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
SUV420H1	51111	hgsc.bcm.edu	37	11	67925696	67925697	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_017635	exon11	c.2117_2118del	p.706_706del	.	.	123.0	31.0	111.0	0.0	.	.	.	Pindel,Atlas-Indel
PI4K2A	55361	hgsc.bcm.edu	37	10	99410611	99410729	+	Frame_Shift_Del	DEL	ATTTCTTTCCAGATTCCTGCTGACTTGGTCTGTGGGCTATTTTGGTCAACTCGGATTTAACATCCTCTTTTTCTTTGGTCTCTGTAGAGGATCATTGCTGTCTTCAAACCCAAGAATGA	ATTTCTTTCCAGATTCCTGCTGACTTGGTCTGTGGGCTATTTTGGTCAACTCGGATTTAACATCCTCTTTTTCTTTGGTCTCTGTAGAGGATCATTGCTGTCTTCAAACCCAAGAATGA	-	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	ATTTCTTTCCAGATTCCTGCTGACTTGGTCTGTGGGCTATTTTGGTCAACTCGGATTTAACATCCTCTTTTTCTTTGGTCTCTGTAGAGGATCATTGCTGTCTTCAAACCCAAGAATGA	ATTTCTTTCCAGATTCCTGCTGACTTGGTCTGTGGGCTATTTTGGTCAACTCGGATTTAACATCCTCTTTTTCTTTGGTCTCTGTAGAGGATCATTGCTGTCTTCAAACCCAAGAATGA	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_018425	exon2	c.436_466del	p.146_156del	.	.	38.0	10.0	81.0	0.0	.	.	.	Pindel
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651442	1651442	+	Silent	SNP	G	G	C	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	KRTAP5-5,bladder,carcinoma,0,4	KRTAP5-5	NM_001001480	exon1	c.G372C	p.G124G	TGGGGGGTCCAAG	.	28.0	3.0	37.0	1.0	.	0	4	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152321277	152321277	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_018151	exon30	c.G5243C	p.G1748A	TCATTGGGTTAAA	.	143.0	43.0	107.0	0.0	.	.	.	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	37	1	152749008	152749008	+	Missense_Mutation	SNP	C	C	G	rs200931119	bycluster;byfrequency	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	LCE1F,colon,carcinoma,0,2	LCE1F	NM_178354	exon1	c.C161G	p.S54C	GTGGCTCCAGCTC	.	209.0	12.0	223.0	0.0	0.004	0	2	Atlas-SNP
PPP6R3	55291	hgsc.bcm.edu	37	11	68359128	68359128	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001164160	exon18	c.G1870C	p.E624Q	ATATGGGAGGAAA	.	51.0	10.0	53.0	0.0	.	.	.	Atlas-SNP
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382423	24382423	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001136234	exon1	c.G1546C	p.A516P	GCTGCTGCTGCTC	.	149.0	10.0	53.0	0.0	.	.	.	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765173	66765173	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_000044	exon1	c.A185T	p.Q62L	AGCAGCAGCAGCA	.	152.0	23.0	56.0	0.0	.	.	.	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921136	12921136	+	Silent	SNP	C	C	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	PRAMEF2,pharynx,carcinoma,0,1	PRAMEF2	NM_023014	exon4	c.C927T	p.D309D	AGAGGACTTGAAG	.	104.0	6.0	66.0	0.0	.	0	1	Atlas-SNP
DIP2B	57609	hgsc.bcm.edu	37	12	51034560	51034560	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_173602	exon3	c.G226T	p.A76S	CCATCTGCAGCTC	.	107.0	5.0	84.0	0.0	.	.	.	Atlas-SNP
SALL2	6297	hgsc.bcm.edu	37	14	21991589	21991589	+	Missense_Mutation	SNP	G	G	T	rs372214185	alternate_allele	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	SALL2,colon,carcinoma,0,1	SALL2	NM_005407	exon2	c.C2273A	p.P758Q	TCTTCCGGTGATG	.	62.0	5.0	64.0	0.0	.	0	1	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65596686	65596686	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001142800	exon19	c.G2896C	p.D966H	TTACATCAAGTTC	.	85.0	34.0	122.0	0.0	.	.	.	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	15575	15575	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	ENST00000361789	exon1	c.G829A	p.A277T	CTATTCGCCTACA	.	12.0	10.0	8.0	0.0	.	.	.	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765170	66765170	+	Missense_Mutation	SNP	A	A	T	rs62636528	byfrequency	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_000044	exon1	c.A182T	p.Q61L	AGCAGCAGCAGCA	.	156.0	16.0	57.0	0.0	0.043	.	.	Atlas-SNP
NYNRIN	57523	hgsc.bcm.edu	37	14	24880356	24880356	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_025081	exon5	c.G2489A	p.R830Q	GACACCGAGAGGT	.	86.0	17.0	106.0	0.0	.	.	.	Atlas-SNP
USP4	7375	hgsc.bcm.edu	37	3	49318243	49318243	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_003363	exon20	c.G2578C	p.A860P	GCCTTGCTGACAG	.	79.0	25.0	84.0	0.0	.	.	.	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32367149	32367149	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_130806	exon16	c.T1710A	p.N570K	GAAAAATGGAGTA	.	73.0	15.0	125.0	0.0	.	.	.	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145741150	145741150	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_004260	exon6	c.C1256T	p.P419L	TCACCTGGCCGGG	.	97.0	32.0	74.0	0.0	.	.	.	Atlas-SNP
THSD1	55901	hgsc.bcm.edu	37	13	52952281	52952281	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_018676	exon5	c.T1824A	p.D608E	ATTTAGATCCAGC	.	66.0	7.0	119.0	0.0	.	.	.	Atlas-SNP
PSMC3	5702	hgsc.bcm.edu	37	11	47445698	47445698	+	Silent	SNP	G	G	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_002804	exon6	c.C490T	p.L164L	TGGGCAGCGTCTC	.	80.0	12.0	97.0	0.0	.	.	.	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95542364	95542364	+	Silent	SNP	G	G	A	rs113812263	bycluster;byfrequency;by1000genomes	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	TEKT4,caecum,carcinoma,0,3	TEKT4	NM_144705	exon6	c.G1158A	p.A386A	AGAAGCGGAGCAG	.	24.0	3.0	20.0	0.0	0.028	0	3	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789342	117789342	+	Missense_Mutation	SNP	T	T	C	rs75037497	bycluster	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001206790	exon2	c.A233G	p.Q78R	GATGCCTGGGCTG	.	51.0	10.0	58.0	0.0	0.500	.	.	Atlas-SNP
VSIG2	23584	hgsc.bcm.edu	37	11	124619734	124619734	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_014312	exon4	c.G456C	p.Q152H	TCCACTCTGACTG	.	42.0	14.0	39.0	0.0	.	.	.	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789345	117789345	+	Missense_Mutation	SNP	G	G	C	rs61900347	bycluster;by1000genomes	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	TMPRSS13_ENST00000445164,NS,carcinoma,0,2	TMPRSS13_ENST00000445164	NM_001206790	exon2	c.C230G	p.A77G	GCCTGGGCTGGAG	.	50.0	10.0	57.0	0.0	0.101	0	2	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789327	117789327	+	Missense_Mutation	SNP	T	T	C	rs61900346	bycluster;byfrequency;by1000genomes	TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	TMPRSS13_ENST00000445164,NS,carcinoma,0,4	TMPRSS13_ENST00000445164	NM_001206790	exon2	c.A248G	p.Q83R	GATGCCTGGGCTG	.	54.0	9.0	43.0	0.0	0.186	0	4	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36937224	36937224	+	Silent	SNP	G	G	A	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_156039	exon10	c.C1095T	p.S365S	CCGTCCGCTGTCT	.	110.0	6.0	114.0	0.0	.	.	.	Atlas-SNP
CD1E	913	hgsc.bcm.edu	37	1	158325337	158325337	+	Silent	SNP	G	G	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001042584	exon3	c.G603T	p.G201G	AGCAGGGGAGTCA	.	86.0	4.0	56.0	0.0	.	.	.	Atlas-SNP
DPY19L2P1	554236	hgsc.bcm.edu	37	7	35163774	35163774	+	RNA	SNP	A	A	T	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	.	.	.	.	CATAGAAAAAATT	.	83.0	34.0	62.0	0.0	.	.	.	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96119761	96119761	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AALQ-01A-12D-A42Y-10	TCGA-2G-AALQ-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3a396cd3-efe4-4bfb-9ade-41334932b612	0cd78c24-0592-4be8-8ef7-6b1c1858fc01	.	.	NM_001198541	exon14	c.A1967G	p.K656R	AAGGCCTTTTCAA	.	83.0	4.0	107.0	0.0	.	.	.	Atlas-SNP
