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
TAS1R3	83756	hgsc.bcm.edu	hg19	1	1267767	1267767	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TAS1R3	NM_152228	exon3	c.T856C	p.Y286H	TTCAACTACAGCA	.	54.0	19.0	133.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	hg19	1	66088612	66088612	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	LEPR	NM_001003680	exon19	c.A2621G	p.D874G	GGGAAGATGTTCC	.	92.0	32.0	59.0	0.0	.	284	.	.	.	none	.	.	PASS	Atlas-SNP
PRCC	5546	hgsc.bcm.edu	hg19	1	156767106	156767106	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PRCC	NM_005973	exon6	c.A1362C	p.K454N	GCGGAAACACCAG	.	118.0	44.0	77.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	hg19	1	179310206	179310206	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	SOAT1	NM_003101	exon7	c.T541G	p.F181V	GGCAAATTTCCTA	.	85.0	41.0	57.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
SMG7	9887	hgsc.bcm.edu	hg19	1	183495889	183495889	+	Silent	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	SMG7	NM_201569	exon5	c.C471T	p.H157H	CGTCCACCTTGGA	.	59.0	24.0	51.0	0.0	.	165	.	.	.	none	.	.	PASS	Atlas-SNP
IRF2BP2	359948	hgsc.bcm.edu	hg19	1	234743069	234743069	+	Silent	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	IRF2BP2	NM_182972	exon2	c.G1578C	p.S526S	CTTGTGCGAAGGG	.	64.0	29.0	115.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
DESI2	51029	hgsc.bcm.edu	hg19	1	244849928	244849928	+	Silent	SNP	T	T	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	.	NM_016076	exon2	c.T72A	p.I24I	ATCCATTGGAATT	.	37.0	10.0	46.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	hg19	2	27456276	27456276	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CAD	NM_004341	exon20	c.C3088A	p.Q1030K	CATCGGCAGCAGT	.	88.0	4.0	53.0	0.0	.	199	.	.	.	none	.	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	hg19	2	86272888	86272888	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	POLR1A	NM_015425	exon20	c.C2738T	p.S913L	AGGCACGAGATCT	.	337.0	96.0	183.0	0.0	.	137	.	.	.	none	.	.	PASS	Atlas-SNP
PAX8	7849	hgsc.bcm.edu	hg19	2	114000281	114000281	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PAX8	NM_013952	exon5	c.C464A	p.P155H	TGTCCGGGACTCA	.	155.0	39.0	126.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
HOXD1	3231	hgsc.bcm.edu	hg19	2	177054137	177054137	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	HOXD1	NM_024501	exon1	c.G608T	p.S203I	CCTTCAGCACGTT	.	152.0	91.0	258.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
CAPN7	23473	hgsc.bcm.edu	hg19	3	15287046	15287046	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CAPN7	NM_014296	exon17	c.A1878G	p.P626P	ACCTCCATACATT	.	86.0	27.0	64.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
UBE2K	3093	hgsc.bcm.edu	hg19	4	39779353	39779353	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	UBE2K	NM_005339	exon6	c.G451A	p.V151M	GCACATGTGTATG	.	181.0	52.0	144.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	hg19	4	66535302	66535302	+	Silent	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	EPHA5	NM_004439	exon1	c.C159A	p.L53L	GGCCAGGAGGGTC	.	183.0	120.0	275.0	0.0	.	315	.	.	.	none	.	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	hg19	4	126239708	126239708	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	FAT4	NM_024582	exon1	c.T2142C	p.T714T	TGCCACTGACCCA	.	120.0	30.0	84.0	0.0	.	1752	.	.	.	none	.	.	PASS	Atlas-SNP
POU5F2	134187	hgsc.bcm.edu	hg19	5	93076747	93076747	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	POU5F2	NM_153216	exon1	c.G523A	p.A175T	TGTTGGCGACGCT	.	44.0	26.0	31.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
GLRA1	2741	hgsc.bcm.edu	hg19	5	151231003	151231003	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	GLRA1	NM_000171	exon7	c.C860T	p.T287I	AGCACAGTGGTGA	.	155.0	39.0	83.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
NEDD9	4739	hgsc.bcm.edu	hg19	6	11185765	11185765	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	NEDD9	NM_001142393	exon8	c.A2135G	p.Y712C	TGGTCATAGTAGA	.	56.0	25.0	54.0	0.0	.	191	.	.	.	none	.	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152497619	152497619	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	SYNE1	NM_182961	exon130	c.C23537T	p.A7846V	TGGCTGGCTTTAG	.	82.0	29.0	65.0	0.0	.	3227	.	.	.	none	.	.	PASS	Atlas-SNP
BUD31	8896	hgsc.bcm.edu	hg19	7	99008752	99008752	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	BUD31	NM_003910	exon3	c.G37A	p.D13N	CCCCCAGATGGCT	.	148.0	90.0	136.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
MBLAC1	255374	hgsc.bcm.edu	hg19	7	99725163	99725163	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MBLAC1	NM_203397	exon2	c.C145T	p.P49S	GTCCTACCCCAGA	.	94.0	31.0	169.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
KLHDC10	23008	hgsc.bcm.edu	hg19	7	129760626	129760626	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	KLHDC10	NM_014997	exon4	c.T513C	p.G171G	TGGAGGTACGGGC	.	164.0	51.0	96.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	hg19	7	158528197	158528197	+	Silent	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ESYT2	NM_020728	exon20	c.C2583T	p.G861G	TACTTTGCCAAGG	.	50.0	10.0	69.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
RB1CC1	9821	hgsc.bcm.edu	hg19	8	53596456	53596456	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	RB1CC1	NM_001083617	exon4	c.T189C	p.S63S	CCCAGCACTGTAG	.	61.0	17.0	47.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	hg19	9	35714845	35714845	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TLN1	NM_006289	exon22	c.C2783A	p.A928D	TGTGTGGCTGAGG	.	21.0	6.0	29.0	0.0	.	185	.	.	.	none	.	.	PASS	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	hg19	9	101546386	101546386	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ANKS6	NM_173551	exon4	c.T961G	p.L321V	TGACCAAGTTCAC	.	27.0	6.0	49.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	hg19	9	130742371	130742371	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	FAM102A	NM_001035254	exon1	c.T46G	p.F16V	GGGTGAAAGTAGT	.	93.0	30.0	183.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf96	169436	hgsc.bcm.edu	hg19	9	136253234	136253234	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	C9orf96	NM_153710	exon5	c.T298G	p.S100A	CAGATCTCTTCTC	.	68.0	30.0	109.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
ARID5B	84159	hgsc.bcm.edu	hg19	10	63829547	63829547	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ARID5B	NM_032199	exon8	c.A1190G	p.H397R	GCAGACATTATGA	.	100.0	53.0	53.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
DPYSL4	10570	hgsc.bcm.edu	hg19	10	134011925	134011925	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	DPYSL4	NM_006426	exon7	c.A628T	p.K210X	GAGCAGAAGCGGT	.	41.0	25.0	63.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	hg19	10	135438923	135438923	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	FRG2B	NM_001080998	exon4	c.A517G	p.K173E	AGCTTTTTCGAAT	.	293.0	127.0	303.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
KCNQ1	3784	hgsc.bcm.edu	hg19	11	2608884	2608884	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	KCNQ1	NM_000218	exon9	c.C1213G	p.L405V	CACACTCTGCTGT	.	65.0	23.0	122.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	hg19	11	51411524	51411524	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	OR4A5	NM_001005272	exon1	c.T872G	p.M291R	TTTCTCATCTCTG	.	104.0	45.0	39.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	hg19	11	65395000	65395000	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PCNXL3	NM_032223	exon22	c.C3649G	p.L1217V	CCGCGCCTCTCCC	.	25.0	10.0	72.0	0.0	.	140	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1377	57562	hgsc.bcm.edu	hg19	11	101829047	101829047	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	KIAA1377	NM_020802	exon5	c.C655G	p.L219V	CTTAAACTGGAGG	.	102.0	32.0	68.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	hg19	12	6103203	6103203	+	Silent	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	VWF	NM_000552	exon37	c.C6423A	p.V2141V	GAGGAGGACCTGG	.	141.0	40.0	62.0	0.0	.	338	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL42	57542	hgsc.bcm.edu	hg19	12	27950834	27950834	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	.	NM_020782	exon3	c.T1253A	p.V418E	TCACCGTGCAGTC	.	264.0	86.0	91.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SMAGP	57228	hgsc.bcm.edu	hg19	12	51639787	51639787	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	SMAGP	NM_001031628	exon4	c.G232A	p.A78T	CGATGGCACTGGG	.	198.0	113.0	82.0	0.0	.	7	.	.	.	none	.	.	PASS	Atlas-SNP
CUX2	23316	hgsc.bcm.edu	hg19	12	111729279	111729279	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CUX2	NM_015267	exon5	c.G359A	p.S120N	CCCCCAGCTTTGA	.	133.0	20.0	100.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
MSI1	4440	hgsc.bcm.edu	hg19	12	120795647	120795647	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MSI1	NM_002442	exon8	c.T506A	p.I169N	AAATGAATTTCAC	.	143.0	29.0	125.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
PAN3	255967	hgsc.bcm.edu	hg19	13	28794514	28794514	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PAN3	NM_175854	exon6	c.A999G	p.P333P	AGCGCCAGGTAAG	.	55.0	24.0	38.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	hg19	13	32808840	32808840	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	FRY	NM_023037	exon42	c.T5657C	p.L1886S	ATGCCTTATCTGA	.	104.0	14.0	71.0	0.0	.	312	.	.	.	none	.	.	PASS	Atlas-SNP
SAV1	60485	hgsc.bcm.edu	hg19	14	51111608	51111608	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	SAV1	NM_021818	exon3	c.T660A	p.H220Q	TGTGTTATGATCT	.	58.0	27.0	46.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP11A	9824	hgsc.bcm.edu	hg19	15	32928491	32928491	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ARHGAP11A	NM_014783	exon12	c.T1517C	p.L506S	AAACCTTACTAAC	.	90.0	33.0	88.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	hg19	15	43769942	43769942	+	Silent	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TP53BP1	NM_001141980	exon8	c.T804G	p.P268P	GCTAAAAGGCATG	.	62.0	21.0	89.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
MEX3B	84206	hgsc.bcm.edu	hg19	15	82336360	82336360	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MEX3B	NM_032246	exon2	c.A851G	p.Y284C	TTGCGGTAGCTAG	.	25.0	10.0	45.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
GTF3C1	2975	hgsc.bcm.edu	hg19	16	27523094	27523094	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	GTF3C1	NM_001520	exon7	c.A1102G	p.M368V	TGAGCATATCCCG	.	103.0	55.0	79.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF629	23361	hgsc.bcm.edu	hg19	16	30795034	30795034	+	Silent	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ZNF629	NM_001080417	exon3	c.C615T	p.P205P	CTTGTAGGGCTTC	.	60.0	39.0	132.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
IRX6	79190	hgsc.bcm.edu	hg19	16	55359021	55359021	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	IRX6	NM_024335	exon1	c.T18G	p.F6L	ACACTTTGGACAC	.	50.0	25.0	96.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
KARS	3735	hgsc.bcm.edu	hg19	16	75674216	75674216	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	KARS	NM_001130089	exon4	c.A338G	p.H113R	AGCTGATGAATTG	.	76.0	46.0	58.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM88	92162	hgsc.bcm.edu	hg19	17	7758984	7758984	+	Silent	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TMEM88	NM_203411	exon2	c.C432G	p.A144A	CCGGGCCTCACCA	.	36.0	8.0	87.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
AOC2	314	hgsc.bcm.edu	hg19	17	41002294	41002294	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	AOC2	NM_009590	exon4	c.C2200T	p.P734S	ATCAATCCTGTGG	.	76.0	43.0	84.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
FZD2	2535	hgsc.bcm.edu	hg19	17	42636200	42636200	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	FZD2	NM_001466	exon1	c.G1144A	p.V382I	CCGGCCGTCAAGA	.	48.0	13.0	80.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
MYL12A	10627	hgsc.bcm.edu	hg19	18	3254019	3254019	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MYL12A	NM_006471	exon3	c.C314T	p.A105V	GAAATGCCTTTGC	.	199.0	73.0	223.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	hg19	18	7016662	7016662	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	LAMA1	NM_005559	exon21	c.T2817C	p.Y939Y	CCCATAATAGCCA	.	42.0	14.0	21.0	0.0	.	458	.	.	.	none	.	.	PASS	Atlas-SNP
DUS3L	56931	hgsc.bcm.edu	hg19	19	5786483	5786483	+	Silent	SNP	A	A	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	DUS3L	NM_020175	exon10	c.T1557A	p.I519I	CCGGGCAATCATG	.	28.0	12.0	74.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF565	147929	hgsc.bcm.edu	hg19	19	36674230	36674230	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ZNF565	NM_001042474	exon5	c.A638T	p.H213L	CTCTGATGCTGAA	.	56.0	22.0	58.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	hg19	19	50747513	50747513	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MYH14	NM_001077186	exon11	c.G1129A	p.V377I	CGGATGGTCTCAG	.	66.0	30.0	125.0	0.0	.	261	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	hg19	20	40713469	40713469	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PTPRT	NM_133170	exon30	c.G4046A	p.R1349H	ACTATACGATAAC	.	109.0	43.0	39.0	0.0	.	372	.	.	.	none	.	.	PASS	Atlas-SNP
PARD6B	84612	hgsc.bcm.edu	hg19	20	49354557	49354557	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PARD6B	NM_032521	exon2	c.A230C	p.N77T	ATGATAATTATCA	.	244.0	87.0	132.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP27-1	643812	hgsc.bcm.edu	hg19	21	31709386	31709386	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	KRTAP27-1	NM_001077711	exon1	c.G601T	p.G201C	GAGAACCACCAGT	.	166.0	35.0	59.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
BCL2L13	23786	hgsc.bcm.edu	hg19	22	18138483	18138483	+	Silent	SNP	G	G	C	rs144712899	byfrequency;alternate_allele	TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	BCL2L13,NS,adenocarcinoma,0,2	BCL2L13	NM_001270732	exon2	c.G6C	p.A2A	AATGGCGTCCTCT	.	58.0	26.0	69.0	1.0	.	27	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
RANBP1	5902	hgsc.bcm.edu	hg19	22	20109854	20109854	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	RANBP1	NM_002882	exon3	c.G220T	p.D74Y	ACTGGTGACGTCA	.	84.0	29.0	132.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
CSNK1E	1454	hgsc.bcm.edu	hg19	22	38690505	38690505	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CSNK1E	NM_001894	exon8	c.G921C	p.E307D	TCGCCGCTCCCGG	.	52.0	24.0	146.0	0.0	.	143	.	.	.	none	.	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	hg19	22	50591546	50591546	+	Silent	SNP	A	A	C	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	MOV10L1	NM_018995	exon22	c.A2965C	p.R989R	TACCACAGGGAAC	.	79.0	32.0	163.0	0.0	.	238	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	hg19	X	27765728	27765728	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	DCAF8L2	NM_001136533	exon1	c.G716A	p.R239H	ACCAGCGTGGCAC	.	83.0	69.0	45.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6955	6955	+	Missense_Mutation	SNP	G	G	A	rs11510102		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	.	ENST00000361624	exon1	c.G1052A	p.G351D	CCGTAGGTGGCCT	.	22.0	13.0	3.0	0.0	.	.	.	.	.	weak	.	.	PASS	Atlas-SNP
PHF3	23469	hgsc.bcm.edu	hg19	6	64421622	64421622	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PHF3	NM_015153	exon15	c.4137delT	p.D1379fs	.	.	185.0	76.0	86.0	0.0	.	191	.	0.410811	0	none	.	.	PASS	Atlas-Indel,Pindel
AHCTF1	25909	hgsc.bcm.edu	hg19	1	247081550	247081560	+	Splice_Site	DEL	TTATGTTTACC	TTATGTTTACC	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	TTATGTTTACC	TTATGTTTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	AHCTF1	.	.	.	.	.	.	139.0	25.0	147.0	0.0	.	187	.	0.179856	0	none	.	.	PASS	Atlas-Indel,Pindel
USH1G	124590	hgsc.bcm.edu	hg19	17	72919094	72919094	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	USH1G	NM_173477	exon1	c.76delA	p.N26fs	.	.	123.0	41.0	192.0	0.0	.	40	.	0.333333	0	none	.	.	PASS	Atlas-INDEL
GGH	8836	hgsc.bcm.edu	hg19	8	63936714	63936714	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	GGH	NM_003878	exon6	c.532delC	p.P178fs	.	.	248.0	61.0	111.0	0.0	.	32	.	0.245968	0	none	.	.	PASS	Atlas-Indel,Pindel
ASPN	54829	hgsc.bcm.edu	hg19	9	95237024	95237025	+	In_Frame_Ins	INS	-	-	TCCTCA	rs111419727	bycluster;byfrequency;alternate_allele	TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.,2	ASPN	NM_001193335	exon2	c.156_157insTGAGGA	p.E52delinsDEE	.	.	67.0	24.0	49.0	0.0	.	52	.	0.358209	0	alt	-|0.500;TCA|0.500	.	PASS	Atlas-INDEL
PHF16	9767	hgsc.bcm.edu	hg19	X	46918210	46918210	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PHF16	NM_014735	exon11	c.2202delG	p.V734fs	.	.	45.0	36.0	28.0	0.0	.	72	.	0.8	0	none	.	.	PASS	Atlas-INDEL
DNAH1	25981	hgsc.bcm.edu	hg19	3	52392687	52392687	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	DNAH1	NM_015512	exon25	c.4199delA	p.E1400fs	.	.	131.0	62.0	216.0	0.0	.	534	.	0.473282	0	none	.	.	PASS	Atlas-Indel,Pindel
CEP95	90799	hgsc.bcm.edu	hg19	17	62518864	62518864	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CEP95	NM_138363	exon8	c.759delA	p.L253fs	.	.	141.0	75.0	89.0	0.0	.	103	.	0.531915	0	none	.	.	PASS	Atlas-Indel,Pindel
VTA1	51534	hgsc.bcm.edu	hg19	6	142491530	142491530	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	VTA1	NM_016485	exon4	c.382delA	p.I128X	.	.	28.0	10.0	15.0	0.0	.	29	.	0.357143	0	none	.	.	PASS	Atlas-INDEL
ROCK1	6093	hgsc.bcm.edu	hg19	18	18600173	18600174	+	Frame_Shift_Del	DEL	TA	TA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ROCK1	NM_005406	exon12	c.1300_1301del	p.434_434del	.	.	20.0	10.0	40.0	0.0	.	162	.	0.5	0	none	.	.	PASS	Atlas-INDEL
CEP290	80184	hgsc.bcm.edu	hg19	12	88523531	88523532	+	Frame_Shift_Ins	INS	-	-	AAAA	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CEP290	NM_025114	exon10	c.792_793insTTTT	p.V264fs	.	.	145.0	12.0	56.0	0.0	.	195	.	0.0827586	0	none	.	.	PASS	Atlas-INDEL
LIAS	11019	hgsc.bcm.edu	hg19	4	39465225	39465225	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	LIAS	NM_194451	exon4	c.392delT	p.M131fs	.	.	53.0	40.0	50.0	0.0	.	26	.	0.754717	0	none	.	.	PASS	Atlas-Indel,Pindel
TPR	7175	hgsc.bcm.edu	hg19	1	186289494	186289494	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	TPR_ENST00000367478,NS,carcinoma,0,2	TPR	NM_003292	exon46	c.6519delA	p.P2173fs	.	.	85.0	38.0	53.0	0.0	.	441	.	0.447059	0	none	.	.	PASS	Atlas-Indel,Pindel
TMPRSS7	344805	hgsc.bcm.edu	hg19	3	111799843	111799844	+	Frame_Shift_Del	DEL	GA	GA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TMPRSS7	NM_001042575	exon16	c.2065_2066del	p.689_689del	.	.	147.0	43.0	197.0	0.0	.	126	.	0.292517	0	none	.	.	PASS	Atlas-INDEL
CEP290	80184	hgsc.bcm.edu	hg19	12	88523533	88523534	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CEP290	NM_025114	exon10	c.790_791insT	p.V264fs	.	.	144.0	12.0	56.0	0.0	.	195	.	0.0833333	0	none	.	.	PASS	Atlas-INDEL
ZNF540	163255	hgsc.bcm.edu	hg19	19	38102608	38102609	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	ZNF540	NM_152606	exon5	c.426_427del	p.142_143del	.	.	137.0	55.0	127.0	0.0	.	75	.	0.40146	0	none	.	.	PASS	Atlas-Indel,Pindel
TMPRSS7	344805	hgsc.bcm.edu	hg19	3	111799843	111799845	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	TMPRSS7	NM_001042575	exon16	c.2065_2067del	p.689_689del	.	.	148.0	36.0	200.0	0.0	.	126	.	0.243	.	none	.	.	PASS	Pindel
PHF16	9767	hgsc.bcm.edu	hg19	X	46918210	46918211	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	PHF16	NM_014735	exon11	c.2202_2203del	p.734_735del	.	.	45.0	26.0	28.0	0.0	.	72	.	0.578	.	none	.	.	PASS	Pindel
USH1G	124590	hgsc.bcm.edu	hg19	17	72919094	72919095	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	USH1G	NM_173477	exon1	c.75_76del	p.25_26del	.	.	127.0	30.0	194.0	0.0	.	40	.	0.236	.	none	.	.	PASS	Pindel
CEP290	80184	hgsc.bcm.edu	hg19	12	88523533	88523533	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	.	CEP290	NM_025114	exon10	c.791delT	p.V264fs	.	.	145.0	12.0	56.0	0.0	.	195	.	0.083	.	none	.	.	PASS	Pindel
