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	dbSNP_AF	Algorithm
NRD1	4898	hgsc.bcm.edu	hg19	1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	rs62648104	bycluster	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NRD1	NM_002525	exon2	c.A449T	p.E150V	TCTTCCTCCACCT	.	298.0	18.0	111.0	0.0	.	89	.	T|0.024;A|0.976	Atlas-SNP
PTPN22	26191	hgsc.bcm.edu	hg19	1	114380291	114380291	+	Silent	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PTPN22	NM_015967	exon13	c.T1731C	p.Y577Y	ATTGTAATAAGAG	.	162.0	60.0	63.0	0.0	.	90	.	.	Atlas-SNP
SYCP1	6847	hgsc.bcm.edu	hg19	1	115524051	115524051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYCP1	NM_003176	exon29	c.C2477T	p.S826L	TCACATCAGTTGA	.	215.0	96.0	74.0	0.0	.	149	.	.	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	hg19	1	161596059	161596059	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FCGR3B	NM_001244753	exon4	c.T561G	p.F187L	ATGATGAAAATAC	.	199.0	160.0	100.0	0.0	.	35	.	.	Atlas-SNP
GPR137B	7107	hgsc.bcm.edu	hg19	1	236368456	236368456	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	GPR137B	NM_003272	exon6	c.T997A	p.F333I	CATGGATTCAGTC	.	151.0	56.0	47.0	0.0	.	57	.	.	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	hg19	1	237774079	237774079	+	Silent	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RYR2	NM_001035	exon36	c.G4701T	p.S1567S	TCTCTCGGCGGGA	.	181.0	52.0	67.0	0.0	.	1273	.	.	Atlas-SNP
OR2L13	284521	hgsc.bcm.edu	hg19	1	248263611	248263611	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2L13	NM_175911	exon3	c.G934T	p.E312X	CTGAAAGAATAAT	.	110.0	27.0	32.0	0.0	.	261	.	.	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	hg19	1	248525404	248525404	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2T4	NM_001004696	exon1	c.C522T	p.L174L	GTGTCTCTTCCTG	.	1540.0	69.0	172.0	0.0	.	126	.	.	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	hg19	1	248525411	248525411	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2T4	NM_001004696	exon1	c.T529G	p.S177A	TTCCTGTCATCAG	.	1529.0	62.0	174.0	0.0	.	126	.	.	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	hg19	2	71047619	71047619	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CLEC4F	NM_173535	exon1	c.C37A	p.Q13K	CACACTGGTTATC	.	100.0	49.0	54.0	0.0	.	95	.	.	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	hg19	2	85043137	85043137	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DNAH6	NM_001370	exon76	c.G12303A	p.K4101K	CTATAAGCCAAGC	.	228.0	85.0	75.0	0.0	.	194	.	.	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	hg19	3	440785	440785	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CHL1	NM_006614	exon26	c.A3339T	p.L1113F	ACTATTATTAACT	.	456.0	196.0	120.0	0.0	.	242	.	.	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	hg19	3	41266100	41266100	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	CTNNB1,gallbladder,other,-1,1	CTNNB1	NM_001098209	exon3	c.T97G	p.S33A	CTGGACTCTGGAA	.	238.0	105.0	89.0	0.0	.	4904	.	.	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	hg19	3	126733602	126733602	+	Silent	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PLXNA1	NM_032242	exon13	c.C2805A	p.A935A	TGACGCCCTGGTG	.	87.0	37.0	31.0	0.0	.	185	.	.	Atlas-SNP
TSC22D2	9819	hgsc.bcm.edu	hg19	3	150128513	150128513	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TSC22D2	NM_014779	exon1	c.C1376T	p.P459L	TGCCCCCGGCTAC	.	40.0	19.0	7.0	0.0	.	42	.	.	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	hg19	3	172098773	172098773	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FNDC3B	NM_001135095	exon25	c.T3193C	p.L1065L	ACACAGTTAGAAG	.	101.0	31.0	51.0	0.0	.	118	.	.	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	hg19	4	39310299	39310299	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RFC1	NM_002913	exon13	c.G1842T	p.W614C	TCGGAGCCAGCGT	.	563.0	248.0	141.0	0.0	.	114	.	.	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	hg19	4	135121534	135121534	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PABPC4L	NM_001114734	exon2	c.G815T	p.G272V	GTTTTGCCATATT	.	195.0	87.0	62.0	0.0	.	60	.	.	Atlas-SNP
EDNRA	1909	hgsc.bcm.edu	hg19	4	148457097	148457097	+	Silent	SNP	G	G	A	rs200693894		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	EDNRA	NM_001957	exon5	c.G816A	p.A272A	CACTGCGATCTTC	.	297.0	127.0	109.0	0.0	.	48	.	.	Atlas-SNP
TNPO1	3842	hgsc.bcm.edu	hg19	5	72168474	72168474	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	TNPO1,colon,carcinoma,0,1	TNPO1	NM_002270	exon7	c.C605T	p.A202V	CTCACGCTGTTGC	.	223.0	100.0	96.0	0.0	.	90	.	.	Atlas-SNP
TTC37	9652	hgsc.bcm.edu	hg19	5	94839530	94839530	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TTC37	NM_014639	exon31	c.G3205A	p.E1069K	TGCTCTCTTTATA	.	154.0	63.0	86.0	0.0	.	128	.	.	Atlas-SNP
CDO1	1036	hgsc.bcm.edu	hg19	5	115146946	115146946	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	CDO1,NS,carcinoma,0,1	CDO1	NM_001801	exon3	c.A315G	p.T105T	AAATAATGTCTCC	.	302.0	120.0	106.0	0.0	.	29	.	.	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	hg19	5	140182753	140182753	+	Silent	SNP	C	C	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCDHA3	NM_031497	exon1	c.C1971G	p.P657P	TGAACCCTCATTG	.	106.0	48.0	50.0	0.0	.	396	.	.	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	hg19	5	169685155	169685155	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	LCP2	NM_005565	exon16	c.T986C	p.L329S	TGGGGCAAAGGTC	.	154.0	63.0	75.0	0.0	.	133	.	.	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	hg19	5	175772304	175772304	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_198567	exon9	c.C1230A	p.F410L	GGCCTTCCGCAGC	.	191.0	81.0	73.0	0.0	.	.	.	.	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	hg19	5	175772305	175772305	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_198567	exon9	c.C1231A	p.R411S	GCCTTCCGCAGCC	.	193.0	80.0	72.0	0.0	.	.	.	.	Atlas-SNP
TRIM52	84851	hgsc.bcm.edu	hg19	5	180687428	180687428	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRIM52	NM_032765	exon1	c.G387A	p.E129E	ATCTTCCTCTTCT	.	184.0	18.0	59.0	0.0	.	20	.	.	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	hg19	6	33657110	33657110	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ITPR3	NM_002224	exon50	c.C6790A	p.L2264I	CGCCCCCTCATCG	.	75.0	32.0	57.0	0.0	.	409	.	.	Atlas-SNP
CYP39A1	51302	hgsc.bcm.edu	hg19	6	46607278	46607278	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CYP39A1	NM_016593	exon3	c.G441A	p.L147L	ATTCTCCAGTTGT	.	336.0	138.0	108.0	0.0	.	41	.	.	Atlas-SNP
CDK13	8621	hgsc.bcm.edu	hg19	7	40085553	40085553	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDK13	NM_003718	exon6	c.T2472C	p.G824G	GGAGGGTCTGGAT	.	154.0	74.0	60.0	0.0	.	114	.	.	Atlas-SNP
PHTF2	57157	hgsc.bcm.edu	hg19	7	77569480	77569480	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PHTF2	NM_001127357	exon12	c.C1499A	p.S500X	CTGCTTCAGAACT	.	495.0	183.0	126.0	0.0	.	104	.	.	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	hg19	7	100678724	100678724	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC17	NM_001040105	exon3	c.C4027A	p.P1343T	AGTATACCTGTCA	.	198.0	10.0	66.0	0.0	.	804	.	.	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	hg19	7	107824934	107824934	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NRCAM	NM_001037132	exon18	c.C2160T	p.R720R	CATCACGCGGAAG	.	106.0	39.0	42.0	0.0	.	267	.	.	Atlas-SNP
HYAL4	23553	hgsc.bcm.edu	hg19	7	123508467	123508467	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	HYAL4,NS,carcinoma,0,1	HYAL4	NM_012269	exon3	c.C140A	p.P47H	GGAAACCTTTTAT	.	162.0	70.0	60.0	0.0	.	65	.	.	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	hg19	7	151962169	151962169	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	MLL3_ENST00000355193,extremity,malignant_melanoma,+1,2	MLL3	NM_170606	exon8	c.C1138T	p.R380C	CTGCACGTTTTAA	.	367.0	16.0	134.0	0.0	.	1564	.	.	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	hg19	10	85960359	85960359	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDHR1	NM_001171971	exon6	c.C441T	p.D147D	TCAGGACATACCT	.	123.0	62.0	76.0	0.0	.	122	.	.	Atlas-SNP
CUTC	51076	hgsc.bcm.edu	hg19	10	101503802	101503802	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	CUTC,NS,carcinoma,0,2	CUTC	NM_015960	exon5	c.C412T	p.R138C	ATTTGCCGCCCTC	.	174.0	85.0	62.0	0.0	.	32	.	.	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	hg19	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC6	NM_005961	exon31	c.A5950G	p.M1984V	CAGTCATAGGACC	.	1978.0	89.0	186.0	0.0	.	408	.	.	Atlas-SNP
EFEMP2	30008	hgsc.bcm.edu	hg19	11	65638628	65638628	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	EFEMP2	NM_016938	exon4	c.G367T	p.D123Y	ACTCACCCACACA	.	58.0	20.0	23.0	0.0	.	42	.	.	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	hg19	12	31255209	31255209	+	Silent	SNP	G	G	A	rs71447572		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DDX11	NM_030653	exon22	c.G2235A	p.V745V	CCAGGTGGAGCAG	.	236.0	12.0	105.0	0.0	.	188	.	G|0.500;A|0.500	Atlas-SNP
TMTC2	160335	hgsc.bcm.edu	hg19	12	83358835	83358835	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TMTC2	NM_152588	exon5	c.C1631G	p.A544G	GGTTTGCAGAAGC	.	498.0	193.0	131.0	0.0	.	100	.	.	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	hg19	12	89916794	89916794	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	GALNT4	NM_003774	exon1	c.T1533G	p.N511K	CACATAATTTTTT	.	169.0	85.0	59.0	0.0	.	38	.	.	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	hg19	12	117768410	117768410	+	Silent	SNP	G	G	A	rs369224010		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NOS1	NM_000620	exon2	c.C465T	p.P155P	ATTCCCGGGACCC	.	55.0	22.0	25.0	0.0	.	240	.	.	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	hg19	12	125453127	125453127	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DHX37	NM_032656	exon10	c.G1361T	p.G454V	CACTCGCCACTGT	.	32.0	16.0	19.0	0.0	.	114	.	.	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	hg19	13	103390332	103390332	+	Missense_Mutation	SNP	C	C	T	rs200872789	bycluster	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001146197	exon4	c.G12715A	p.E4239K	CAACTTCGTGATC	.	924.0	375.0	166.0	0.0	.	.	.	.	Atlas-SNP
SYNDIG1L	646658	hgsc.bcm.edu	hg19	14	74876039	74876039	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYNDIG1L	NM_001105579	exon2	c.G409A	p.E137K	CCTCTTCCTCCTG	.	88.0	54.0	72.0	0.0	.	24	.	.	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	hg19	16	88776355	88776355	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CTU2	NM_001012759	exon3	c.C153T	p.F51F	CTGTTTCAAGGCC	.	102.0	44.0	62.0	0.0	.	66	.	.	Atlas-SNP
DLG4	1742	hgsc.bcm.edu	hg19	17	7097812	7097812	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DLG4	NM_001365	exon14	c.C1433T	p.A478V	AACAGGGCCCTGG	.	45.0	30.0	35.0	0.0	.	110	.	.	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	hg19	17	39525703	39525703	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	KRT33B	NM_002279	exon1	c.C300T	p.C100C	GCTGGGGCACAGC	.	112.0	10.0	40.0	0.0	.	46	.	.	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	hg19	17	80115731	80115731	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CCDC57	NM_198082	exon14	c.C2134T	p.Q712X	CCACCTGCTTCCG	.	49.0	28.0	25.0	0.0	.	102	.	.	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	hg19	18	10471887	10471887	+	Silent	SNP	C	C	T	rs145453912	byfrequency;alternate_allele	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	APCDD1,NS,carcinoma,0,1	APCDD1	NM_153000	exon3	c.C603T	p.A201A	CAAGGCCGTGAAC	.	69.0	26.0	30.0	0.0	.	57	.	C|1.000;G|0.000	Atlas-SNP
ZNF527	84503	hgsc.bcm.edu	hg19	19	37879212	37879212	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ZNF527	NM_032453	exon5	c.G261T	p.W87C	AGACTGGGAGTCT	.	240.0	92.0	88.0	0.0	.	78	.	.	Atlas-SNP
HNRNPL	3191	hgsc.bcm.edu	hg19	19	39328060	39328060	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	HNRNPL	NM_001533	exon12	c.C1675G	p.L559V	AGCCCAGAGTCTC	.	172.0	68.0	69.0	0.0	.	67	.	.	Atlas-SNP
OSCAR	126014	hgsc.bcm.edu	hg19	19	54602893	54602893	+	Splice_Site	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OSCAR	NM_130771	exon4	c.71-1G>T	.	TGGCCACTAAGGG	.	117.0	50.0	44.0	0.0	.	22	.	.	Atlas-SNP
COX4I2	84701	hgsc.bcm.edu	hg19	20	30227827	30227827	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	COX4I2	NM_032609	exon3	c.C174T	p.N58N	ACTCAACGCTGAG	.	22.0	11.0	15.0	0.0	.	18	.	.	Atlas-SNP
TRPC4AP	26133	hgsc.bcm.edu	hg19	20	33598060	33598060	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRPC4AP	NM_015638	exon12	c.C1441G	p.L481V	CATTCAGCTCCTG	.	277.0	107.0	106.0	0.0	.	64	.	.	Atlas-SNP
LCA5L	150082	hgsc.bcm.edu	hg19	21	40800132	40800132	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	LCA5L	NM_152505	exon4	c.A288G	p.K96K	ATACTTTTTCTTC	.	303.0	123.0	109.0	0.0	.	57	.	.	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	hg19	21	47773060	47773060	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCNT	NM_006031	exon10	c.A1499G	p.D500G	TGGAAGATTTAGA	.	92.0	25.0	56.0	0.0	.	283	.	.	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	hg19	22	32111160	32111160	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PRR14L	NM_173566	exon4	c.A2665C	p.T889P	GAATGGTTTTGTT	.	438.0	208.0	123.0	0.0	.	198	.	.	Atlas-SNP
PNMA3	29944	hgsc.bcm.edu	hg19	X	152225435	152225435	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PNMA3	NM_013364	exon2	c.A23G	p.D8G	TACAGGACTGGTG	.	117.0	104.0	40.0	0.0	.	81	.	.	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9329	9329	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	ENST00000362079	exon1	c.G123A	p.T41T	CATAACGCTCCTC	.	243.0	17.0	24.0	0.0	.	.	.	.	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	11120	11120	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	ENST00000361381	exon1	c.T361C	p.F121L	TATATCTTCTTCG	.	226.0	10.0	20.0	0.0	.	.	.	.	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	hg19	22	29885573	29885574	+	In_Frame_Ins	INS	-	-	CCTGAGAAGGCCAAGTCC	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NEFH	NM_021076	exon4	c.1944_1945insCCTGAGAAGGCCAAGTCC	p.S648delinsSPEKAKS	.	.	152.0	19.0	46.0	0.0	.	178	.	.	Atlas-INDEL
MYH11	4629	hgsc.bcm.edu	hg19	16	15808930	15808930	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MYH11	NM_001040114	exon41	c.5644delG	p.G1882fs	.	.	92.0	39.0	49.0	0.0	.	520	.	.	Atlas-Indel,Pindel
C2orf62	375307	hgsc.bcm.edu	hg19	2	219222268	219222286	+	Frame_Shift_Del	DEL	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	C2orf62	NM_198559	exon3	c.129_147del	p.43_49del	.	.	41.0	16.0	37.0	0.0	.	28	.	.	Atlas-INDEL
METTL2B	55798	hgsc.bcm.edu	hg19	7	128140983	128140984	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	METTL2B	NM_018396	exon8	c.943_944insT	p.V315fs	.	.	254.0	41.0	79.0	0.0	.	34	.	.	Atlas-INDEL
TRMT1L	81627	hgsc.bcm.edu	hg19	1	185089286	185089287	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRMT1L	NM_030934	exon15	c.2067_2068insT	p.L689fs	.	.	412.0	102.0	84.0	0.0	.	50	.	.	Atlas-Indel,Pindel
CRELD2	79174	hgsc.bcm.edu	hg19	22	50315943	50315980	+	Frame_Shift_Del	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CRELD2	NM_001135101	exon6	c.593_620del	p.198_207del	.	.	77.0	23.0	33.0	0.0	.	57	.	.	Atlas-Indel,Pindel
SMURF1	57154	hgsc.bcm.edu	hg19	7	98655111	98655111	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SMURF1	NM_020429	exon4	c.268delC	p.Q90fs	.	.	247.0	89.0	93.0	0.0	.	58	.	.	Atlas-Indel,Pindel
BCAP29	55973	hgsc.bcm.edu	hg19	7	107254121	107254122	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	BCAP29	NM_001008405	exon7	c.713_714insA	p.L238fs	.	.	199.0	15.0	72.0	0.0	.	46	.	.	Atlas-INDEL
APOB	338	hgsc.bcm.edu	hg19	2	21231993	21231994	+	Frame_Shift_Ins	INS	-	-	CTCTACC	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	APOB	NM_000384	exon26	c.7747_7748insGGTAGAG	p.Q2583fs	.	.	146.0	33.0	59.0	0.0	.	761	.	.	Atlas-Indel,Pindel
C2orf62	375307	hgsc.bcm.edu	hg19	2	219222270	219222288	+	Frame_Shift_Del	DEL	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	C2orf62	NM_198559	exon3	c.131_149del	p.44_50del	.	.	10.0	10.0	0.0	0.0	.	28	.	.	Pindel
METTL2B	55798	hgsc.bcm.edu	hg19	7	128140982	128140983	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	METTL2B	NM_018396	exon8	c.941_942del	p.314_314del	.	.	25.0	25.0	0.0	0.0	.	34	.	.	Pindel
CDC27	996	hgsc.bcm.edu	hg19	17	45234594	45234729	+	Frame_Shift_Del	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDC27	NM_001114091	exon6	c.601_631del	p.201_211del	.	.	19.0	19.0	0.0	0.0	.	337	.	.	Pindel
NCAM1	4684	hgsc.bcm.edu	hg19	11	112832332	112832363	+	Frame_Shift_Del	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NCAM1	NM_001242607	wholegene	.	.	.	.	27.0	27.0	0.0	0.0	.	372	.	.	Pindel