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
ITGA10	8515	hgsc.bcm.edu	hg19	1	145532515	145532515	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ITGA10	NM_003637	exon9	c.G968A	p.R323K	AAATTAGAACTAT	.	170.0	66.0	143.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA6C	10500	hgsc.bcm.edu	hg19	1	151109386	151109386	+	Silent	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SEMA6C	NM_001178061	exon11	c.G921A	p.V307V	CAGGTTCACAGGC	.	165.0	47.0	184.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	hg19	1	156877993	156877993	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PEAR1	NM_001080471	exon9	c.C976T	p.R326C	GACGCCCGTTGCT	.	22.0	11.0	31.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	hg19	1	167096129	167096129	+	Silent	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	DUSP27	NM_001080426	exon5	c.A1761G	p.T587T	CCTGACAGCCTAC	.	63.0	29.0	68.0	0.0	.	235	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf112	55732	hgsc.bcm.edu	hg19	1	169806133	169806133	+	Silent	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	C1orf112	NM_018186	exon17	c.C1605T	p.S535S	TATTTCCTTCCAG	.	65.0	23.0	63.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
PPFIA4	8497	hgsc.bcm.edu	hg19	1	203025587	203025587	+	Silent	SNP	C	C	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	PPFIA4_ENST00000272198,colon,carcinoma,0,3	PPFIA4	NM_015053	exon5	c.C673A	p.R225R	ACGCTGCGGCTAG	.	47.0	3.0	51.0	0.0	.	139	.	.	.	none	.	.	PASS	Atlas-SNP
EMILIN1	11117	hgsc.bcm.edu	hg19	2	27306240	27306240	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	EMILIN1	NM_007046	exon4	c.C1801A	p.R601S	GTGGAGCGCTGCT	.	88.0	4.0	98.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
EIF2AK2	5610	hgsc.bcm.edu	hg19	2	37365711	37365711	+	Silent	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	EIF2AK2	NM_001135652	exon5	c.C534T	p.S178S	ACCAGAGGACAGG	.	71.0	32.0	75.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1841	84542	hgsc.bcm.edu	hg19	2	61310382	61310382	+	Missense_Mutation	SNP	C	C	A	rs140620846	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	KIAA1841_ENST00000402291,colon,carcinoma,0,2	KIAA1841	NM_032506	exon8	c.C823A	p.R275S	CTCACACGTATAG	.	45.0	2.0	48.0	0.0	.	95	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
GPAT2	150763	hgsc.bcm.edu	hg19	2	96687959	96687959	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	GPAT2,trunk,malignant_melanoma,0,2	GPAT2	NM_207328	exon22	c.T2336A	p.L779Q	TTGTCCAGGCTGG	.	35.0	2.0	34.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
CNNM4	26504	hgsc.bcm.edu	hg19	2	97428127	97428127	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CNNM4	NM_020184	exon1	c.A1391G	p.E464G	TGGAGGAGTTCAA	.	81.0	36.0	82.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM131	23505	hgsc.bcm.edu	hg19	2	98413329	98413329	+	Silent	SNP	T	T	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TMEM131	NM_015348	exon27	c.A2991T	p.A997A	TAACAATGCTTCC	.	65.0	23.0	59.0	0.0	.	258	.	.	.	none	.	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	hg19	2	238280361	238280361	+	Silent	SNP	C	C	T	rs373893821		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	COL6A3	NM_057165	exon8	c.G3681A	p.A1227A	CTCCGACGCCCCC	.	171.0	54.0	147.0	0.0	.	608	.	.	.	weak	.	.	PASS	Atlas-SNP
CAPN7	23473	hgsc.bcm.edu	hg19	3	15288921	15288921	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CAPN7	NM_014296	exon19	c.A2161G	p.I721V	TTCCATATAGAAA	.	116.0	46.0	121.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ACAA1	30	hgsc.bcm.edu	hg19	3	38168151	38168151	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ACAA1	NM_001607	exon8	c.A667C	p.I223L	GCACAATCTCAGC	.	125.0	54.0	117.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	hg19	3	44926858	44926858	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TGM4	NM_003241	exon2	c.G61T	p.A21S	GACAACGCCGTTT	.	44.0	13.0	48.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
SETD2	29072	hgsc.bcm.edu	hg19	3	47127778	47127778	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SETD2	NM_014159	exon11	c.G5304T	p.K1768N	AAAGGACTTCAGG	.	57.0	22.0	72.0	0.0	.	721	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM175	84286	hgsc.bcm.edu	hg19	4	947053	947053	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TMEM175	NM_032326	exon8	c.C538G	p.L180V	AGGGCTCTGTACC	.	65.0	33.0	52.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	hg19	4	1805487	1805487	+	Silent	SNP	C	C	T	rs370530264		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	FGFR3,colon,carcinoma,0,1	FGFR3	NM_000142	exon8	c.C999T	p.D333D	TGAGGACGCCGGG	.	70.0	3.0	65.0	0.0	.	3320	.	.	.	weak	.	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	hg19	4	3443800	3443800	+	Silent	SNP	G	G	C	rs372137428		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	HGFAC	NM_001528	exon1	c.G72C	p.L24L	CCTCCTGCTGCTG	.	55.0	5.0	39.0	0.0	.	69	.	.	.	weak	.	.	PASS	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	hg19	4	9784197	9784197	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	DRD5	NM_000798	exon1	c.A544T	p.R182W	TGGCACAGGGACC	.	84.0	33.0	92.0	0.0	.	119	.	.	.	none	.	.	PASS	Atlas-SNP
ANK2	287	hgsc.bcm.edu	hg19	4	114232517	114232517	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ANK2	NM_001148	exon24	c.T2655A	p.N885K	TATGAATTACCTG	.	73.0	39.0	95.0	0.0	.	576	.	.	.	none	.	.	PASS	Atlas-SNP
TRPC3	7222	hgsc.bcm.edu	hg19	4	122825594	122825594	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TRPC3	NM_001130698	exon8	c.T2136G	p.D712E	TTTGTGATCATAT	.	52.0	20.0	74.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	hg19	5	74026107	74026107	+	Silent	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	GFM2	NM_032380	exon17	c.C1704A	p.I568I	GTTTAGGATGGTC	.	114.0	32.0	69.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
POC5	134359	hgsc.bcm.edu	hg19	5	74981182	74981182	+	Silent	SNP	G	G	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	POC5	NM_001099271	exon10	c.C1257G	p.S419S	TGGTGGGGATGGC	.	199.0	47.0	120.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	hg19	5	98195710	98195710	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CHD1	NM_001270	exon32	c.A4490G	p.Y1497C	TGCTTATATAATT	.	67.0	42.0	62.0	0.0	.	137	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	hg19	5	140724210	140724210	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PCDHGA3	NM_032011	exon1	c.A610T	p.K204X	CGTGAGAAAAAAG	.	136.0	39.0	111.0	0.0	.	246	.	.	.	none	.	.	PASS	Atlas-SNP
PCDH1	5097	hgsc.bcm.edu	hg19	5	141233788	141233788	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	PCDH1,NS,carcinoma,0,1	PCDH1	NM_032420	exon5	c.G3533A	p.R1178Q	GTGTTCCGGTCTT	.	39.0	3.0	18.0	0.0	.	119	.	.	.	none	.	.	PASS	Atlas-SNP
SLC22A7	10864	hgsc.bcm.edu	hg19	6	43266249	43266249	+	Silent	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	SLC22A7,NS,carcinoma,0,1	SLC22A7	NM_006672	exon1	c.G153A	p.L51L	TGCCCTGCCGGGT	.	89.0	35.0	116.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC1	55227	hgsc.bcm.edu	hg19	6	53660212	53660212	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	LRRC1	NM_018214	exon1	c.A158T	p.E53V	TGCCCGAGGTAAG	.	31.0	9.0	26.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	hg19	6	74407130	74407130	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CD109	NM_133493	exon2	c.T82C	p.F28L	CCTCGGTTTCTGG	.	118.0	49.0	113.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	hg19	6	79724879	79724879	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PHIP	NM_017934	exon15	c.C1444T	p.L482F	AAAAGAGAACTCT	.	82.0	10.0	93.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
GPNMB	10457	hgsc.bcm.edu	hg19	7	23306207	23306207	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	GPNMB	NM_001005340	exon7	c.C1126A	p.H376N	TATGGCCACTTTC	.	52.0	19.0	52.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	hg19	7	42063171	42063171	+	Missense_Mutation	SNP	C	C	T	rs35488756	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	GLI3	NM_000168	exon10	c.G1393A	p.G465R	TGTCCCCTTCCTC	.	102.0	41.0	103.0	0.0	.	312	.	.	.	alt	C|0.997;G|0.003	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	hg19	7	121651018	121651018	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PTPRZ1	NM_001206838	exon12	c.G1918C	p.E640Q	GGTTCAGAAGAAT	.	105.0	45.0	113.0	0.0	.	605	.	.	.	none	.	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	hg19	8	144942527	144942527	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	EPPK1	NM_031308	exon1	c.G4895C	p.G1632A	AACATTCCTGCTT	.	128.0	42.0	104.0	0.0	.	199	.	.	.	none	.	.	PASS	Atlas-SNP
CNTRL	11064	hgsc.bcm.edu	hg19	9	123900898	123900898	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CNTRL	NM_007018	exon14	c.T2278G	p.F760V	GCCCAGTTCTCAG	.	101.0	42.0	93.0	0.0	.	161	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	hg19	9	136305499	136305499	+	Silent	SNP	G	G	T	rs371209152	alternate_allele	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ADAMTS13	NM_139027	exon16	c.G1821T	p.G607G	GGCTGGGAAGATG	.	103.0	32.0	107.0	0.0	.	113	.	.	.	alt	.	.	PASS	Atlas-SNP
SLC18A3	6572	hgsc.bcm.edu	hg19	10	50819621	50819621	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SLC18A3	NM_003055	exon1	c.G835C	p.G279R	CCAGTGGGCACTC	.	126.0	31.0	120.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	hg19	10	70450862	70450862	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TET1	NM_030625	exon12	c.T5702G	p.I1901S	CTGGCATTTCACA	.	167.0	91.0	118.0	0.0	.	255	.	.	.	none	.	.	PASS	Atlas-SNP
H2AFY2	55506	hgsc.bcm.edu	hg19	10	71868875	71868875	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	H2AFY2	NM_018649	exon8	c.C865A	p.Q289K	GAAGAACAGCTTG	.	167.0	24.0	92.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM8	81603	hgsc.bcm.edu	hg19	10	104415049	104415049	+	Silent	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TRIM8	NM_030912	exon3	c.G879A	p.T293T	TAAGACGGAGGAT	.	92.0	8.0	74.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	hg19	10	115372127	115372127	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	NRAP,caecum,carcinoma,0,1	NRAP	NM_001261463	exon30	c.G3364C	p.A1122P	CCAGGGCGGCCAT	.	157.0	44.0	99.0	0.0	.	208	.	.	.	none	.	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	hg19	11	21594920	21594920	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	NELL1	NM_006157	exon19	c.A2347T	p.M783L	TGGACGATGGCTG	.	211.0	75.0	211.0	0.0	.	179	.	.	.	none	.	.	PASS	Atlas-SNP
IMMP1L	196294	hgsc.bcm.edu	hg19	11	31482191	31482191	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	IMMP1L	NM_144981	exon4	c.A176G	p.H59R	TAAAAATGTCGAC	.	36.0	11.0	59.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC73	493860	hgsc.bcm.edu	hg19	11	32676507	32676507	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	CCDC73,NS,carcinoma,-2,1	CCDC73	NM_001008391	exon10	c.T657G	p.D219E	GGCTGCTTTTTTT	.	25.0	2.0	42.0	0.0	.	136	.	.	.	none	.	.	PASS	Atlas-SNP
PRR5L	79899	hgsc.bcm.edu	hg19	11	36472765	36472765	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	PRR5L,NS,carcinoma,0,1	PRR5L	NM_024841	exon9	c.C592T	p.H198Y	AGTGTTCACGAGC	.	156.0	67.0	145.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
AAMDC	28971	hgsc.bcm.edu	hg19	11	77580812	77580812	+	Silent	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	.	NM_024684	exon3	c.G177A	p.E59E	TGTTGAGAAGGGT	.	264.0	91.0	338.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	hg19	11	82877724	82877724	+	Silent	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PCF11	NM_015885	exon5	c.A1785G	p.K595K	TGCCAAAAGATGG	.	125.0	55.0	142.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	hg19	11	128840894	128840894	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ARHGAP32	NM_001142685	exon22	c.G4172A	p.R1391Q	GGGACCCGGGCAC	.	61.0	25.0	58.0	0.0	.	307	.	.	.	none	.	.	PASS	Atlas-SNP
AKAP3	10566	hgsc.bcm.edu	hg19	12	4737430	4737430	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	AKAP3	NM_006422	exon4	c.A638C	p.K213T	TTGTATTTCAAAT	.	202.0	121.0	173.0	0.0	.	212	.	.	.	none	.	.	PASS	Atlas-SNP
GTSF1	121355	hgsc.bcm.edu	hg19	12	54856511	54856511	+	Splice_Site	SNP	T	T	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	GTSF1	NM_144594	exon6	c.245-2A>T	.	GTTGACTGCAAGA	.	168.0	46.0	93.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
WIF1	11197	hgsc.bcm.edu	hg19	12	65460514	65460514	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	WIF1	NM_007191	exon6	c.C637A	p.L213I	TACAAAGGGCTTA	.	54.0	14.0	44.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN11	5781	hgsc.bcm.edu	hg19	12	112892407	112892407	+	Missense_Mutation	SNP	T	T	G	rs79068130	bycluster	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	PTPN11,NS,carcinoma,0,1	PTPN11	NM_080601	exon5	c.T565G	p.S189A	TTTGATTCTTTGA	.	121.0	6.0	72.0	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-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	PTPN11,NS,carcinoma,0,2	PTPN11	NM_080601	exon5	c.T616C	p.L206L	GAAACATTGGGTA	.	99.0	5.0	60.0	0.0	.	623	.	.	.	weak	.	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	hg19	13	25029240	25029240	+	Silent	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PARP4	NM_006437	exon22	c.A2673G	p.T891T	CAAGAATGTCACA	.	286.0	104.0	257.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
CPB2	1361	hgsc.bcm.edu	hg19	13	46658419	46658419	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CPB2	NM_001872	exon3	c.T210G	p.F70L	TACAAAAAAATGG	.	171.0	74.0	166.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
AP1G2	8906	hgsc.bcm.edu	hg19	14	24032848	24032848	+	Splice_Site	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	AP1G2	NM_003917	exon14	c.1233-1G>A	.	GCAAACCTAGGGG	.	68.0	46.0	103.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	hg19	14	45711249	45711249	+	Silent	SNP	A	A	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	MIS18BP1	NM_018353	exon4	c.T1131G	p.L377L	TTTTTTAAGTCCA	.	47.0	30.0	110.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
SERINC4	619189	hgsc.bcm.edu	hg19	15	44090645	44090645	+	Silent	SNP	A	A	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SERINC4	NM_001258031	exon4	c.T516A	p.I172I	ATCAGGAATGCAG	.	91.0	44.0	102.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	hg19	15	101529603	101529603	+	Silent	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	LRRK1	NM_024652	exon6	c.A762G	p.T254T	AAAAACAGTGAGT	.	64.0	30.0	59.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
RAB11FIP3	9727	hgsc.bcm.edu	hg19	16	570232	570232	+	Silent	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	RAB11FIP3	NM_014700	exon12	c.C1971T	p.R657R	CAGCCGCGCCCGG	.	11.0	6.0	8.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
ARL6IP1	23204	hgsc.bcm.edu	hg19	16	18810023	18810023	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ARL6IP1	NM_015161	exon2	c.T170C	p.L57P	ACTTACAGAAACA	.	168.0	63.0	147.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
PRSS53	339105	hgsc.bcm.edu	hg19	16	31098021	31098021	+	Silent	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PRSS53	NM_001039503	exon4	c.G441A	p.Q147Q	GGCGGGCTGGGGC	.	94.0	44.0	78.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
DDX19B	11269	hgsc.bcm.edu	hg19	16	70346536	70346536	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	RP11-529K1.3,NS,carcinoma,0,2	DDX19B	NM_001257172	exon2	c.G97C	p.E33Q	AAGGAAGAGAAAA	.	35.0	2.0	55.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
TXNL4B	54957	hgsc.bcm.edu	hg19	16	72120699	72120699	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TXNL4B	NM_001142318	exon4	c.C287A	p.S96Y	TCTGGAGATCTAG	.	61.0	26.0	68.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
SLC2A4	6517	hgsc.bcm.edu	hg19	17	7189210	7189210	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SLC2A4	NM_001042	exon10	c.G1309C	p.G437R	GGCATGGGTTTCC	.	71.0	24.0	62.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
POLR2A	5430	hgsc.bcm.edu	hg19	17	7399344	7399344	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	POLR2A	NM_000937	exon2	c.C178G	p.P60A	ATGGACCCGAGGC	.	100.0	36.0	79.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
TAF15	8148	hgsc.bcm.edu	hg19	17	34172014	34172014	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TAF15	NM_139215	exon15	c.G1711T	p.G571C	GACCGAGGTGGCT	.	165.0	55.0	168.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	hg19	17	35567392	35567392	+	Silent	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ACACA	NM_198834	exon30	c.T3696C	p.P1232P	TAGCGTAGGGATG	.	97.0	4.0	104.0	0.0	.	395	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC46	90506	hgsc.bcm.edu	hg19	17	45914207	45914207	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	LRRC46	NM_033413	exon8	c.G687A	p.M229I	GGAGATGCAGCCC	.	132.0	38.0	97.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
ACSF2	80221	hgsc.bcm.edu	hg19	17	48549793	48549793	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ACSF2	NM_025149	exon12	c.G1328A	p.R443Q	AGGCCCGGATCAT	.	53.0	31.0	34.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PITPNC1	26207	hgsc.bcm.edu	hg19	17	65665781	65665781	+	Splice_Site	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PITPNC1	NM_181671	exon7	c.618+2T>C	.	ACAAGGTAAGTGG	.	20.0	12.0	10.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	hg19	17	76491997	76491997	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	DNAH17	NM_173628	exon38	c.G5863C	p.G1955R	CGCGTCCGGCGTA	.	82.0	20.0	77.0	0.0	.	347	.	.	.	none	.	.	PASS	Atlas-SNP
PNPLA6	10908	hgsc.bcm.edu	hg19	19	7615223	7615223	+	Silent	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PNPLA6	NM_001166111	exon17	c.G1881A	p.A627A	TGCGGCGCACACG	.	149.0	53.0	113.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
JUNB	3726	hgsc.bcm.edu	hg19	19	12902787	12902787	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	JUNB	NM_002229	exon1	c.T202C	p.Y68H	GGCAGCTACTTTT	.	31.0	13.0	15.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF681	148213	hgsc.bcm.edu	hg19	19	23927146	23927146	+	Silent	SNP	A	A	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	ZNF681,bladder,carcinoma,0,8	ZNF681	NM_138286	exon4	c.T1206C	p.A402A	GTTAAAAGCTTTG	.	62.0	3.0	53.0	1.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
LSM14A	26065	hgsc.bcm.edu	hg19	19	34712486	34712486	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	LSM14A	NM_001114093	exon9	c.G1211T	p.R404L	CAAACCGTGGCCG	.	63.0	20.0	87.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	hg19	19	38572702	38572702	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SIPA1L3	NM_015073	exon3	c.T497C	p.L166P	TCCCCCTTCGGCA	.	125.0	52.0	105.0	0.0	.	150	.	.	.	none	.	.	PASS	Atlas-SNP
MYL9	10398	hgsc.bcm.edu	hg19	20	35177592	35177592	+	Silent	SNP	C	C	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	MYL9	NM_006097	exon4	c.C459T	p.N153N	AGGCAACTTCAAC	.	69.0	20.0	49.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
UBA1	7317	hgsc.bcm.edu	hg19	X	47069022	47069022	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	UBA1	NM_153280	exon17	c.T1939G	p.W647G	CTGCAGTGGGCTC	.	32.0	26.0	21.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	hg19	X	153037078	153037078	+	Missense_Mutation	SNP	G	G	C	rs375202688		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	PLXNB3	NM_001163257	exon15	c.G2554C	p.E852Q	GCTGTGGAGCTGC	.	12.0	12.0	14.0	0.0	.	208	.	.	.	weak	.	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	hg19	MT	3776	3776	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	.	ENST00000361390	exon1	c.G470A	p.S157N	TAATAAGTGGCTC	.	10.0	10.0	1.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	hg19	MT	13814	13814	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	.	ENST00000361567	exon1	c.T1478C	p.V493A	TCGCTGTCACTTT	.	15.0	14.0	0.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
UEVLD	55293	hgsc.bcm.edu	hg19	11	18568448	18568448	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	UEVLD	NM_018314	exon8	c.866delT	p.L289fs	.	.	98.0	35.0	125.0	0.0	.	58	.	0.357143	0	none	.	.	PASS	Atlas-INDEL
FAM208B	54906	hgsc.bcm.edu	hg19	10	5790239	5790239	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	.	NM_017782	exon15	c.4854delC	p.L1618fs	.	.	133.0	29.0	91.0	0.0	.	.	.	0.218045	0	none	.	.	PASS	Atlas-INDEL
GALNT5	11227	hgsc.bcm.edu	hg19	2	158115698	158115699	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	GALNT5	NM_014568	exon1	c.1104_1105insT	p.S368fs	.	.	147.0	49.0	186.0	0.0	.	112	.	0.333333	0	none	.	.	PASS	Atlas-INDEL
ATP1B1	481	hgsc.bcm.edu	hg19	1	169100749	169100768	+	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	ATP1B1	NM_001677	exon6	c.867_886del	p.289_296del	.	.	79.0	26.0	113.0	0.0	.	29	.	0.329114	0	none	.	.	PASS	Atlas-INDEL
STAG2	10735	hgsc.bcm.edu	hg19	X	123211859	123211862	+	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	AGAT	AGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	STAG2	NM_001042749	exon27	c.2725_2728del	p.909_910del	.	.	58.0	45.0	69.0	0.0	.	309	.	0.775862	0	none	.	.	PASS	Atlas-INDEL
CENPH	64946	hgsc.bcm.edu	hg19	5	68505552	68505552	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	CENPH	NM_022909	exon9	c.669delT	p.S223fs	.	.	57.0	31.0	57.0	0.0	.	28	.	0.54386	0	none	.	.	PASS	Atlas-INDEL
ADAM29	11086	hgsc.bcm.edu	hg19	4	175898831	175898832	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	ADAM29,NS,malignant_melanoma,0,1	ADAM29	NM_014269	exon5	c.2155_2156insA	p.E719fs	.	.	73.0	46.0	101.0	0.0	.	262	.	0.630137	0	none	.	.	PASS	Atlas-INDEL
UFL1	23376	hgsc.bcm.edu	hg19	6	96996102	96996102	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	.	NM_015323	exon13	c.1464delA	p.K488fs	.	.	35.0	17.0	45.0	0.0	.	.	.	0.485714	0	none	.	.	PASS	Atlas-INDEL
MSH3	4437	hgsc.bcm.edu	hg19	5	80160742	80160743	+	Frame_Shift_Ins	INS	-	-	GAAA	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	MSH3	NM_002439	exon22	c.3111_3112insGAAA	p.D1037fs	.	.	171.0	38.0	143.0	0.0	.	129	.	0.222222	0	none	.	.	PASS	Atlas-INDEL
TGIF2	60436	hgsc.bcm.edu	hg19	20	35219568	35219569	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	TGIF2	NM_021809	exon3	c.448_449insA	p.E150fs	.	.	104.0	42.0	101.0	0.0	.	26	.	0.403846	0	none	.	.	PASS	Atlas-INDEL
SLC26A8	116369	hgsc.bcm.edu	hg19	6	35923086	35923086	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	SLC26A8	NM_001193476	exon17	c.2076delC	p.N692fs	.	.	108.0	45.0	122.0	0.0	.	95	.	0.416667	0	none	.	.	PASS	Atlas-INDEL
NCOA2	10499	hgsc.bcm.edu	hg19	8	71039066	71039067	+	Frame_Shift_Ins	INS	-	-	AAAC	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	.	NCOA2	NM_006540	exon19	c.3898_3899insGTTT	p.P1300fs	.	.	50.0	11.0	43.0	0.0	.	147	.	0.22	0	none	.	.	PASS	Atlas-INDEL
LGR4	55366	hgsc.bcm.edu	hg19	11	27412675	27412676	+	In_Frame_Ins	INS	-	-	AAG	novel		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	LGR4,NS,carcinoma,0,1	LGR4	NM_018490	exon4	c.367_368insCTT	p.E123delinsLE	.	.	83.0	21.0	85.0	0.0	.	87	.	0.253012	0	none	.	.	PASS	Atlas-INDEL