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
ATP13A2	23400	hgsc.bcm.edu	hg19	1	17322884	17322884	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ATP13A2	NM_022089	exon13	c.C1303A	p.L435M	CACCCAGGACAGA	.	90.0	35.0	97.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	hg19	1	201030589	201030589	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CACNA1S	NM_000069	exon25	c.T3061C	p.Y1021H	CCTTGTACAGCAG	.	83.0	17.0	54.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
NAV1	89796	hgsc.bcm.edu	hg19	1	201781618	201781618	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NAV1	NM_020443	exon27	c.G5050T	p.E1684X	AACGTGGAGCCAG	.	182.0	84.0	107.0	0.0	.	143	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	hg19	1	204236626	204236626	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PLEKHA6	NM_014935	exon5	c.A257T	p.D86V	CAGCGATCCACCA	.	125.0	40.0	73.0	0.0	.	115	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	hg19	1	233518317	233518317	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	KIAA1804	NM_032435	exon10	c.A2971G	p.R991G	AAGGAGAGAACTA	.	149.0	39.0	94.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
TBCE	6905	hgsc.bcm.edu	hg19	1	235599915	235599915	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	TBCE	NM_003193	exon11	c.A955C	p.I319L	AATCAGATATCAC	.	158.0	34.0	126.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
TFCP2L1	29842	hgsc.bcm.edu	hg19	2	121991738	121991738	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	TFCP2L1	NM_014553	exon12	c.G1127A	p.C376Y	TCCTGACAGACAT	.	87.0	32.0	90.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
CNPPD1	27013	hgsc.bcm.edu	hg19	2	220039577	220039577	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CNPPD1	NM_015680	exon5	c.A433C	p.N145H	CGTCGTTGAAGAC	.	91.0	31.0	77.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
AGXT	189	hgsc.bcm.edu	hg19	2	241808770	241808770	+	Missense_Mutation	SNP	G	G	A	rs180177208	alternate_allele	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	AGXT	NM_000030	exon2	c.G349A	p.E117K	ATCGGGGAGCGCA	.	87.0	32.0	82.0	0.0	.	50	.	.	.	alt	.	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	hg19	2	242065794	242065794	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PASK	NM_015148	exon10	c.C2536T	p.H846Y	GAACGTGTCCTGG	.	165.0	59.0	132.0	0.0	.	230	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	hg19	3	44763320	44763320	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ZNF502	NM_001134440	exon4	c.C1011G	p.N337K	GGCAAACCTCTCT	.	117.0	79.0	124.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	hg19	3	47032943	47032943	+	Silent	SNP	G	G	T	rs181297174	bycluster;by1000genomes;alternate_allele	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NBEAL2	NM_015175	exon8	c.G690T	p.L230L	CCTGCTGAGTGTG	.	29.0	22.0	20.0	0.0	.	267	.	.	.	alt	G|1.000;C|0.000	.	PASS	Atlas-SNP
SETD2	29072	hgsc.bcm.edu	hg19	3	47143047	47143047	+	Splice_Site	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	NM_014159	exon9	c.4918-2A>G	.	GTCCACTGAGATG	.	139.0	102.0	115.0	0.0	.	721	.	.	.	none	.	.	PASS	Atlas-SNP
NPHP3	27031	hgsc.bcm.edu	hg19	3	132410108	132410108	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NPHP3	NM_153240	exon18	c.A2498G	p.E833G	AGGTACTCCAATC	.	308.0	175.0	251.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
STX18	53407	hgsc.bcm.edu	hg19	4	4436571	4436571	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	STX18	NM_016930	exon7	c.G628A	p.E210K	GTGTTTCAGCCAA	.	71.0	18.0	88.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
YTHDC1	91746	hgsc.bcm.edu	hg19	4	69185877	69185877	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	YTHDC1	NM_001031732	exon12	c.A1648G	p.R550G	CAATCCTTGGTTT	.	81.0	25.0	113.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
ELOVL6	79071	hgsc.bcm.edu	hg19	4	111119479	111119479	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ELOVL6	NM_001130721	exon2	c.G13T	p.V5L	TCAACACTGACAT	.	147.0	45.0	204.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	hg19	4	143181690	143181690	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	INPP4B,NS,carcinoma,0,1	INPP4B	NM_003866	exon12	c.C643A	p.P215T	TTTCCGGGGCTGT	.	52.0	16.0	47.0	0.0	.	132	.	.	.	none	.	.	PASS	Atlas-SNP
TIGD4	201798	hgsc.bcm.edu	hg19	4	153691640	153691640	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	TIGD4	NM_145720	exon2	c.G517A	p.D173N	GATAATCATTTAA	.	56.0	18.0	87.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
SORBS2	8470	hgsc.bcm.edu	hg19	4	186545113	186545113	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	SORBS2	NM_001270771	exon16	c.C1758T	p.H586H	GTCCTTGTGCTGC	.	117.0	49.0	106.0	0.0	.	300	.	.	.	none	.	.	PASS	Atlas-SNP
SORBS2	8470	hgsc.bcm.edu	hg19	4	186545114	186545114	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	SORBS2	NM_001270771	exon16	c.A1757C	p.H586P	TCCTTGTGCTGCT	.	114.0	49.0	108.0	0.0	.	300	.	.	.	none	.	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	hg19	5	41048530	41048530	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	.	NM_173489	exon16	c.G1580A	p.G527E	CCAGCCCCACGTA	.	58.0	31.0	63.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL3	26249	hgsc.bcm.edu	hg19	5	136975648	136975648	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	KLHL3	NM_017415	exon9	c.G922A	p.G308S	CCTGGCCGCCAAC	.	90.0	20.0	78.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
FAM13B	51306	hgsc.bcm.edu	hg19	5	137289855	137289855	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	FAM13B	NM_001101800	exon14	c.G1652C	p.R551T	ATATACCTAGTAA	.	77.0	17.0	64.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
GABRA1	2554	hgsc.bcm.edu	hg19	5	161281260	161281260	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	GABRA1	NM_001127643	exon4	c.G171A	p.L57L	TCGCCTGAGACCA	.	112.0	23.0	73.0	0.0	.	132	.	.	.	none	.	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	hg19	6	32049190	32049190	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	NM_019105	exon10	c.C3997T	p.R1333C	TGCCACGAAGCCC	.	8.0	5.0	5.0	0.0	.	553	.	.	.	none	.	.	PASS	Atlas-SNP
SCUBE3	222663	hgsc.bcm.edu	hg19	6	35213120	35213120	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	SCUBE3	NM_152753	exon19	c.G2517A	p.K839K	ACCCAAGCGCAAG	.	122.0	39.0	117.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	hg19	6	42932546	42932546	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PEX6	NM_000287	exon16	c.G2788A	p.V930I	CATGAACCCTGCG	.	148.0	54.0	143.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	hg19	6	51882414	51882414	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PKHD1	NM_170724	exon34	c.C5394T	p.F1798F	ACACAGGAAGGCC	.	103.0	42.0	102.0	0.0	.	927	.	.	.	none	.	.	PASS	Atlas-SNP
ENPP1	5167	hgsc.bcm.edu	hg19	6	132206107	132206107	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ENPP1	NM_006208	exon23	c.A2348C	p.K783T	TGCGAAAGTATGC	.	96.0	34.0	84.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
TNFAIP3	7128	hgsc.bcm.edu	hg19	6	138200458	138200458	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.,1	TNFAIP3	NM_001270507	exon7	c.C1876A	p.L626M	TGCACACTGTGTT	.	52.0	32.0	85.0	0.0	.	340	.	.	.	none	.	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	hg19	7	102110042	102110042	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	LRWD1	NM_152892	exon10	c.T1250G	p.I417S	AGCGGATCATCCT	.	127.0	26.0	143.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	hg19	7	102110043	102110043	+	Silent	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	LRWD1	NM_152892	exon10	c.C1251A	p.I417I	GCGGATCATCCTC	.	127.0	27.0	144.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	hg19	8	3216707	3216707	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CSMD1	NM_033225	exon21	c.C3271T	p.R1091C	ACACACGGCGGCC	.	120.0	33.0	117.0	0.0	.	1469	.	.	.	none	.	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	hg19	8	24357759	24357759	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ADAM7	NM_003817	exon18	c.A1992C	p.L664F	AACCTTACATGTT	.	66.0	26.0	43.0	0.0	.	165	.	.	.	none	.	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	hg19	8	24357760	24357760	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ADAM7	NM_003817	exon18	c.C1993A	p.H665N	ACCTTACATGTTA	.	68.0	26.0	43.0	0.0	.	165	.	.	.	none	.	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	hg19	9	84608073	84608073	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	.	NM_001001670	exon4	c.T2688G	p.S896R	CCTTAGTTCCAAC	.	66.0	26.0	56.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TXN	7295	hgsc.bcm.edu	hg19	9	113013695	113013695	+	Silent	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	TXN	NM_001244938	exon2	c.A72G	p.V24V	GTCAACTACTACA	.	46.0	12.0	41.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
MVB12B	89853	hgsc.bcm.edu	hg19	9	129143362	129143362	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	.	NM_001011703	exon3	c.G224C	p.G75A	CAGATGGTGTGGA	.	93.0	28.0	103.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CYP2C18	1562	hgsc.bcm.edu	hg19	10	96443672	96443672	+	Silent	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CYP2C18	NM_000772	exon1	c.C96A	p.G32G	GTCTGGCCCCACT	.	78.0	9.0	52.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	hg19	10	124351862	124351862	+	Silent	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	DMBT1	NM_007329	exon20	c.C2251A	p.R751R	CTATACCGAGGCT	.	437.0	141.0	397.0	1.0	.	677	.	.	.	none	.	.	PASS	Atlas-SNP
CD81	975	hgsc.bcm.edu	hg19	11	2417109	2417109	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CD81	NM_004356	exon6	c.G470T	p.C157F	ACTGCTGTGGCTC	.	75.0	32.0	70.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	hg19	11	21581738	21581738	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NELL1	NM_006157	exon17	c.T1790G	p.I597S	CAGACATTGATGA	.	144.0	60.0	181.0	0.0	.	179	.	.	.	none	.	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	hg19	11	26742996	26742996	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	SLC5A12	NM_178498	exon1	c.T266A	p.L89Q	ACAAATAGGTAAG	.	66.0	28.0	81.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	hg19	11	63884401	63884401	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	FLRT1	NM_013280	exon2	c.T662A	p.L221H	AGGGCCTCAACAG	.	44.0	13.0	50.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PITPNM1	9600	hgsc.bcm.edu	hg19	11	67265787	67265787	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PITPNM1	NM_001130848	exon11	c.C1491T	p.S497S	GTAAGGGCTCAGG	.	23.0	8.0	24.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	hg19	12	977170	977170	+	Missense_Mutation	SNP	C	C	T	rs200794710	bycluster	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	WNK1	NM_213655	exon10	c.C2533T	p.R845C	CAGCGGCGTAAGA	.	148.0	7.0	101.0	0.0	.	403	.	.	.	weak	.	.	PASS	Atlas-SNP
KCNC2	3747	hgsc.bcm.edu	hg19	12	75441966	75441966	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	KCNC2	NM_139137	exon4	c.T1747G	p.Y583D	ACGTGTAATCACC	.	286.0	108.0	284.0	0.0	.	239	.	.	.	none	.	.	PASS	Atlas-SNP
NUAK1	9891	hgsc.bcm.edu	hg19	12	106460987	106460987	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NUAK1	NM_014840	exon7	c.C1579A	p.H527N	TGCTGTGTTTCAA	.	121.0	53.0	113.0	0.0	.	196	.	.	.	none	.	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	hg19	13	25352542	25352542	+	Silent	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	RNF17	NM_001184993	exon4	c.T427C	p.L143L	GTAATGTTGGTAT	.	197.0	60.0	171.0	0.0	.	259	.	.	.	none	.	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	hg19	15	75981607	75981607	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CSPG4	NM_001897	exon3	c.G1799A	p.G600D	GGGAGGCCAGAGG	.	49.0	23.0	47.0	0.0	.	175	.	.	.	none	.	.	PASS	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	hg19	15	94884070	94884070	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	MCTP2	NM_001159643	exon6	c.G886T	p.D296Y	CTGGAAGATCCAA	.	56.0	25.0	63.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
PRSS21	10942	hgsc.bcm.edu	hg19	16	2868724	2868724	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PRSS21	NM_144957	exon4	c.C304G	p.Q102E	TTTGGCCAGCTGA	.	184.0	35.0	98.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF597	146434	hgsc.bcm.edu	hg19	16	3487524	3487524	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	ZNF597,NS,malignant_melanoma,0,1	ZNF597	NM_152457	exon4	c.C175G	p.P59A	TCTCAGGCTTGCC	.	145.0	91.0	82.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	hg19	16	23083424	23083424	+	Silent	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	USP31	NM_020718	exon15	c.C2430A	p.T810T	CAGGGAGGTGCGT	.	232.0	20.0	134.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
NUP93	9688	hgsc.bcm.edu	hg19	16	56792502	56792502	+	Silent	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	NUP93	NM_014669	exon3	c.T232C	p.L78L	CAGCGATTGGAGA	.	98.0	37.0	112.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
COG8	84342	hgsc.bcm.edu	hg19	16	69368791	69368791	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	COG8	NM_032382	exon3	c.G1046C	p.C349S	TACATGCACTGGC	.	93.0	34.0	103.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF778	197320	hgsc.bcm.edu	hg19	16	89294017	89294017	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ZNF778	NM_001201407	exon7	c.C1321T	p.R441X	CACGTACGAACAC	.	80.0	23.0	71.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
DEF8	54849	hgsc.bcm.edu	hg19	16	90015887	90015887	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	DEF8	NM_207514	exon2	c.C14A	p.S5Y	TCCTGTCCCTGCG	.	90.0	31.0	86.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
KDM6B	23135	hgsc.bcm.edu	hg19	17	7755372	7755372	+	Silent	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	KDM6B	NM_001080424	exon18	c.T4269G	p.A1423A	CAGCGCTTTCTGT	.	63.0	19.0	57.0	0.0	.	95	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA9	10350	hgsc.bcm.edu	hg19	17	66981100	66981100	+	Silent	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ABCA9	NM_080283	exon34	c.C4305T	p.I1435I	CCCCAGGATGCTC	.	174.0	31.0	116.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA10	10349	hgsc.bcm.edu	hg19	17	67170778	67170778	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ABCA10	NM_080282	exon25	c.C3018A	p.F1006L	AAGCTGGAATCCC	.	231.0	71.0	143.0	0.0	.	209	.	.	.	none	.	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	hg19	17	80050833	80050833	+	Missense_Mutation	SNP	G	G	A	rs200752265	alternate_allele	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	FASN	NM_004104	exon6	c.C718T	p.R240W	CCCGCCGGGCCAG	.	37.0	12.0	24.0	0.0	.	154	.	.	.	alt	G|0.998;T|0.002	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	hg19	19	879943	879943	+	Missense_Mutation	SNP	G	G	C	rs76403059	bycluster	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	MED16,colon,carcinoma,0,1	MED16	NM_005481	exon8	c.C1347G	p.H449Q	CTTCCCGTGGCTG	.	19.0	2.0	15.0	1.0	.	61	.	.	.	weak	.	.	PASS	Atlas-SNP
CD97	976	hgsc.bcm.edu	hg19	19	14513447	14513447	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	CD97	NM_078481	exon12	c.A1222G	p.T408A	AACATGACGACAT	.	91.0	4.0	121.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	hg19	19	49379135	49379135	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PPP1R15A	NM_014330	exon3	c.G1930A	p.V644I	TCCCCAGTCCAGA	.	284.0	91.0	247.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF773	374928	hgsc.bcm.edu	hg19	19	58018434	58018434	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	ZNF773	NM_198542	exon4	c.T971C	p.V324A	AGAGAGTTCACAC	.	200.0	47.0	219.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	hg19	20	8741054	8741054	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PLCB1	NM_015192	exon25	c.A2657T	p.Q886L	TTACAGGTTCTGT	.	69.0	21.0	71.0	0.0	.	394	.	.	.	none	.	.	PASS	Atlas-SNP
KCNS1	3787	hgsc.bcm.edu	hg19	20	43726464	43726464	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	KCNS1	NM_002251	exon4	c.T949A	p.Y317N	TGAGATAGAAGGG	.	29.0	16.0	32.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
WFDC2	10406	hgsc.bcm.edu	hg19	20	44108666	44108666	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	WFDC2	NM_006103	exon3	c.G308A	p.C103Y	GCCAGTGTCCTGG	.	181.0	74.0	217.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
DNTTIP1	116092	hgsc.bcm.edu	hg19	20	44424050	44424050	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	DNTTIP1	NM_052951	exon4	c.A340G	p.I114V	CAGCTGATCCAGG	.	18.0	7.0	29.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
PSMA7	5688	hgsc.bcm.edu	hg19	20	60714841	60714841	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PSMA7	NM_002792	exon3	c.A344C	p.K115T	ACCTGCTTCAGAC	.	64.0	21.0	59.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
PRPF6	24148	hgsc.bcm.edu	hg19	20	62642772	62642772	+	Silent	SNP	G	G	C	rs199552405	by1000genomes;alternate_allele	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PRPF6	NM_012469	exon11	c.G1440C	p.T480T	GAACACGCAGATG	.	46.0	12.0	52.0	0.0	.	88	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
SON	6651	hgsc.bcm.edu	hg19	21	34925625	34925625	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	SON	NM_032195	exon3	c.C4088T	p.S1363L	AGTCTTCGGCTGT	.	68.0	17.0	54.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
STAG2	10735	hgsc.bcm.edu	hg19	X	123200037	123200037	+	Silent	SNP	T	T	C	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	STAG2	NM_001042749	exon22	c.T2109C	p.L703L	TGACCTTTCAAAG	.	65.0	44.0	76.0	0.0	.	309	.	.	.	none	.	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	10971	10971	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	.	ENST00000361381	exon1	c.G212A	p.W71X	CTACCTGACTCCT	.	141.0	127.0	51.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	hg19	3	52696272	52696272	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	PBRM1	NM_018313	exon5	c.406delG	p.A136fs	.	.	91.0	61.0	149.0	0.0	.	1252	.	0.67033	0	none	.	.	PASS	Atlas-INDEL
HOXA2	3199	hgsc.bcm.edu	hg19	7	27140389	27140390	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	HOXA2	NM_006735	exon2	c.1087_1088insT	p.T363fs	.	.	177.0	23.0	177.0	0.0	.	56	.	0.129944	0	none	.	.	PASS	Atlas-INDEL
COL14A1	7373	hgsc.bcm.edu	hg19	8	121219275	121219276	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	.	COL14A1	NM_021110	exon10	c.1133_1134insA	p.G378fs	.	.	59.0	19.0	49.0	0.0	.	292	.	0.322034	0	none	.	.	PASS	Atlas-INDEL
