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	Algorithm
USP12	219333	hgsc.bcm.edu	37	13	27664080	27664081	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	USP12	NM_182488	exon6	c.674_675del	p.225_225del	.	.	225.0	40.0	260.0	0.0	.	35	.	Atlas-Indel
NCOA6	23054	hgsc.bcm.edu	37	20	33345720	33345721	+	In_Frame_Ins	INS	-	-	TGC	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	-	-	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	NCOA6	NM_014071	exon7	c.831_832insGCA	p.Q277delinsQQ	.	.	100.0	12.0	58.0	0.0	.	219	.	Atlas-Indel
CDK12	51755	hgsc.bcm.edu	37	17	37627847	37627850	+	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	ACTC	ACTC	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	CDK12	NM_016507	exon2	c.1761_1764del	p.587_588del	.	.	269.0	58.0	244.0	0.0	.	161	.	Pindel,Atlas-Indel
DST	667	hgsc.bcm.edu	37	6	56368856	56368856	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_015548	exon59	c.C11636T	p.A3879V	ATTGAAGCTAATT	.	124.0	14.0	129.0	0.0	.	.	.	Atlas-SNP
PRDM7	11105	hgsc.bcm.edu	37	16	90124710	90124710	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	PRDM7_ENST00000449207,NS,carcinoma,0,1	PRDM7_ENST00000449207	NM_001098173	exon10	c.G1466C	p.G489A	TTTGGACCTTTCT	.	97.0	32.0	96.0	0.0	.	0	1	Atlas-SNP
FLJ36000	0	hgsc.bcm.edu	37	17	21904869	21904869	+	RNA	SNP	A	A	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	.	.	.	.	ACGGCAACAAGCC	.	57.0	8.0	74.0	0.0	.	.	.	Atlas-SNP
DCDC5	100506627	hgsc.bcm.edu	37	11	30937241	30937241	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_020869	exon8	c.G791T	p.S264I	AATTTACTATGCT	.	125.0	35.0	127.0	0.0	.	.	.	Atlas-SNP
FKBP4	2288	hgsc.bcm.edu	37	12	2908333	2908333	+	Silent	SNP	G	G	C	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_002014	exon5	c.G594C	p.L198L	GAACCTGGATCTG	.	109.0	19.0	52.0	0.0	.	.	.	Atlas-SNP
tRNA-Tyr	0	hgsc.bcm.edu	37	MT	5881	5881	+	RNA	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	.	.	.	.	CACTCAGCCATTT	.	115.0	11.0	108.0	0.0	.	.	.	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186283154	186283154	+	Silent	SNP	C	C	T	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_003292	exon51	c.G7041A	p.V2347V	ATGGCTCACACCT	.	105.0	15.0	84.0	0.0	.	.	.	Atlas-SNP
DNM2	1785	hgsc.bcm.edu	37	19	10940946	10940946	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_001005361	exon20	c.G2435T	p.R812L	CATCCCGGCCTGG	.	177.0	20.0	96.0	0.0	.	.	.	Atlas-SNP
ZNF277	11179	hgsc.bcm.edu	37	7	111980956	111980956	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_021994	exon11	c.G1039A	p.V347I	AAACTGGTCAATT	.	233.0	54.0	228.0	0.0	.	.	.	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28890347	28890347	+	Silent	SNP	A	A	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_015594	exon5	c.A357G	p.Q119Q	AGGACAACAAGCC	.	95.0	4.0	156.0	0.0	.	.	.	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51096836	51096836	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_015198	exon10	c.G1957T	p.G653C	CACAGCCATACAC	.	270.0	87.0	176.0	0.0	.	.	.	Atlas-SNP
KRT19	3880	hgsc.bcm.edu	37	17	39680453	39680453	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_002276	exon5	c.C890T	p.T297I	AGGTCAGTAACCT	.	113.0	30.0	140.0	0.0	.	.	.	Atlas-SNP
ERICH1	157697	hgsc.bcm.edu	37	8	642586	642586	+	Nonsense_Mutation	SNP	G	G	A	rs150434775	bycluster	TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_207332	exon3	c.C196T	p.R66X	GCCGTCGGGCAGT	.	450.0	93.0	333.0	0.0	0.000	.	.	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5212059	5212059	+	Silent	SNP	T	T	C	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_004703	exon2	c.T105C	p.L35L	GCAGCTTGAACAA	.	382.0	56.0	430.0	0.0	.	.	.	Atlas-SNP
PITX1	5307	hgsc.bcm.edu	37	5	134364535	134364535	+	Silent	SNP	C	C	G	rs61751190	bycluster;alternate_allele	TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_002653	exon3	c.G879C	p.S293S	AAACGACGAGTGC	.	62.0	18.0	72.0	0.0	.	.	.	Atlas-SNP
GPR39	2863	hgsc.bcm.edu	37	2	133174783	133174783	+	Silent	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_001508	exon1	c.G168A	p.Q56Q	CACCCAGGTGCTG	.	186.0	21.0	154.0	0.0	.	.	.	Atlas-SNP
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357586	39357586	+	Silent	SNP	T	T	C	rs202076860	bycluster	TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	APOBEC3A,caecum,carcinoma,+1,1	APOBEC3A	NM_145699	exon3	c.T369C	p.R123R	ACTGCGTATCTTC	.	54.0	6.0	78.0	1.0	0.001	+1	1	Atlas-SNP
CCSER2	54462	hgsc.bcm.edu	37	10	86131820	86131820	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_018999	exon2	c.G1012A	p.G338R	GTTGATGGAAATA	.	114.0	17.0	118.0	0.0	.	.	.	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	37	16	28914470	28914470	+	Splice_Site	SNP	T	T	A	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_173201	exon20	c.2862+2T>A	.	TGCCGGTGAGGTT	.	51.0	13.0	46.0	0.0	.	.	.	Atlas-SNP
ZNF85	7639	hgsc.bcm.edu	37	19	21132152	21132152	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_001256171	exon5	c.A922T	p.I308L	CATAAGATAATTC	.	99.0	14.0	69.0	0.0	.	.	.	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122420415	122420415	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_017554	exon6	c.A3014G	p.K1005R	GGGAAAAAGGAAG	.	137.0	23.0	119.0	0.0	.	.	.	Atlas-SNP
EPB41	2035	hgsc.bcm.edu	37	1	29314195	29314195	+	Silent	SNP	A	A	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	EPB41_ENST00000343067,NS,carcinoma,+2,1	EPB41_ENST00000343067	NM_203343	exon2	c.A246G	p.L82L	ACGACTATTCTCC	.	401.0	47.0	315.0	0.0	.	+2	1	Atlas-SNP
CHRDL1	91851	hgsc.bcm.edu	37	X	109924730	109924730	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_001143981	exon10	c.A1136G	p.H379R	CAAACGTGGACCT	.	164.0	79.0	154.0	0.0	.	.	.	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	116901	116901	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_207305	exon1	c.C1219G	p.L407V	ATGTCAGCCCAGA	.	181.0	14.0	180.0	0.0	.	.	.	Atlas-SNP
C11orf35	256329	hgsc.bcm.edu	37	11	557032	557032	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	NM_173573	exon8	c.G779A	p.R260Q	TGATGCCGCTCGG	.	37.0	6.0	41.0	0.0	.	.	.	Atlas-SNP
RAPGEF4-AS1	91149	hgsc.bcm.edu	37	2	173600785	173600785	+	RNA	SNP	C	C	G	novel		TCGA-YU-A90W-01A-11D-A435-10	TCGA-YU-A90W-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e283c8-569b-4e2a-81ec-1d38873ec4f8	1374f899-bff2-4251-a5f5-309ce22bb20f	.	.	.	.	.	.	AGCTCGCCGGGGG	.	28.0	5.0	37.0	0.0	.	.	.	Atlas-SNP
