Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	TTotCov	TVarCov	NTotCov	NVarCov	TVarRat	NVarRat	dbSNP_AF	dbSNP_PopFreq	dbSNP_Strength	COSMIC_Codon	COSMIC_Gene	COSMIC_Gene_Freq	COSMIC_Site_Freq	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	Confidence	Algorithm
E2F1	1869	hgsc.bcm.edu	37	20	32267687	32267690	+	Frame_Shift_Del	DEL	CCGT	CCGT	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	CCGT	CCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	91.0	12.0	125.0	0.0	0.131868	0	.	.	none	.	E2F1	41	.	NM_005225	exon3	c.444_447del	p.148_149del	.	.	PASS	Atlas-Indel
TNFAIP3	7128	hgsc.bcm.edu	37	6	138198239	138198240	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	165.0	12.0	286.0	0.0	0.0727273	0	.	.	none	.	TNFAIP3	340	.	NM_001270508	exon6	c.831_832del	p.277_278del	.	.	PASS	Atlas-Indel
SCN9A	6335	hgsc.bcm.edu	37	2	167055184	167055185	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	243.0	22.0	372.0	0.0	0.090535	0	.	.	none	.	SCN9A	296	.	NM_002977	exon27	c.5932_5933insA	p.X1978delinsI	.	.	PASS	Atlas-Indel
ARID1A	8289	hgsc.bcm.edu	37	1	27101417	27101417	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	119.0	28.0	124.0	0.0	0.235294	0	.	.	none	.	ARID1A	842	.	NM_006015	exon18	c.4698delG	p.R1566fs	.	.	PASS	Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49436376	49436377	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	66.0	11.0	87.0	0.0	0.166667	0	.	.	none	.	MLL2	1173	.	NM_003482	exon27	c.5835_5836insC	p.P1945fs	.	.	PASS	Atlas-Indel
CTSH	1512	hgsc.bcm.edu	37	15	79221796	79221797	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	129.0	12.0	226.0	0.0	0.0930233	0	.	.	none	.	CTSH	23	.	NM_004390	exon8	c.588_589insA	p.N196fs	.	.	PASS	Atlas-Indel
OR2T34	127068	hgsc.bcm.edu	37	1	248737510	248737511	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	230.0	39.0	333.0	0.0	0.169565	0	.	.	none	OR2T34,NS,haematopoietic_neoplasm,-1,2	OR2T34	72	2	NM_001001821	exon1	c.549_550insT	p.F183fs	.	.	PASS	Atlas-Indel
RIMS1	22999	hgsc.bcm.edu	37	6	73023228	73023228	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	78.0	19.0	93.0	0.0	0.24359	0	.	.	none	.	RIMS1	278	.	NM_014989	exon28	c.A3983G	p.Q1328R	AAGATCAGTACAG	.	PASS	Atlas-SNP
SMAD9	4093	hgsc.bcm.edu	37	13	37453460	37453460	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	52.0	6.0	81.0	0.0	0.115385	0	.	.	none	.	SMAD9	91	.	NM_005905	exon2	c.G367A	p.E123K	ACACTTCTTTCTG	.	PASS	Atlas-SNP
KCNN4	3783	hgsc.bcm.edu	37	19	44278489	44278489	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	98.0	11.0	119.0	0.0	0.112245	0	.	.	none	.	KCNN4	37	.	NM_002250	exon3	c.C538G	p.R180G	TGCTGCGGTAGGA	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	394899	394899	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	46.0	8.0	55.0	0.0	0.173913	0	.	.	none	IRF4_ENST00000380956,NS,carcinoma,-1,1	IRF4	65	1	NM_001195286	exon3	c.T295C	p.C99R	CTGCGGTGCGCTT	.	PASS	Atlas-SNP
KCTD3	51133	hgsc.bcm.edu	37	1	215751396	215751396	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	184.0	23.0	297.0	0.0	0.125	0	.	.	none	.	KCTD3	101	.	NM_016121	exon6	c.C369T	p.V123V	CAGTGTCCTTTTT	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187539303	187539303	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	103.0	14.0	151.0	0.0	0.135922	0	.	.	none	.	FAT1	500	.	NM_005245	exon10	c.C8437A	p.P2813T	CATATGGACTAGA	.	PASS	Atlas-SNP
GPC1	2817	hgsc.bcm.edu	37	2	241401695	241401695	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	111.0	11.0	147.0	0.0	0.0990991	0	.	.	none	.	GPC1	32	.	NM_002081	exon3	c.C413T	p.A138V	AGAACGCGAGGGC	.	PASS	Atlas-SNP
XRCC2	7516	hgsc.bcm.edu	37	7	152346254	152346254	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	35.0	5.0	59.0	0.0	0.142857	0	.	.	none	.	XRCC2	30	.	NM_005431	exon3	c.G316T	p.E106X	TTATTTCTTCAGA	.	PASS	Atlas-SNP
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158776	26158776	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105.0	14.0	163.0	0.0	0.133333	0	.	.	none	.	HIST1H2BD	45	.	NM_021063	exon1	c.T379C	p.X127Q	TCCAAGTAACTTT	.	PASS	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35729913	35729913	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	64.0	9.0	118.0	0.0	0.140625	0	.	.	none	.	NBEA	340	.	NM_015678	exon19	c.C2448A	p.I816I	TCAGATCTTGACA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804886	804886	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	63.0	3.0	60.0	0.0	0.047619	0	.	.	none	PTBP1,larynx,carcinoma,-2,1	PTBP1	43	1	NM_031990	exon7	c.T664C	p.F222L	AACCAGTTCCAGG	.	scavenged	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52877609	52877609	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	138.0	13.0	118.0	0.0	0.0942029	0	.	.	none	.	ZNF880	45	.	NM_001145434	exon3	c.G197A	p.R66Q	ATCCCCGGAATCT	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	81046571	81046571	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	117.0	5.0	145.0	0.0	0.042735	0	.	.	none	.	PTPRQ	119	.	NM_001145026	exon35	c.C5557G	p.P1853A	GATCTGCCTTGGA	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3089200	3089200	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	316.0	52.0	492.0	0.0	0.164557	0	.	.	none	.	MYOM1	192	.	NM_003803	exon29	c.G4109T	p.G1370V	CATTCACCAGTCA	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42674280	42674280	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	127.0	18.0	214.0	0.0	0.141732	0	.	.	none	.	NKTR	116	.	NM_005385	exon9	c.A738C	p.E246D	TTCAGAAGAGCCA	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55626476	55626476	+	Silent	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	145.0	6.0	214.0	0.0	0.0413793	0	.	.	none	.	PCDH15	1715	.	NM_001142763	exon28	c.A3658C	p.R1220R	AGGATCTCCTCAT	.	PASS	Atlas-SNP
CTNNA3	29119	hgsc.bcm.edu	37	10	67829199	67829199	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	150.0	16.0	260.0	0.0	0.106667	0	.	.	none	.	CTNNA3	401	.	NM_013266	exon15	c.C2026A	p.Q676K	CAACTTGCTCAGC	.	PASS	Atlas-SNP
DLX4	1748	hgsc.bcm.edu	37	17	48051195	48051195	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	70.0	11.0	92.0	0.0	0.157143	0	.	.	none	.	DLX4	25	.	NM_138281	exon3	c.T611C	p.L204P	CCTCCCTCTGGGA	.	PASS	Atlas-SNP
NAA25	80018	hgsc.bcm.edu	37	12	112516526	112516526	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	153.0	10.0	219.0	0.0	0.0653595	0	.	.	none	.	NAA25	105	.	NM_024953	exon6	c.A497G	p.E166G	AGGTTTTCATCCT	.	PASS	Atlas-SNP
LRRC4	64101	hgsc.bcm.edu	37	7	127669744	127669744	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	110.0	17.0	135.0	0.0	0.154545	0	.	.	none	.	LRRC4	72	.	NM_022143	exon2	c.A950G	p.E317G	ATATACTCTCGAA	.	PASS	Atlas-SNP
AGTR2	186	hgsc.bcm.edu	37	X	115304549	115304549	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	215.0	12.0	334.0	0.0	0.055814	0	.	.	none	.	AGTR2	62	.	NM_000686	exon3	c.G1016T	p.W339L	TTACTTGGCTCCA	.	PASS	Atlas-SNP
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857825	149857825	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	166.0	9.0	160.0	0.0	0.0542169	0	.	.	none	.	HIST2H2BE	33	.	NM_003528	exon1	c.C366T	p.Y122Y	GCTGGTGTACTTG	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18491371	18491371	+	Silent	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	124.0	7.0	171.0	0.0	0.0564516	0	.	.	none	.	PIK3C2G	315	.	NM_004570	exon9	c.T1284C	p.Y428Y	CGTGTATAATATT	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20683092	20683092	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	149.0	17.0	214.0	0.0	0.114094	0	.	.	none	.	ABCB5	357	.	NM_001163941	exon7	c.A515G	p.D172G	ACATTGACAAAAT	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78923585	78923585	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105.0	5.0	163.0	0.0	0.047619	0	.	.	none	.	PCSK5	329	.	NM_001190482	exon28	c.G3548C	p.C1183S	AGCCTTGTCATTC	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16255388	16255388	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	66.0	6.0	92.0	0.0	0.0909091	0	.	.	none	.	SPEN	374	.	NM_015001	exon11	c.G2653T	p.E885X	GTGAAAGAGAAAG	.	PASS	Atlas-SNP
NPAS3	64067	hgsc.bcm.edu	37	14	34270175	34270175	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	55.0	7.0	65.0	0.0	0.127273	0	.	.	none	.	NPAS3	266	.	NM_001164749	exon12	c.G2662A	p.A888T	GGCGGCGCAGTGA	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48688529	48688529	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	135.0	9.0	163.0	0.0	0.0666667	0	.	.	none	.	SLC5A9	82	.	NM_001135181	exon1	c.G121C	p.V41L	AGCGTGGTGGTCA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508026	37508026	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	160.0	12.0	216.0	0.0	0.075	0	.	.	none	.	ANKRD30A	448	.	NM_052997	exon34	c.A3218T	p.E1073V	AAAAGGAAAATAA	.	PASS	Atlas-SNP
EFNB1	1947	hgsc.bcm.edu	37	X	68058642	68058642	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	195.0	9.0	389.0	0.0	0.0461538	0	.	.	none	.	EFNB1	37	.	NM_004429	exon2	c.C311A	p.P104Q	ATAGGCCAGAGCA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152768599	152768599	+	Silent	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	69.0	7.0	105.0	0.0	0.101449	0	.	.	none	.	SYNE1	3227	.	NM_033071	exon29	c.G3684C	p.L1228L	CTCTGACAGCAGC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825160	34825160	+	Missense_Mutation	SNP	C	C	T	rs201864059		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105.0	9.0	152.0	0.0	0.0857143	0	.	.	weak	.	UHRF1BP1	102	.	NM_017754	exon12	c.C1486T	p.R496W	TGCAGTCGGAAAC	.	PASS	Atlas-SNP
PYY	5697	hgsc.bcm.edu	37	17	42030694	42030694	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	178.0	13.0	188.0	0.0	0.0730337	0	.	.	none	.	PYY	11	.	NM_004160	exon5	c.G158A	p.R53H	TAGTGGCGCAGGG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	102.0	14.0	117.0	0.0	0.137255	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G176A	p.S59N	GAAGCAGCCGATC	.	PASS	Atlas-SNP
OR4S1	256148	hgsc.bcm.edu	37	11	48328231	48328231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	113.0	10.0	191.0	0.0	0.0884956	0	.	.	none	.	OR4S1	52	.	NM_001004725	exon1	c.C457T	p.H153Y	TTCCTGCATTCCA	.	PASS	Atlas-SNP
KCNH1	3756	hgsc.bcm.edu	37	1	210856924	210856924	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	136.0	6.0	166.0	0.0	0.0441176	0	.	.	none	.	KCNH1	199	.	NM_172362	exon11	c.G2669A	p.R890H	TCCAGGCGCAAGT	.	PASS	Atlas-SNP
HNF4G	3174	hgsc.bcm.edu	37	8	76471075	76471075	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	89.0	9.0	117.0	0.0	0.101124	0	.	.	none	.	HNF4G	111	.	NM_004133	exon8	c.T896C	p.M299T	AGAACATGAGGTT	.	PASS	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113773002	113773002	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	100.0	22.0	122.0	0.0	0.22	0	.	.	none	.	F7	49	.	NM_000131	exon9	c.A1081G	p.N361D	GTCCTCAACGTGC	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31768074	31768074	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	90.0	19.0	125.0	0.0	0.211111	0	.	.	none	.	TSHZ3	549	.	NM_020856	exon2	c.C2625T	p.D875D	GGCCCCGTCAATG	.	PASS	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58979509	58979509	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	117.0	11.0	119.0	0.0	0.0940171	0	.	.	none	.	MPEG1	72	.	NM_001039396	exon1	c.G830A	p.S277N	CCAATGCTCTGCA	.	PASS	Atlas-SNP
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005633	118005633	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	179.0	18.0	225.0	0.0	0.100559	0	.	.	none	.	TRAM1L1	55	.	NM_152402	exon1	c.C917T	p.T306M	TGGATCGTGCAAC	.	PASS	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22052356	22052356	+	Silent	SNP	G	G	A	rs11552824	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	70.0	10.0	84.0	0.0	0.142857	0	.	.	alt	.	BMP1	131	.	NM_001199	exon12	c.G1563A	p.T521T	GAGCACGTCCAGC	.	PASS	Atlas-SNP
NPAT	4863	hgsc.bcm.edu	37	11	108044437	108044437	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	391.0	34.0	543.0	0.0	0.0869565	0	.	.	none	.	NPAT	124	.	NM_002519	exon13	c.A1274T	p.K425I	GCCTTTTTCTGTA	.	PASS	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	37	16	68716273	68716273	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	63.0	8.0	76.0	0.0	0.126984	0	.	.	none	.	CDH3	68	.	NM_001793	exon9	c.C1065T	p.D355D	TCTGGACGCCCCC	.	PASS	Atlas-SNP
CD36	948	hgsc.bcm.edu	37	7	80285936	80285936	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	126.0	22.0	156.0	0.0	0.174603	0	.	.	none	.	CD36	185	.	NM_001127444	exon2	c.C201A	p.I67I	TTGGATCTTTGAT	.	PASS	Atlas-SNP
UTS2B	257313	hgsc.bcm.edu	37	3	190999976	190999976	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	120.0	5.0	145.0	0.0	0.0416667	0	.	.	none	.	.	.	.	NM_198152	exon5	c.G3T	p.M1I	CTTGTTCATGTTA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79328899	79328899	+	Silent	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	98.0	8.0	121.0	0.0	0.0816327	0	.	.	none	.	FRAS1	779	.	NM_001166133	exon31	c.C4212G	p.T1404T	AGCTACCCCCACC	.	PASS	Atlas-SNP
DDC	1644	hgsc.bcm.edu	37	7	50531011	50531011	+	Missense_Mutation	SNP	G	G	A	rs147562019		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	165.0	14.0	218.0	0.0	0.0848485	0	G|1.000;A|0.000	0.000	weak	.	DDC	100	.	NM_001082971	exon14	c.C1361T	p.T454M	TCCACCGTGCGAG	.	PASS	Atlas-SNP
TLX1	3195	hgsc.bcm.edu	37	10	102896618	102896618	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	124.0	18.0	144.0	0.0	0.145161	0	.	.	none	TLX1,NS,carcinoma,-1,1	TLX1	20	1	NM_005521	exon3	c.A941G	p.D314G	GGTCTGACGACTC	.	PASS	Atlas-SNP
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126812	19126812	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	44.0	4.0	54.0	0.0	0.0909091	0	.	.	none	.	ITPRIPL2	40	.	NM_001034841	exon1	c.G1029A	p.A343A	GCGTGCGGAGGCA	.	PASS	Atlas-SNP
BICC1	80114	hgsc.bcm.edu	37	10	60549152	60549152	+	Missense_Mutation	SNP	G	G	A	rs192860241	bycluster;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	155.0	10.0	221.0	0.0	0.0645161	0	G|1.000;A|0.000	0.000	strong	BICC1,colon,carcinoma,+1,1	BICC1	121	1	NM_001080512	exon7	c.G731A	p.R244H	AACAGCGTTCCCG	.	PASS	Atlas-SNP
SLC6A14	11254	hgsc.bcm.edu	37	X	115588850	115588850	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	136.0	8.0	252.0	0.0	0.0588235	0	.	.	none	.	SLC6A14	56	.	NM_007231	exon13	c.G1690A	p.A564T	GGAGTTGCTTTAG	.	PASS	Atlas-SNP
ATN1	1822	hgsc.bcm.edu	37	12	7045906	7045906	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	46.0	5.0	58.0	0.0	0.108696	0	.	.	none	.	ATN1	95	.	NM_001007026	exon5	c.G1476A	p.Q492Q	GCAGCAGCAGCAG	.	PASS	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58978519	58978519	+	Missense_Mutation	SNP	G	G	A	rs376216311	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	126.0	15.0	119.0	0.0	0.119048	0	.	.	alt	.	MPEG1	72	.	NM_001039396	exon1	c.C1820T	p.T607I	GTATTGGTGGCAG	.	PASS	Atlas-SNP
PADI1	29943	hgsc.bcm.edu	37	1	17566209	17566209	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	128.0	14.0	203.0	0.0	0.109375	0	.	.	none	.	PADI1	77	.	NM_013358	exon14	c.C1563G	p.H521Q	AAAACACCAGGCA	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158935181	158935181	+	Silent	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	190.0	21.0	264.0	0.0	0.110526	0	.	.	none	.	VIPR2	53	.	NM_003382	exon2	c.A108G	p.T36T	ACATTTTGTTTCT	.	PASS	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58979544	58979544	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	133.0	12.0	128.0	0.0	0.0902256	0	.	.	none	.	MPEG1	72	.	NM_001039396	exon1	c.C795T	p.S265S	GAGGTAGCTCTTG	.	PASS	Atlas-SNP
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117576	46117576	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	64.0	4.0	88.0	0.0	0.0625	0	.	.	none	KRTAP10-12,rectum,carcinoma,0,2	KRTAP10-12	21	2	NM_198699	exon1	c.C460T	p.P154S	TGTGTGCCCGTCT	.	scavenged	Atlas-SNP
HS6ST2	90161	hgsc.bcm.edu	37	X	132091067	132091067	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	100.0	8.0	134.0	0.0	0.08	0	.	.	none	.	HS6ST2	89	.	NM_001077188	exon3	c.G716T	p.G239V	GTGGTGCCCCCGG	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539203	92539203	+	Silent	SNP	G	G	A	rs369374957	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	181.0	8.0	187.0	0.0	0.0441989	0	.	.	alt	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	NM_001731	exon1	c.C109T	p.L37L	TCTGCAGCTGTCG	.	PASS	Atlas-SNP
KIF25	3834	hgsc.bcm.edu	37	6	168443315	168443315	+	Missense_Mutation	SNP	G	G	A	rs146787013	bycluster;byfrequency;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	62.0	12.0	91.0	0.0	0.193548	0	G|0.993;A|0.007	0.007	strong	KIF25,NS,carcinoma,-2,1	KIF25	75	1	NM_030615	exon8	c.G904A	p.V302I	GCAGGCGTCCTGG	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58209024	58209024	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	41.0	5.0	58.0	0.0	0.121951	0	.	.	none	.	PCDH17	304	.	NM_001040429	exon1	c.G2344A	p.V782I	ATGAACGTCATGA	.	PASS	Atlas-SNP
ITCH	83737	hgsc.bcm.edu	37	20	32996580	32996580	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105.0	10.0	151.0	0.0	0.0952381	0	.	.	none	.	ITCH	73	.	NM_001257137	exon4	c.G194A	p.W65X	CCAAGTGGAAGCA	.	PASS	Atlas-SNP
SFR1	119392	hgsc.bcm.edu	37	10	105883796	105883796	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	203.0	24.0	297.0	0.0	0.118227	0	.	.	none	MEIR5,NS,carcinoma,-2,1	.	.	1	NM_001002759	exon3	c.G460A	p.A154T	TTAAACGCTGAAA	.	PASS	Atlas-SNP
TAB3	257397	hgsc.bcm.edu	37	X	30873153	30873153	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	170.0	22.0	243.0	0.0	0.129412	0	.	.	none	.	TAB3	82	.	NM_152787	exon6	c.C629A	p.P210Q	GCTCTTGGTACAG	.	PASS	Atlas-SNP
ELOVL6	79071	hgsc.bcm.edu	37	4	111119485	111119485	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	102.0	7.0	126.0	0.0	0.0686275	0	.	.	none	.	ELOVL6	27	.	NM_001130721	exon2	c.A7C	p.M3L	CTGACATGTTCAT	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	64981740	64981740	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	162.0	15.0	190.0	0.0	0.0925926	0	.	.	none	.	CDH11	260	.	NM_001797	exon13	c.C2157A	p.D719E	GATGAAGTCATCG	.	PASS	Atlas-SNP
ITLN1	55600	hgsc.bcm.edu	37	1	160850422	160850422	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	91.0	22.0	132.0	0.0	0.241758	0	.	.	none	ITLN1,caecum,carcinoma,+1,1	ITLN1	45	1	NM_017625	exon6	c.G641A	p.G214D	GCGTCGCCAAAAT	.	PASS	Atlas-SNP
KLHDC4	54758	hgsc.bcm.edu	37	16	87748161	87748161	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	138.0	7.0	169.0	0.0	0.0507246	0	.	.	none	.	KLHDC4	45	.	NM_017566	exon8	c.G778A	p.D260N	CCTTGTCCACGTC	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38355355	38355355	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	122.0	6.0	177.0	0.0	0.0491803	0	.	.	none	.	INPP5B	76	.	NM_005540	exon9	c.C671T	p.S224F	GTGGAGGAGCGAA	.	PASS	Atlas-SNP
PRPF31	26121	hgsc.bcm.edu	37	19	54632434	54632434	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	51.0	8.0	53.0	0.0	0.156863	0	.	.	none	.	PRPF31	48	.	NM_015629	exon12	c.C1149A	p.I383I	CTAGATCGAGGAG	.	PASS	Atlas-SNP
CYBB	1536	hgsc.bcm.edu	37	X	37663373	37663373	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	196.0	24.0	324.0	0.0	0.122449	0	.	.	none	.	CYBB	62	.	NM_000397	exon9	c.A1141T	p.K381X	GCGTGGAAACTAC	.	PASS	Atlas-SNP
LYRM5	144363	hgsc.bcm.edu	37	12	25357062	25357062	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	194.0	26.0	260.0	0.0	0.134021	0	.	.	none	.	LYRM5	10	.	NM_001001660	exon3	c.A89C	p.D30A	GAGCAGACTATTT	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46419037	46419037	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	50.0	6.0	64.0	1.0	0.12	0.015625	.	.	none	AMBRA1_ENST00000458649,bladder,carcinoma,0,2	AMBRA1	201	2	NM_001267782	exon20	c.A3869G	p.D1290G	GCAGCGTCCCCCC	.	scavenged	Atlas-SNP
SORCS3	22986	hgsc.bcm.edu	37	10	106959775	106959775	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	81.0	9.0	91.0	0.0	0.111111	0	.	.	none	.	SORCS3	282	.	NM_014978	exon15	c.C2028T	p.S676S	CTTCAGCCTCCGC	.	PASS	Atlas-SNP
ZNF496	84838	hgsc.bcm.edu	37	1	247492064	247492064	+	Silent	SNP	G	G	A	rs146066456	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	93.0	5.0	102.0	0.0	0.0537634	0	G|1.000;T|0.000	.	alt	.	ZNF496	80	.	NM_032752	exon4	c.C495T	p.N165N	ATCCTGGTTCTTT	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107977810	107977810	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	76.0	7.0	103.0	0.0	0.0921053	0	.	.	none	.	IRS4	253	.	NM_003604	exon1	c.G1765T	p.G589W	CCCCCCCAGAGTT	.	PASS	Atlas-SNP
MYBL1	4603	hgsc.bcm.edu	37	8	67492515	67492515	+	Silent	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	87.0	6.0	116.0	0.0	0.0689655	0	.	.	none	.	MYBL1	73	.	NM_001080416	exon9	c.T954C	p.T318T	CTCACTAGTGTGC	.	PASS	Atlas-SNP
