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	dbSNP_AF	Algorithm
DMAP1	55929	hgsc.bcm.edu	hg19	1	44684030	44684030	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	DMAP1	NM_001034023	exon5	c.C441T	p.L147L	TTATCTCCACGAT	.	143.0	38.0	306.0	0.0	.	35	.	.	Atlas-SNP
SLC35A3	23443	hgsc.bcm.edu	hg19	1	100483326	100483326	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	SLC35A3,bile_duct,carcinoma,0,1	SLC35A3	NM_001271685	exon7	c.C968T	p.S323L	TATTATCAACATT	.	495.0	75.0	913.0	2.0	.	25	.	.	Atlas-SNP
HIST2H3D	653604	hgsc.bcm.edu	hg19	1	149784882	149784882	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	HIST2H3D,bile_duct,carcinoma,0,1	HIST2H3D	NM_001123375	exon1	c.A355G	p.T119A	TGATGGTCACGCG	.	209.0	62.0	277.0	1.0	.	15	.	.	Atlas-SNP
WDR26	80232	hgsc.bcm.edu	hg19	1	224585919	224585919	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	WDR26_ENST00000414423,bile_duct,carcinoma,0,2	WDR26	NM_025160	exon12	c.T1654A	p.L552I	CCCATAAATGAAC	.	95.0	30.0	156.0	0.0	.	104	.	.	Atlas-SNP
HK2	3099	hgsc.bcm.edu	hg19	2	75104368	75104368	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	HK2	NM_000189	exon8	c.G951A	p.E317E	GGAGGAGCTGCTC	.	105.0	25.0	133.0	0.0	.	85	.	.	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	hg19	2	109380447	109380447	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	RANBP2_ENST00000283195,bile_duct,carcinoma,0,2	RANBP2	NM_006267	exon20	c.A3452G	p.N1151S	CAGCAAACAAGAA	.	131.0	71.0	165.0	0.0	.	488	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179412302	179412302	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	TTN	NM_001267550	exon339	c.T94051C	p.S31351P	TACCCGATTCACG	.	166.0	31.0	246.0	0.0	.	18412	.	.	Atlas-SNP
IDH1	3417	hgsc.bcm.edu	hg19	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499	bycluster	TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	NM_005896	exon4	c.C394T	p.R132C	CATGACGACCTAT	.	189.0	89.0	298.0	0.0	.	6310	.	.	Atlas-SNP
CXCR7	57007	hgsc.bcm.edu	hg19	2	237489915	237489915	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	CXCR7	NM_020311	exon2	c.C807T	p.H269H	CTACCACGTGGCG	.	111.0	23.0	141.0	0.0	.	72	.	.	Atlas-SNP
RAF1	5894	hgsc.bcm.edu	hg19	3	12645687	12645687	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	RAF1,bile_duct,carcinoma,0,1	RAF1	NM_002880	exon7	c.C782G	p.P261R	ACATTAGGTGTGG	.	126.0	57.0	173.0	0.0	.	66	.	.	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	hg19	3	184001717	184001717	+	Missense_Mutation	SNP	G	G	A	rs370460271		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	ECE2	NM_014693	exon8	c.G1315A	p.D439N	CGGCGCGACGAGG	.	164.0	30.0	168.0	0.0	.	303	.	.	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	hg19	7	48315045	48315045	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	ABCA13	NM_152701	exon17	c.G5782T	p.V1928F	CCGTTTGTCCCAC	.	222.0	106.0	280.0	0.0	.	1192	.	.	Atlas-SNP
TPST1	8460	hgsc.bcm.edu	hg19	7	65705902	65705902	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	TPST1,bile_duct,carcinoma,0,1	TPST1	NM_003596	exon2	c.C490G	p.L164V	TTTGCCCTGAAAT	.	82.0	32.0	126.0	0.0	.	25	.	.	Atlas-SNP
STEAP4	79689	hgsc.bcm.edu	hg19	7	87912274	87912274	+	Missense_Mutation	SNP	G	G	C	rs370475892	bycluster;alternate_allele	TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	STEAP4,colon,carcinoma,0,2	STEAP4	NM_001205315	exon4	c.C666G	p.D222E	GATTACGTCTCTT	.	103.0	43.0	189.0	0.0	.	54	.	.	Atlas-SNP
ARID5B	84159	hgsc.bcm.edu	hg19	10	63817024	63817024	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	ARID5B	NM_032199	exon6	c.T995C	p.M332T	AATACATGAAAGA	.	72.0	52.0	166.0	0.0	.	125	.	.	Atlas-SNP
MLL	4297	hgsc.bcm.edu	hg19	11	118373507	118373507	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	MLL	NM_001197104	exon27	c.G6900A	p.V2300V	CTTGGTGTCCAAG	.	51.0	13.0	103.0	0.0	.	548	.	.	Atlas-SNP
SNX19	399979	hgsc.bcm.edu	hg19	11	130785772	130785772	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	SNX19	NM_014758	exon1	c.T63C	p.N21N	CAGGTTATTGAGG	.	53.0	11.0	108.0	0.0	.	84	.	.	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	hg19	14	58605153	58605153	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	C14orf37	NM_001001872	exon2	c.T924A	p.S308S	TAAGGCAGAGGCA	.	98.0	45.0	227.0	0.0	.	87	.	.	Atlas-SNP
TRPV3	162514	hgsc.bcm.edu	hg19	17	3417232	3417232	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	TRPV3	NM_001258205	exon18	c.A2355G	p.E785E	CGGGAATTCCTCG	.	217.0	71.0	314.0	1.0	.	85	.	.	Atlas-SNP
ANKFY1	51479	hgsc.bcm.edu	hg19	17	4082167	4082167	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	ANKFY1	NM_001257999	exon18	c.C2709T	p.S903S	AGCCCCGGACTCT	.	85.0	20.0	135.0	0.0	.	81	.	.	Atlas-SNP
MYH2	4620	hgsc.bcm.edu	hg19	17	10432777	10432777	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	MYH2	NM_017534	exon25	c.G3139T	p.E1047X	TCTTTTCTTGCTC	.	136.0	15.0	246.0	0.0	.	390	.	.	Atlas-SNP
TPM4	7171	hgsc.bcm.edu	hg19	19	16186928	16186928	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	TPM4	NM_001145160	exon2	c.G186C	p.E62D	TTCCGAGGACCTG	.	179.0	95.0	194.0	0.0	.	28	.	.	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	hg19	19	39010081	39010081	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	RYR1	NM_001042723	exon67	c.G10246A	p.V3416M	CGCTACGTGGACA	.	46.0	17.0	62.0	0.0	.	708	.	.	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	hg19	19	53014251	53014251	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	.	NM_001099694	exon6	c.A617C	p.N206T	CTCCTAATAACTA	.	233.0	14.0	398.0	0.0	.	.	.	.	Atlas-SNP
TARM1	441864	hgsc.bcm.edu	hg19	19	54573362	54573362	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	TARM1	NM_001135686	exon5	c.G711A	p.L237L	CAGACCCAGTCGT	.	67.0	8.0	73.0	0.0	.	10	.	.	Atlas-SNP
U2AF2	11338	hgsc.bcm.edu	hg19	19	56185355	56185355	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	U2AF2,bile_duct,carcinoma,0,1	U2AF2	NM_007279	exon12	c.C1349T	p.T450M	GCCTGACGGGCCG	.	106.0	22.0	123.0	0.0	.	62	.	.	Atlas-SNP
ZMYND8	23613	hgsc.bcm.edu	hg19	20	45920579	45920579	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	ZMYND8	NM_183047	exon6	c.A621G	p.E207E	GATGTATTCCGCA	.	82.0	31.0	144.0	0.0	.	166	.	.	Atlas-SNP
PKNOX1	5316	hgsc.bcm.edu	hg19	21	44450022	44450022	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	PKNOX1	NM_004571	exon11	c.G1122A	p.T374T	CACCACGCCCGTG	.	97.0	40.0	152.0	0.0	.	40	.	.	Atlas-SNP
PHKA2	5256	hgsc.bcm.edu	hg19	X	18919622	18919622	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	PHKA2	NM_000292	exon27	c.T3008A	p.L1003Q	CTCCTCAGTCTGT	.	210.0	101.0	315.0	0.0	.	122	.	.	Atlas-SNP
BMP15	9210	hgsc.bcm.edu	hg19	X	50653812	50653812	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	BMP15	NM_005448	exon1	c.T29G	p.L10R	GAATTCTTTTTCT	.	236.0	47.0	269.0	0.0	.	62	.	.	Atlas-SNP
HTATSF1	27336	hgsc.bcm.edu	hg19	X	135593729	135593729	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	HTATSF1	NM_001163280	exon10	c.A1825C	p.K609Q	TCTGAAAAAGTGT	.	127.0	40.0	244.0	0.0	.	66	.	.	Atlas-SNP
DUSP9	1852	hgsc.bcm.edu	hg19	X	152914788	152914788	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	DUSP9	NM_001395	exon3	c.G475A	p.V159M	GTGCCCGTGGTGG	.	100.0	12.0	117.0	0.0	.	41	.	.	Atlas-SNP
ND1	10625	hgsc.bcm.edu	hg19	MT	3918	3918	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	.	ENST00000361390	exon1	c.G612C	p.E204D	AGGGGAGTCCGAA	.	146.0	40.0	466.0	0.0	.	.	.	.	Atlas-SNP
COX2	5743	hgsc.bcm.edu	hg19	MT	8184	8184	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	.	ENST00000361739	exon1	c.G599A	p.C200Y	AAATCTGTGGAGC	.	167.0	13.0	519.0	0.0	.	.	.	.	Atlas-SNP
CYTB	0	hgsc.bcm.edu	hg19	MT	15276	15276	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	.	ENST00000361789	exon1	c.G530A	p.R177Q	TCACACGATTCTT	.	165.0	158.0	497.0	1.0	.	.	.	.	Atlas-SNP
BAP1	8314	hgsc.bcm.edu	hg19	3	52440340	52440348	+	In_Frame_Del	DEL	TGCGGTCGG	TGCGGTCGG	-	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	TGCGGTCGG	TGCGGTCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	BAP1	NM_004656	exon9	c.705_713del	p.235_238del	.	.	37.0	16.0	111.0	0.0	.	371	.	.	Atlas-INDEL
CYLC1	1538	hgsc.bcm.edu	hg19	X	83128315	83128316	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	CYLC1	NM_021118	exon4	c.598_599del	p.200_200del	.	.	250.0	79.0	428.0	0.0	.	272	.	.	Atlas-INDEL
DIP2C	22982	hgsc.bcm.edu	hg19	10	460026	460026	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	DIP2C	NM_014974	exon8	c.885delA	p.P295fs	.	.	68.0	24.0	57.0	0.0	.	195	.	.	Atlas-Indel,Pindel
TNPO1	3842	hgsc.bcm.edu	hg19	5	72144303	72144303	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	.	TNPO1	NM_002270	exon2	c.106delA	p.T36fs	.	.	67.0	30.0	46.0	0.0	.	90	.	.	Atlas-Indel,Pindel
