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
FAM110D	79927	hgsc.bcm.edu	hg19	1	26488081	26488081	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	NM_024869	exon2	c.A299G	p.E100G	ACAAAGAGAACGC	.	124.0	62.0	124.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZC3H12A	80149	hgsc.bcm.edu	hg19	1	37948519	37948519	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ZC3H12A	NM_025079	exon6	c.A1107T	p.T369T	GCTAACAGAGAGT	.	159.0	76.0	196.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
PRPF3	9129	hgsc.bcm.edu	hg19	1	150325324	150325324	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PRPF3	NM_004698	exon16	c.C1921A	p.R641R	AAAGACCGGAGCT	.	438.0	180.0	460.0	1.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
MCL1	4170	hgsc.bcm.edu	hg19	1	150551933	150551933	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	MCL1	NM_021960	exon1	c.G74T	p.S25I	CCGCCGCTGCCGG	.	205.0	83.0	181.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
TDRKH	11022	hgsc.bcm.edu	hg19	1	151748012	151748012	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	TDRKH	NM_001083965	exon10	c.G1290C	p.Q430H	TTCCCACTGGTCA	.	120.0	59.0	137.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	hg19	1	176863825	176863825	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ASTN1	NM_004319	exon17	c.G2813C	p.R938P	GGGCATCGTCCCT	.	73.0	31.0	75.0	0.0	.	314	.	.	.	none	.	.	PASS	Atlas-SNP
RASAL2	9462	hgsc.bcm.edu	hg19	1	178063695	178063695	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	RASAL2	NM_170692	exon1	c.T68C	p.L23P	CGGCGCTGGAGTC	.	124.0	58.0	148.0	0.0	.	334	.	.	.	none	.	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	hg19	1	228528466	228528466	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	OBSCN	NM_001271223	exon83	c.G20445A	p.A6815A	CTGCGCGCTGCTG	.	190.0	87.0	225.0	1.0	.	2142	.	.	.	none	.	.	PASS	Atlas-SNP
EML6	400954	hgsc.bcm.edu	hg19	2	55054726	55054726	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	EML6	NM_001039753	exon5	c.C549A	p.A183A	AAATGCCCTGACT	.	94.0	40.0	76.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
ITPRIPL1	150771	hgsc.bcm.edu	hg19	2	96993651	96993651	+	Missense_Mutation	SNP	A	A	G	rs35855657	bycluster;byfrequency;alternate_allele	TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ITPRIPL1	NM_178495	exon1	c.A1306G	p.S436G	ATTTTAAGTCTCC	.	93.0	35.0	91.0	0.0	.	58	.	.	.	alt	A|0.643;T|0.357	.	PASS	Atlas-SNP
CCNT2	905	hgsc.bcm.edu	hg19	2	135710229	135710229	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	CCNT2	NM_058241	exon8	c.T722C	p.L241P	AGTTTCTACAAAT	.	287.0	126.0	346.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
MUC13	56667	hgsc.bcm.edu	hg19	3	124632081	124632081	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	MUC13	NM_033049	exon8	c.G1088A	p.S363N	TTGAGACTGGAAG	.	112.0	28.0	84.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
ISY1	57461	hgsc.bcm.edu	hg19	3	128852942	128852942	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ISY1	NM_001199469	exon10	c.A704G	p.N235S	TAGATGTTGATCT	.	92.0	54.0	57.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	hg19	3	183756384	183756384	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	HTR3D	NM_001163646	exon7	c.C1107T	p.G369G	TAAGGGCCCGGGT	.	234.0	60.0	150.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
FAM131A	131408	hgsc.bcm.edu	hg19	3	184062687	184062687	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	FAM131A	NM_144635	exon6	c.C1030A	p.Q344K	CAGCGGCAAGCCT	.	90.0	46.0	59.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	hg19	4	995927	995927	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	IDUA	NM_000203	exon7	c.C950T	p.T317I	ACGTGACCTACGC	.	120.0	55.0	107.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	hg19	4	3076668	3076668	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	HTT	NM_002111	exon1	c.C116A	p.P39Q	AACAGCCGCCACC	.	16.0	4.0	11.0	0.0	.	221	.	.	.	none	.	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	hg19	5	147484531	147484531	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SPINK5	NM_001127699	exon16	c.G1447A	p.A483T	GAAAGAGCAAGAG	.	323.0	146.0	332.0	1.0	.	245	.	.	.	none	.	.	PASS	Atlas-SNP
SLU7	10569	hgsc.bcm.edu	hg19	5	159831848	159831848	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SLU7	NM_006425	exon14	c.G1432T	p.E478X	CAGATTCTTCCCC	.	94.0	36.0	74.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
F12	2161	hgsc.bcm.edu	hg19	5	176831333	176831333	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	F12,NS,carcinoma,0,1	F12	NM_000505	exon9	c.G882A	p.Q294Q	CTGGCACTGTGCC	.	160.0	81.0	204.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
SCGN	10590	hgsc.bcm.edu	hg19	6	25665199	25665199	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SCGN	NM_006998	exon4	c.A275C	p.E92A	AGGATGAAAACTT	.	40.0	15.0	33.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
HIST1H2AD	3013	hgsc.bcm.edu	hg19	6	26199103	26199103	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	HIST1H2AD	NM_021065	exon1	c.T369G	p.S123R	GTGGTGACTCTCA	.	131.0	58.0	151.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
HSD17B8	7923	hgsc.bcm.edu	hg19	6	33173455	33173455	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	HSD17B8	NM_014234	exon5	c.G519A	p.K173K	ATCCAAGGCTGGA	.	101.0	42.0	80.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152462387	152462387	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SYNE1	NM_182961	exon139	c.G25197A	p.E8399E	AAGGCTCTCCTCT	.	82.0	36.0	92.0	0.0	.	3227	.	.	.	none	.	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149499004	149499004	+	Missense_Mutation	SNP	C	C	T	rs376985175		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	NM_198455	exon50	c.C7456T	p.R2486W	GACCTGCGGCCTG	.	70.0	27.0	40.0	0.0	.	.	.	.	.	weak	.	.	PASS	Atlas-SNP
FPGS	2356	hgsc.bcm.edu	hg19	9	130570589	130570589	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	FPGS	NM_004957	exon9	c.C821A	p.S274X	AGATCTCAGTAAG	.	48.0	18.0	52.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
PRKG1	5592	hgsc.bcm.edu	hg19	10	54053646	54053646	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PRKG1	NM_006258	exon18	c.G2047T	p.D683Y	GGATGGGATATAG	.	70.0	34.0	69.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
SMPD1	6609	hgsc.bcm.edu	hg19	11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	rs78250081	bycluster	TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SMPD1	NM_000543	exon1	c.C113T	p.A38V	TGCTGGCGCTGGC	.	102.0	11.0	74.0	0.0	.	108	.	.	.	weak	.	.	PASS	Atlas-SNP
PLEKHA7	144100	hgsc.bcm.edu	hg19	11	16816490	16816490	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PLEKHA7	NM_175058	exon18	c.T2485C	p.F829L	TTCTGAAGTTCTC	.	94.0	42.0	77.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGAP2	84364	hgsc.bcm.edu	hg19	11	47198367	47198367	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ARFGAP2	NM_001242832	exon1	c.T38C	p.L13P	TTAAAAAGAGTCT	.	79.0	40.0	57.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	hg19	11	118772132	118772132	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	BCL9L	NM_182557	exon6	c.A2320G	p.M774V	CATTCATGTTCAT	.	43.0	22.0	34.0	0.0	.	254	.	.	.	none	.	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	hg19	11	134038058	134038058	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	NCAPD3	NM_015261	exon27	c.C3406G	p.L1136V	CGTCCAGGTCCAG	.	70.0	43.0	71.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
KRT82	3888	hgsc.bcm.edu	hg19	12	52789833	52789833	+	Missense_Mutation	SNP	C	C	T	rs377127392		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	KRT82	NM_033033	exon7	c.G1252A	p.A418T	AGGTGGCGATCTC	.	76.0	32.0	91.0	0.0	.	45	.	.	.	weak	.	.	PASS	Atlas-SNP
RDH5	5959	hgsc.bcm.edu	hg19	12	56115699	56115699	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	RDH5	NM_001199771	exon3	c.A537C	p.K179N	CTCCAAATTTGGC	.	365.0	142.0	345.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
PAN2	9924	hgsc.bcm.edu	hg19	12	56720417	56720417	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PAN2	NM_014871	exon7	c.T1246C	p.S416P	GAGCAGAGTTGGC	.	127.0	53.0	131.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
ATP5B	506	hgsc.bcm.edu	hg19	12	57033773	57033773	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ATP5B	NM_001686	exon8	c.G1278T	p.K426N	CAGGATCTTTTGC	.	85.0	31.0	74.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
SCYL2	55681	hgsc.bcm.edu	hg19	12	100717393	100717393	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SCYL2	NM_017988	exon11	c.T1486A	p.C496S	AATGCTTGTCTAC	.	80.0	30.0	73.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
HPD	3242	hgsc.bcm.edu	hg19	12	122295709	122295709	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	HPD	NM_002150	exon3	c.T47C	p.F16S	TGGAGGAATCGGC	.	160.0	68.0	168.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
B3GNT4	79369	hgsc.bcm.edu	hg19	12	122691299	122691299	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	B3GNT4	NM_030765	exon3	c.A501T	p.P167P	TCCCCCAGCCCAG	.	43.0	17.0	37.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	hg19	12	133385055	133385055	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	GOLGA3	NM_001172557	exon5	c.G600T	p.R200S	ACTGGCCCTTGGT	.	110.0	54.0	95.0	0.0	.	234	.	.	.	none	.	.	PASS	Atlas-SNP
COG3	83548	hgsc.bcm.edu	hg19	13	46066332	46066332	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	COG3	NM_031431	exon11	c.G1134T	p.Q378H	CTGCCAGGATGAA	.	106.0	5.0	107.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
ACTR10	55860	hgsc.bcm.edu	hg19	14	58675768	58675768	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ACTR10	NM_018477	exon4	c.A285G	p.V95V	ATCGGTATTATGT	.	62.0	21.0	86.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
SNAPC1	6617	hgsc.bcm.edu	hg19	14	62229244	62229244	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SNAPC1	NM_003082	exon1	c.C66T	p.D22D	GACGGACAGTGTA	.	61.0	20.0	66.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	hg19	14	64595265	64595265	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SYNE2	NM_182914	exon74	c.G14013A	p.Q4671Q	TGAACAGCTTCAG	.	143.0	55.0	151.0	0.0	.	577	.	.	.	none	.	.	PASS	Atlas-SNP
GPHN	10243	hgsc.bcm.edu	hg19	14	67646373	67646373	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	GPHN	NM_020806	exon22	c.C2158A	p.P720T	CCACTACCTTGGG	.	77.0	41.0	96.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
VRTN	55237	hgsc.bcm.edu	hg19	14	74824607	74824607	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	VRTN	NM_018228	exon2	c.T1121A	p.L374Q	AGGAGCTAGAGAA	.	55.0	23.0	61.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
PLA2G4E	123745	hgsc.bcm.edu	hg19	15	42298282	42298282	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PLA2G4E	NM_001206670	exon4	c.T431C	p.V144A	GGTGTCACTGTGT	.	101.0	52.0	106.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
SLC24A1	9187	hgsc.bcm.edu	hg19	15	65943100	65943100	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SLC24A1	NM_004727	exon7	c.A2613G	p.E871E	GGAGGAAGAGGAG	.	79.0	10.0	84.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
NR2F2	7026	hgsc.bcm.edu	hg19	15	96875660	96875660	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	NR2F2	NM_021005	exon1	c.G326T	p.R109M	TGCGGAGGAACCT	.	86.0	32.0	100.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
NTN3	4917	hgsc.bcm.edu	hg19	16	2522514	2522514	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	NTN3	NM_006181	exon1	c.A812C	p.H271P	AGGGCCACCTGAT	.	47.0	5.0	41.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
TANGO6	79613	hgsc.bcm.edu	hg19	16	68914532	68914532	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	NM_024562	exon7	c.A1376C	p.K459T	TGTTTAAGGTTGG	.	163.0	41.0	115.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
BANP	54971	hgsc.bcm.edu	hg19	16	88039824	88039824	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	BANP	NM_001173542	exon6	c.G608A	p.S203N	CGGGCAGTCAGAG	.	58.0	31.0	49.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
NTN1	9423	hgsc.bcm.edu	hg19	17	9066277	9066277	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	NTN1	NM_004822	exon3	c.G1166T	p.R389L	ACTACCGCGACAT	.	139.0	87.0	83.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	hg19	17	35609953	35609953	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ACACA	NM_198834	exon15	c.G1836T	p.V612V	AGCCACCACCATG	.	93.0	59.0	88.0	0.0	.	395	.	.	.	none	.	.	PASS	Atlas-SNP
UBE2O	63893	hgsc.bcm.edu	hg19	17	74398143	74398143	+	Splice_Site	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	UBE2O	NM_022066	exon6	c.750+2T>C	.	CACACTACCGAGT	.	135.0	85.0	76.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCA4	6597	hgsc.bcm.edu	hg19	19	11138579	11138579	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SMARCA4	NM_003072	exon24	c.T3335G	p.M1112R	CCATCATGGAAGA	.	145.0	71.0	151.0	0.0	.	502	.	.	.	none	.	.	PASS	Atlas-SNP
PAK4	10298	hgsc.bcm.edu	hg19	19	39664225	39664225	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	PAK4	NM_001014832	exon4	c.C673A	p.H225N	GAGCCTCATGACG	.	66.0	22.0	65.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
C20orf144	128864	hgsc.bcm.edu	hg19	20	32251357	32251357	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	C20orf144	NM_080825	exon2	c.T146C	p.L49P	TGATTCTCCCCCT	.	141.0	7.0	106.0	0.0	.	4	.	.	.	none	.	.	PASS	Atlas-SNP
SDF2L1	23753	hgsc.bcm.edu	hg19	22	21996638	21996638	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	SDF2L1	NM_022044	exon1	c.G13A	p.G5S	AGCGCGGGCCGCG	.	49.0	24.0	46.0	0.0	.	5	.	.	.	none	.	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6481	6481	+	Missense_Mutation	SNP	T	T	C	rs199476128	bycluster;alternate_allele	TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	ENST00000361624	exon1	c.T578C	p.V193A	CAGCAGTCCTACT	.	12.0	10.0	42.0	0.0	.	.	.	.	.	alt	A|0.006;G|0.994	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9420	9420	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	ENST00000362079	exon1	c.A214G	p.T72A	CACCACACACCAC	.	16.0	15.0	46.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	hg19	7	24742409	24742409	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	DFNA5	NM_001127453	exon9	c.1228delC	p.L410fs	.	.	120.0	75.0	70.0	0.0	.	51	.	0.625	0	none	.	.	PASS	Atlas-Indel,Pindel
MAGI1	9223	hgsc.bcm.edu	hg19	3	65342733	65342733	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	MAGI1	NM_001033057	exon23	c.3710delG	p.R1237fs	.	.	107.0	40.0	93.0	0.0	.	481	.	0.373832	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF582	147948	hgsc.bcm.edu	hg19	19	56895643	56895643	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ZNF582	NM_144690	exon5	c.1144delC	p.L382fs	.	.	93.0	46.0	125.0	0.0	.	56	.	0.494624	0	none	.	.	PASS	Atlas-Indel,Pindel
USP25	29761	hgsc.bcm.edu	hg19	21	17214827	17214829	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	USP25	NM_013396	exon18	c.2304_2306del	p.768_769del	.	.	217.0	125.0	178.0	0.0	.	156	.	0.576037	0	none	.	.	PASS	Atlas-Indel,Pindel
ZSWIM8	23053	hgsc.bcm.edu	hg19	10	75548546	75548546	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	NM_015037	exon2	c.326delC	p.A109fs	.	.	56.0	19.0	56.0	0.0	.	.	.	0.339286	0	none	.	.	PASS	Atlas-Indel,Pindel
STXBP5L	9515	hgsc.bcm.edu	hg19	3	121100364	121100367	+	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	ATGG	ATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	STXBP5L	NM_014980	exon23	c.2643_2646del	p.881_882del	.	.	118.0	31.0	75.0	0.0	.	159	.	0.262712	0	none	.	.	PASS	Atlas-Indel,Pindel
ARID1A	8289	hgsc.bcm.edu	hg19	1	27105645	27105645	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	ARID1A	NM_006015	exon20	c.5255delA	p.K1752fs	.	.	130.0	55.0	136.0	0.0	.	842	.	0.423077	0	none	.	.	PASS	Atlas-Indel,Pindel
CFC1	55997	hgsc.bcm.edu	hg19	2	131356313	131356313	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	CFC1	NM_001270420	exon3	c.150delG	p.P50fs	.	.	1015.0	120.0	957.0	0.0	.	14	.	0.118	.	none	.	.	PASS	Pindel
CFC1B	653275	hgsc.bcm.edu	hg19	2	131279604	131279604	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	.	.	NM_001079530	exon3	c.147delA	p.S49fs	.	.	381.0	39.0	396.0	0.0	.	.	.	0.102	.	none	.	.	PASS	Pindel
