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
ARID1A	8289	hgsc.bcm.edu	hg19	1	27107195	27107195	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	ARID1A,NS,carcinoma,0,2	ARID1A	NM_006015	exon20	c.C6806A	p.S2269X	TGAACTCATTGGT	.	118.0	47.0	198.0	0.0	.	842	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf194	127003	hgsc.bcm.edu	hg19	1	109649721	109649721	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	C1orf194	NM_001122961	exon3	c.C186T	p.F62F	TAAGCGGAAGTCC	.	217.0	93.0	183.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
RFX5	5993	hgsc.bcm.edu	hg19	1	151314667	151314667	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	RFX5	NM_000449	exon11	c.C1846A	p.P616T	ATCATGGGGGTGT	.	94.0	47.0	129.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	216017693	216017693	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	USH2A	NM_206933	exon46	c.T9201A	p.N3067K	AGGCACATTCATT	.	77.0	24.0	75.0	0.0	.	1168	.	.	.	none	.	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	hg19	1	232650317	232650317	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	SIPA1L2	NM_020808	exon1	c.C769T	p.R257C	AGATGCGGACAAA	.	115.0	44.0	126.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
PELI1	57162	hgsc.bcm.edu	hg19	2	64323347	64323347	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	PELI1,NS,carcinoma,0,1	PELI1	NM_020651	exon6	c.C602T	p.S201F	GGCTTGGAGTCTT	.	124.0	45.0	121.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
IQSEC1	9922	hgsc.bcm.edu	hg19	3	12957106	12957106	+	Silent	SNP	C	C	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	IQSEC1	NM_014869	exon7	c.G2190A	p.V730V	TTTCCCCACAATG	.	94.0	22.0	134.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	hg19	3	37369907	37369907	+	Silent	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	GOLGA4	NM_001172713	exon16	c.A6006G	p.K2002K	ACTCAGACAGGAG	.	185.0	8.0	167.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
MASP1	5648	hgsc.bcm.edu	hg19	3	187009418	187009418	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	MASP1	NM_139125	exon1	c.G3C	p.M1I	GTACCTCATTTTC	.	211.0	46.0	178.0	0.0	.	240	.	.	.	none	.	.	PASS	Atlas-SNP
UGDH	7358	hgsc.bcm.edu	hg19	4	39515753	39515753	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.,2	UGDH	NM_003359	exon3	c.T214C	p.S72P	TGGTAGAAAAAAA	.	98.0	40.0	81.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
SORBS2	8470	hgsc.bcm.edu	hg19	4	186545386	186545386	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	SORBS2	NM_001270771	exon16	c.C1485A	p.F495L	GTCCGGGAAGCTA	.	70.0	30.0	96.0	0.0	.	300	.	.	.	none	.	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	hg19	5	7886796	7886796	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	MTRR	NM_024010	exon8	c.A1207G	p.I403V	CTTGAAATCCGAG	.	79.0	5.0	91.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
FAM46A	55603	hgsc.bcm.edu	hg19	6	82461655	82461655	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	FAM46A	NM_017633	exon2	c.G204T	p.W68C	TTGCTCCCAGTTC	.	124.0	61.0	197.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	hg19	6	90411386	90411386	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	MDN1	NM_014611	exon55	c.A8318T	p.E2773V	TGAACTTCTTTGT	.	52.0	26.0	52.0	0.0	.	478	.	.	.	none	.	.	PASS	Atlas-SNP
ECHDC1	55862	hgsc.bcm.edu	hg19	6	127611395	127611395	+	Silent	SNP	T	T	C	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ECHDC1	NM_001139510	exon6	c.A543G	p.R181R	GACGAATCTGATC	.	93.0	37.0	80.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	hg19	6	159401839	159401839	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	RSPH3	NM_031924	exon6	c.G1252A	p.D418N	CACTATCCCTGAG	.	44.0	18.0	60.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
C7orf26	79034	hgsc.bcm.edu	hg19	7	6639468	6639468	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	C7orf26	NM_024067	exon4	c.A589T	p.I197F	GACCTCATTCCAC	.	218.0	126.0	193.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
HERPUD2	64224	hgsc.bcm.edu	hg19	7	35707133	35707133	+	Silent	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	HERPUD2	NM_022373	exon5	c.T405C	p.G135G	GGAAGAACCCACA	.	179.0	111.0	133.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	hg19	9	20414373	20414373	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	MLLT3,NS,carcinoma,0,4	MLLT3	NM_004529	exon5	c.C471T	p.S157S	GCTGCTGCTACTG	.	67.0	3.0	95.0	1.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
RUSC2	9853	hgsc.bcm.edu	hg19	9	35560975	35560975	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	RUSC2	NM_014806	exon11	c.G4230A	p.L1410L	CTGGCTGAGCCTG	.	52.0	24.0	76.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
GAPVD1	26130	hgsc.bcm.edu	hg19	9	128117063	128117063	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	GAPVD1	NM_015635	exon23	c.G3781A	p.V1261I	ACCACTGTCTGTG	.	177.0	70.0	159.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
ARRDC1	92714	hgsc.bcm.edu	hg19	9	140508526	140508526	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ARRDC1	NM_152285	exon5	c.C478A	p.L160M	TACAAGCTGGTGA	.	183.0	61.0	225.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	hg19	11	47745663	47745663	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	FNBP4	NM_015308	exon14	c.C2381A	p.T794K	ATTTCTGTAGCTT	.	79.0	30.0	89.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	hg19	11	47745665	47745665	+	Silent	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	FNBP4	NM_015308	exon14	c.T2379C	p.A793A	TTCTGTAGCTTTC	.	75.0	29.0	90.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	hg19	11	48142761	48142761	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	PTPRJ	NM_001098503	exon4	c.A559G	p.T187A	TCCATCACTCCAG	.	69.0	20.0	102.0	0.0	.	225	.	.	.	none	.	.	PASS	Atlas-SNP
NCAM1	4684	hgsc.bcm.edu	hg19	11	113103986	113103986	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	NCAM1	NM_001242607	exon15	c.G1718T	p.W573L	CTGAGTGGAGAGC	.	42.0	16.0	45.0	0.0	.	372	.	.	.	none	.	.	PASS	Atlas-SNP
LAG3	3902	hgsc.bcm.edu	hg19	12	6886460	6886460	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	LAG3	NM_002286	exon6	c.C1088G	p.S363C	CTGGATCCCTGGG	.	158.0	67.0	136.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
PRB4	5545	hgsc.bcm.edu	hg19	12	11461501	11461501	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	PRB4	NM_002723	exon3	c.G416T	p.G139V	GGCTTTCCTGGAG	.	566.0	232.0	531.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
TMTC2	160335	hgsc.bcm.edu	hg19	12	83290130	83290130	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	TMTC2	NM_152588	exon3	c.G1188A	p.L396L	TGTTCTGTCTTTA	.	208.0	96.0	214.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	hg19	12	92537939	92537939	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	BTG1	NM_001731	exon2	c.A433G	p.S145G	TTCGGCTGTCTAC	.	116.0	56.0	117.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	hg19	12	94976205	94976205	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	TMCC3	NM_020698	exon2	c.A188T	p.K63M	TTGACCTTGTGGA	.	146.0	62.0	166.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	hg19	13	95886864	95886864	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ABCC4	NM_005845	exon4	c.G531T	p.K177N	ACTTACCTTCCGA	.	44.0	19.0	72.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	hg19	13	95886865	95886865	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ABCC4	NM_005845	exon4	c.A530C	p.K177T	CTTACCTTCCGAT	.	47.0	20.0	74.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
DENND4A	10260	hgsc.bcm.edu	hg19	15	66031104	66031104	+	Silent	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	DENND4A	NM_001144823	exon6	c.T741C	p.N247N	TTTGCTATTTGAT	.	122.0	49.0	88.0	0.0	.	217	.	.	.	none	.	.	PASS	Atlas-SNP
C15orf59	388135	hgsc.bcm.edu	hg19	15	74032301	74032301	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	C15orf59	NM_001039614	exon2	c.T839A	p.L280Q	TAGGGCAGAACCG	.	163.0	72.0	250.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
ACSM1	116285	hgsc.bcm.edu	hg19	16	20682868	20682868	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ACSM1	NM_052956	exon4	c.C737A	p.P246H	AAGGAGGGTTGTA	.	111.0	36.0	61.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	hg19	17	1633711	1633711	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	WDR81	NM_001163809	exon2	c.G3705A	p.K1235K	TGCCAAGCTCGGC	.	69.0	15.0	67.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	hg19	17	4445915	4445915	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	MYBBP1A	NM_014520	exon21	c.A3014G	p.H1005R	ACCGGGTGCCGGG	.	189.0	115.0	137.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	hg19	17	7948982	7948982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ALOX15B	NM_001141	exon8	c.C1178T	p.P393L	AGCTGCCCCACTG	.	78.0	38.0	45.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
MYH2	4620	hgsc.bcm.edu	hg19	17	10433386	10433386	+	Silent	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	MYH2	NM_017534	exon23	c.C2703T	p.A901A	GCCTTCGGCTTCC	.	254.0	82.0	152.0	0.0	.	390	.	.	.	none	.	.	PASS	Atlas-SNP
EPB41L3	23136	hgsc.bcm.edu	hg19	18	5406855	5406855	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	EPB41L3	NM_012307	exon16	c.A2270G	p.K757R	AGCCTCTTCTCCC	.	116.0	49.0	162.0	0.0	.	222	.	.	.	none	.	.	PASS	Atlas-SNP
DSC2	1824	hgsc.bcm.edu	hg19	18	28660278	28660278	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	DSC2	NM_024422	exon10	c.T1304G	p.I435S	ACACCAATTTGCA	.	70.0	30.0	68.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	hg19	19	10403449	10403449	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ICAM5	NM_003259	exon5	c.A1123G	p.N375D	ACCGAGAACGACG	.	56.0	8.0	99.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
ROMO1	140823	hgsc.bcm.edu	hg19	20	34288799	34288799	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ROMO1	NM_080748	exon3	c.A211G	p.M71V	ACATTCATGGCCA	.	127.0	49.0	105.0	0.0	.	5	.	.	.	none	.	.	PASS	Atlas-SNP
SON	6651	hgsc.bcm.edu	hg19	21	34948684	34948684	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.,1	SON	NM_138927	exon12	c.G7235A	p.G2412E	GAAATGGAGCCCT	.	58.0	10.0	32.0	2.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
SUPT20HL1	100130302	hgsc.bcm.edu	hg19	X	24381817	24381817	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	.	NM_001136234	exon1	c.G940T	p.G314W	GCTAAAGGGTATC	.	181.0	119.0	185.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PUS3	83480	hgsc.bcm.edu	hg19	11	125765906	125765922	+	Frame_Shift_Del	DEL	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	PUS3	NM_031307	exon2	c.259_275del	p.87_92del	.	.	194.0	60.0	236.0	0.0	.	33	.	0.309278	0	none	.	.	PASS	Atlas-INDEL
AMY1C	278	hgsc.bcm.edu	hg19	1	104299657	104299658	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	AMY1C	NM_001008219	exon10	c.1232_1233insT	p.N411fs	.	.	398.0	43.0	332.0	0.0	.	11	.	0.10804	0	none	.	.	PASS	Atlas-INDEL
RAD18	56852	hgsc.bcm.edu	hg19	3	8955405	8955406	+	Splice_Site	INS	-	-	TG	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	RAD18	NM_020165	exon9	c.890-1->CA	.	.	.	23.0	13.0	21.0	0.0	.	52	.	0.565217	0	none	.	.	PASS	Atlas-INDEL
ZZEF1	23140	hgsc.bcm.edu	hg19	17	3924472	3924472	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	ZZEF1	NM_015113	exon45	c.7356delG	p.K2452fs	.	.	375.0	106.0	235.0	0.0	.	195	.	0.282667	0	none	.	.	PASS	Atlas-INDEL
C2orf71	388939	hgsc.bcm.edu	hg19	2	29297095	29297096	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	C2orf71	NM_001029883	exon1	c.33_34insT	p.V11fs	.	.	93.0	48.0	119.0	0.0	.	146	.	0.516129	0	none	.	.	PASS	Atlas-INDEL
TRIM37	4591	hgsc.bcm.edu	hg19	17	57078973	57078974	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	TRIM37	NM_015294	exon23	c.2798_2799del	p.933_933del	.	.	188.0	20.0	121.0	0.0	.	105	.	0.106383	0	none	.	.	PASS	Atlas-INDEL
AMY1C	278	hgsc.bcm.edu	hg19	1	104231690	104231691	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	AMY1C	NM_001008219	exon10	c.1236_1237insT	p.F412fs	.	.	357.0	54.0	315.0	0.0	.	11	.	0.151261	0	none	.	.	PASS	Atlas-INDEL
SENP8	123228	hgsc.bcm.edu	hg19	15	72432229	72432229	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	SENP8	NM_001166340	exon2	c.264delA	p.L88fs	.	.	114.0	53.0	122.0	0.0	.	18	.	0.464912	0	none	.	.	PASS	Atlas-INDEL
AP1G1	164	hgsc.bcm.edu	hg19	16	71768532	71768533	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	AP1G1	NM_001030007	exon23	c.2356_2357insT	p.K786_V787delinsX	.	.	657.0	369.0	376.0	0.0	.	83	.	0.561644	0	none	.	.	PASS	Atlas-INDEL
EPHB4	2050	hgsc.bcm.edu	hg19	7	100404084	100404104	+	In_Frame_Del	DEL	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	EPHB4	NM_004444	exon14	c.2423_2443del	p.808_815del	.	.	161.0	14.0	142.0	0.0	.	106	.	0.0869565	0	none	.	.	PASS	Atlas-INDEL
AMY1C	278	hgsc.bcm.edu	hg19	1	104205519	104205520	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	AMY1C	NM_001008219	exon10	c.1232_1233insT	p.N411fs	.	.	381.0	55.0	287.0	0.0	.	11	.	0.144357	0	none	.	.	PASS	Atlas-INDEL
TRIM14	9830	hgsc.bcm.edu	hg19	9	100862406	100862406	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	TRIM14	NM_014788	exon3	c.345delC	p.F115fs	.	.	111.0	52.0	106.0	0.0	.	24	.	0.468468	0	none	.	.	PASS	Atlas-INDEL
HLA-B	3106	hgsc.bcm.edu	hg19	6	31323288	31323288	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	.	HLA-B	NM_005514	exon4	c.702delT	p.P234fs	.	.	162.0	72.0	225.0	0.0	.	54	.	0.444444	0	none	.	.	PASS	Atlas-INDEL