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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
PABPC4	8761	hgsc.bcm.edu	hg19	1	40029530	40029530	+	Silent	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	PABPC4	NM_001135653	exon11	c.G1518A	p.L506L	GTCAGTCAGCCCT	.	116.0	51.0	97.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
BEST4	266675	hgsc.bcm.edu	hg19	1	45250593	45250593	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	BEST4	NM_153274	exon7	c.T977C	p.I326T	CGGTCTATGAGCT	.	135.0	11.0	117.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
STXBP3	6814	hgsc.bcm.edu	hg19	1	109302625	109302625	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	STXBP3	NM_007269	exon6	c.T356G	p.F119C	ATCTCTTTAACAA	.	216.0	94.0	172.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF687	57592	hgsc.bcm.edu	hg19	1	151259373	151259373	+	Silent	SNP	C	C	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ZNF687	NM_020832	exon2	c.C606G	p.A202A	GCTGGCCCAGGAG	.	122.0	59.0	115.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	hg19	1	153004965	153004965	+	Silent	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	SPRR1B	NM_003125	exon2	c.C144T	p.P48P	TGAGCCCTGCCAC	.	264.0	105.0	274.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	hg19	2	33412006	33412006	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	LTBP1	NM_206943	exon6	c.C1285A	p.L429I	GGAAAACTTTGTC	.	57.0	20.0	68.0	0.0	.	317	.	.	.	none	.	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	hg19	2	85777685	85777685	+	Missense_Mutation	SNP	G	G	T	rs372492949	alternate_allele	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	GGCX	NM_000821	exon14	c.C2077A	p.R693S	TGCGGCGAAAGAC	.	92.0	42.0	85.0	0.0	.	44	.	.	.	alt	.	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	hg19	2	152507333	152507333	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	NEB	NM_004543	exon53	c.G6982A	p.D2328N	TTGGGTCATCTTG	.	287.0	142.0	231.0	0.0	.	1697	.	.	.	none	.	.	PASS	Atlas-SNP
RAPGEF4	11069	hgsc.bcm.edu	hg19	2	173832042	173832042	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	RAPGEF4	NM_007023	exon10	c.G874A	p.D292N	CTGGATGATGAGC	.	33.0	18.0	23.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	hg19	2	218712984	218712984	+	Silent	SNP	G	G	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	TNS1	NM_022648	exon17	c.C1881G	p.P627P	CAGCTGGGGTTCA	.	79.0	37.0	59.0	0.0	.	251	.	.	.	none	.	.	PASS	Atlas-SNP
MYEOV2	150678	hgsc.bcm.edu	hg19	2	241073371	241073371	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	MYEOV2,NS,carcinoma,0,1	MYEOV2	NM_138336	exon2	c.G208C	p.V70L	CATGAACGGCCTT	.	168.0	65.0	132.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	hg19	3	9877081	9877081	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	TTLL3	NM_001025930	exon13	c.G2656A	p.V886M	AAACAAGTGAAGT	.	311.0	108.0	160.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
NISCH	11188	hgsc.bcm.edu	hg19	3	52526307	52526307	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	NISCH	NM_007184	exon21	c.C4324A	p.L1442I	CATGACCTCATGG	.	441.0	133.0	309.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	hg19	3	113376680	113376680	+	Silent	SNP	G	G	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	KIAA2018	NM_001009899	exon7	c.C3849A	p.G1283G	TTGACTGCCATAG	.	222.0	140.0	165.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	hg19	4	123254840	123254840	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	KIAA1109	NM_015312	exon66	c.A11522G	p.K3841R	AGAAGAAGTTTCA	.	46.0	23.0	37.0	0.0	.	424	.	.	.	none	.	.	PASS	Atlas-SNP
CBR4	84869	hgsc.bcm.edu	hg19	4	169931208	169931208	+	Silent	SNP	G	G	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	CBR4	NM_032783	exon1	c.C33A	p.S11S	GCCTCGGGAGCCT	.	44.0	22.0	49.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	hg19	4	187540602	187540602	+	Missense_Mutation	SNP	C	C	T	rs201352448	bycluster	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	FAT1	NM_005245	exon10	c.G7138A	p.V2380I	CGGTAACGTCCAC	.	67.0	35.0	52.0	0.0	.	500	.	.	.	weak	C|0.999;T|0.001	0.001	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	hg19	5	73136427	73136427	+	Silent	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	.	NM_001080479	exon11	c.T1269C	p.S423S	AACCAGTCCCAGT	.	57.0	27.0	54.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CDKL3	51265	hgsc.bcm.edu	hg19	5	133695635	133695635	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	CDKL3	NM_001113575	exon3	c.T313G	p.Y105D	AGAGGTATTTTCT	.	17.0	8.0	6.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	hg19	6	38704982	38704982	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	DNAH8	NM_001206927	exon6	c.A902T	p.E301V	AATCTGAAAAACA	.	108.0	50.0	70.0	0.0	.	1239	.	.	.	none	.	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	hg19	7	24745817	24745817	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	DFNA5	NM_001127453	exon8	c.T1169A	p.V390D	GCACTGACCAAGA	.	164.0	95.0	100.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
AEBP1	165	hgsc.bcm.edu	hg19	7	44146299	44146299	+	Silent	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	AEBP1,NS,carcinoma,0,2	AEBP1	NM_001129	exon2	c.T408C	p.P136P	GCCACCTAAGGCC	.	41.0	3.0	31.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	hg19	7	66532281	66532281	+	Silent	SNP	C	C	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	TYW1	NM_018264	exon10	c.C1165A	p.R389R	ATGCTCCGAGGGA	.	162.0	7.0	114.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	hg19	8	8235103	8235103	+	Silent	SNP	A	A	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	.	NM_001080826	exon2	c.T816A	p.T272T	ACCTGCAGTCTGG	.	34.0	22.0	32.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB10	65986	hgsc.bcm.edu	hg19	8	81411997	81411997	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ZBTB10	NM_023929	exon2	c.T1241G	p.V414G	CTGCAGTTCAAGG	.	96.0	4.0	106.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
NIPAL2	79815	hgsc.bcm.edu	hg19	8	99215364	99215364	+	Silent	SNP	A	A	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	NIPAL2	NM_024759	exon8	c.T852A	p.I284I	AAAGAAAATATGA	.	122.0	58.0	99.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf91	203197	hgsc.bcm.edu	hg19	9	117400851	117400851	+	Silent	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	C9orf91	NM_153045	exon8	c.T694C	p.L232L	AGCCAGTTGTGTG	.	175.0	76.0	168.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
PPA1	5464	hgsc.bcm.edu	hg19	10	71969401	71969401	+	Silent	SNP	T	T	C	rs150430650		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	PPA1	NM_021129	exon7	c.A552G	p.E184E	AGTAGCTTCTAAG	.	170.0	10.0	124.0	0.0	.	24	.	.	.	weak	.	.	PASS	Atlas-SNP
CUTC	51076	hgsc.bcm.edu	hg19	10	101507060	101507060	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	CUTC	NM_015960	exon6	c.A486C	p.L162F	CCTCTTAACCTTG	.	179.0	42.0	122.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
MCMBP	79892	hgsc.bcm.edu	hg19	10	121598084	121598084	+	Silent	SNP	A	A	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	MCMBP	NM_024834	exon12	c.T1377C	p.D459D	AGTCTCATCGATT	.	80.0	29.0	60.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
ENDOD1	23052	hgsc.bcm.edu	hg19	11	94862157	94862157	+	Missense_Mutation	SNP	C	C	G	rs61734147	bycluster;by1000genomes;alternate_allele	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	ENDOD1,mouth,carcinoma,0,1	ENDOD1	NM_015036	exon2	c.C917G	p.S306C	CCCTTTCTAGCAC	.	116.0	47.0	121.0	0.0	.	26	.	.	.	alt	C|0.998;T|0.002	.	PASS	Atlas-SNP
UBE4A	9354	hgsc.bcm.edu	hg19	11	118243839	118243839	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	UBE4A	NM_004788	exon7	c.G781A	p.E261K	GTCATTGAAGCCT	.	89.0	42.0	94.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
MCAM	4162	hgsc.bcm.edu	hg19	11	119183001	119183001	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	MCAM	NM_006500	exon8	c.T999G	p.S333R	TGGTTCACTCAGC	.	107.0	38.0	110.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
APOLD1	81575	hgsc.bcm.edu	hg19	12	12940182	12940182	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	APOLD1	NM_001130415	exon2	c.C436T	p.R146W	AACTCCCGGGAGC	.	93.0	23.0	65.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
ANP32D	23519	hgsc.bcm.edu	hg19	12	48866497	48866497	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ANP32D	NM_012404	exon1	c.C50A	p.S17Y	CGCCCTCCGATGT	.	258.0	135.0	167.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
KRT4	3851	hgsc.bcm.edu	hg19	12	53205646	53205646	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	KRT4	NM_002272	exon2	c.G578C	p.S193T	AGGACACTGAGGT	.	124.0	44.0	71.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	hg19	12	85449852	85449852	+	Silent	SNP	G	G	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	LRRIQ1	NM_001079910	exon8	c.G1281T	p.V427V	TCTAGTGGATGAA	.	279.0	34.0	160.0	0.0	.	512	.	.	.	none	.	.	PASS	Atlas-SNP
SYCP3	50511	hgsc.bcm.edu	hg19	12	102125409	102125409	+	Silent	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	SYCP3	NM_001177949	exon7	c.A489G	p.Q163Q	TCTAGATTGTTGA	.	41.0	24.0	29.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN11	5781	hgsc.bcm.edu	hg19	12	112892407	112892407	+	Missense_Mutation	SNP	T	T	G	rs79068130	bycluster	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	PTPN11,NS,carcinoma,0,1	PTPN11	NM_080601	exon5	c.T565G	p.S189A	TTTGATTCTTTGA	.	112.0	5.0	42.0	0.0	.	623	.	.	.	weak	T|0.500;G|0.500	0.500	PASS	Atlas-SNP
PTPN11	5781	hgsc.bcm.edu	hg19	12	112892458	112892458	+	Silent	SNP	T	T	C	rs78376169	bycluster	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	PTPN11,NS,carcinoma,0,2	PTPN11	NM_080601	exon5	c.T616C	p.L206L	GAAACATTGGGTA	.	81.0	4.0	42.0	0.0	.	623	.	.	.	weak	.	.	PASS	Atlas-SNP
GATC	283459	hgsc.bcm.edu	hg19	12	120884511	120884511	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	GATC	NM_176818	exon2	c.C133T	p.L45F	CTAGCGCTTGTGG	.	121.0	34.0	58.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
PSME2	5721	hgsc.bcm.edu	hg19	14	24615760	24615760	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	PSME2	NM_002818	exon1	c.G31T	p.G11W	CTTCCCCGCTCAG	.	109.0	5.0	101.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
MNAT1	4331	hgsc.bcm.edu	hg19	14	61434959	61434959	+	Silent	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	MNAT1	NM_002431	exon8	c.T822C	p.H274H	AAACCATGTCAGA	.	102.0	33.0	110.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
MARK3	4140	hgsc.bcm.edu	hg19	14	103894758	103894758	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	MARK3	NM_001128921	exon3	c.A278G	p.N93S	AGTTGAATCCAAC	.	12.0	8.0	3.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
SLTM	79811	hgsc.bcm.edu	hg19	15	59172211	59172211	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	SLTM	NM_024755	exon21	c.C3092A	p.P1031Q	CGTCGCGGAGGTC	.	95.0	4.0	64.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
TERF2	7014	hgsc.bcm.edu	hg19	16	69402345	69402345	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	TERF2	NM_005652	exon6	c.G881C	p.S294T	CCTGTACTTGAGG	.	160.0	61.0	67.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
GINS2	51659	hgsc.bcm.edu	hg19	16	85715212	85715212	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.,1	GINS2	NM_016095	exon3	c.A281G	p.E94G	GTAAGTTCCATGT	.	130.0	66.0	50.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	hg19	17	14005508	14005508	+	Silent	SNP	T	T	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	COX10	NM_001303	exon4	c.T573A	p.L191L	CCTGCTTACTTCT	.	300.0	190.0	164.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	hg19	19	22940373	22940373	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	ZNF99,NS,carcinoma,0,4	ZNF99	NM_001080409	exon4	c.A2338G	p.K780E	TTATCTTATGTTT	.	74.0	3.0	48.0	0.0	.	273	.	.	.	none	.	.	PASS	Atlas-SNP
FAM187B	148109	hgsc.bcm.edu	hg19	19	35718874	35718874	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	FAM187B	NM_152481	exon1	c.G710A	p.G237E	ATGGATCCTAAGG	.	37.0	13.0	26.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
ATP1A3	478	hgsc.bcm.edu	hg19	19	42492245	42492245	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ATP1A3	NM_001256214	exon4	c.C239T	p.P80L	GCGTTAGGCCCAT	.	133.0	16.0	118.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF836	162962	hgsc.bcm.edu	hg19	19	52660096	52660096	+	Silent	SNP	G	G	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ZNF836	NM_001102657	exon5	c.C840T	p.G280G	GATCTTGCCACAT	.	114.0	46.0	69.0	0.0	.	158	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF264	9422	hgsc.bcm.edu	hg19	19	57724137	57724137	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	ZNF264	NM_003417	exon4	c.C1672G	p.Q558E	CAGCATCAAAGGA	.	114.0	5.0	91.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
PHKA1	5255	hgsc.bcm.edu	hg19	X	71822085	71822085	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	PHKA1	NM_002637	exon27	c.A2956G	p.I986V	CGTGGATAGAAAT	.	39.0	4.0	21.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
LIPA	3988	hgsc.bcm.edu	hg19	10	90974746	90974746	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	LIPA	NM_000235	exon10	c.1040delT	p.L347fs	.	.	156.0	63.0	131.0	0.0	.	29	.	0.403846	0	none	.	.	PASS	Atlas-INDEL
REPIN1	29803	hgsc.bcm.edu	hg19	7	150068863	150068864	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	REPIN1	NM_001099695	exon3	c.704_705insA	p.I235fs	.	.	41.0	10.0	38.0	0.0	.	74	.	0.243902	0	none	.	.	PASS	Atlas-INDEL
C1orf54	79630	hgsc.bcm.edu	hg19	1	150248209	150248212	+	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	GTGA	GTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	C1orf54	NM_024579	exon3	c.189_189del	p.63_63del	.	.	75.0	17.0	48.0	0.0	.	20	.	0.226667	0	none	.	.	PASS	Atlas-INDEL
CSPP1	79848	hgsc.bcm.edu	hg19	8	68070755	68070755	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	CSPP1,colon,carcinoma,0,1	CSPP1	NM_024790	exon18	c.2299delC	p.R767fs	.	.	47.0	13.0	49.0	0.0	.	129	.	0.276596	0	none	.	.	PASS	Atlas-INDEL
LTBP1	4052	hgsc.bcm.edu	hg19	2	33412000	33412000	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	LTBP1	NM_206943	exon6	c.1278delA	p.T426fs	.	.	57.0	20.0	64.0	0.0	.	317	.	0.350877	0	none	.	.	PASS	Atlas-INDEL
BCLAF1	9774	hgsc.bcm.edu	hg19	6	136582550	136582550	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	.	BCLAF1	NM_014739	exon12	c.2611delC	p.R871fs	.	.	614.0	103.0	379.0	0.0	.	203	.	0.167752	0	none	.	.	PASS	Atlas-INDEL