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
CEP128	145508	hgsc.bcm.edu	37	14	81297580	81297612	+	In_Frame_Del	DEL	CAGCTGCACTCTCAAATCTGACATTTGCTTCTC	CAGCTGCACTCTCAAATCTGACATTTGCTTCTC	-	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	CAGCTGCACTCTCAAATCTGACATTTGCTTCTC	CAGCTGCACTCTCAAATCTGACATTTGCTTCTC	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	CEP128	NM_152446	exon12	c.1085_1117del	p.362_373del	.	.	205.0	48.0	470.0	0.0	.	146	.	Pindel,Atlas-Indel
ZNF682	91120	hgsc.bcm.edu	37	19	20117945	20117946	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	ZNF682	NM_033196	exon4	c.366_367del	p.122_123del	.	.	110.0	37.0	136.0	0.0	.	51	.	Pindel,Atlas-Indel
DIS3	22894	hgsc.bcm.edu	37	13	73335570	73335571	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	DIS3	NM_014953	exon19	c.2601_2602del	p.867_868del	.	.	104.0	26.0	151.0	0.0	.	103	.	Pindel,Atlas-Indel
KIF14	9928	hgsc.bcm.edu	37	1	200529865	200529865	+	Silent	SNP	T	T	C	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_014875	exon26	c.A4215G	p.K1405K	GGCAGCTTTATTG	.	206.0	71.0	262.0	0.0	.	.	.	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117266554	117266554	+	Silent	SNP	T	T	C	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_001173425	exon1	c.A528G	p.L176L	CTCAGCTAGAGAG	.	50.0	17.0	110.0	0.0	.	.	.	Atlas-SNP
EMC3	55831	hgsc.bcm.edu	37	3	10012302	10012302	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	TMEM111,bladder,carcinoma,+1,1	TMEM111	NM_018447	exon6	c.C538T	p.R180W	TGCTCCGAAGCCC	.	66.0	30.0	153.0	0.0	.	+1	1	Atlas-SNP
COL4A5	1287	hgsc.bcm.edu	37	X	107929306	107929306	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_000495	exon46	c.G4244A	p.G1415D	TCCCTGGCTTTGA	.	246.0	14.0	205.0	0.0	.	.	.	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	rs55936365		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	NBPF10,NS,carcinoma,0,2	NBPF10	NM_001039703	exon1	c.C130G	p.L44V	TGTTTTCTAACTC	.	54.0	5.0	60.0	2.0	.	0	2	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508174	195508174	+	Missense_Mutation	SNP	G	G	A	rs200854768	byfrequency	TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4_ENST00000463781	NM_018406	exon2	c.C10277T	p.P3426L	GTGACAGGAAGAG	.	50.0	3.0	79.0	1.0	0.008	-1	3	Atlas-SNP
SMS	6611	hgsc.bcm.edu	37	X	21995231	21995231	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_004595	exon5	c.G382C	p.D128H	ACCGCCGACGGGC	.	232.0	11.0	227.0	0.0	.	.	.	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	37	1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	rs199597671		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_014856	exon18	c.C2722G	p.Q908E	GCTGCTGCTGCTG	.	36.0	7.0	34.0	0.0	.	.	.	Atlas-SNP
PPEF1	5475	hgsc.bcm.edu	37	X	18845518	18845518	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_006240	exon19	c.C1875A	p.S625R	TGGAAGCATTGAC	.	213.0	66.0	209.0	0.0	.	.	.	Atlas-SNP
TFAP2D	83741	hgsc.bcm.edu	37	6	50740418	50740418	+	Silent	SNP	A	A	C	rs375378399		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	TFAP2D,NS,carcinoma,+1,2	TFAP2D	NM_172238	exon8	c.A1200C	p.T400T	CCAAACAGTTCTC	.	78.0	28.0	95.0	0.0	.	+1	2	Atlas-SNP
VSIG8	391123	hgsc.bcm.edu	37	1	159827898	159827898	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_001013661	exon3	c.G412T	p.V138F	CAATGACCTTCCG	.	154.0	79.0	282.0	1.0	.	.	.	Atlas-SNP
ABCA6	23460	hgsc.bcm.edu	37	17	67136799	67136799	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_080284	exon2	c.C46A	p.L16M	TGCACAGAAGTGC	.	90.0	4.0	122.0	0.0	.	.	.	Atlas-SNP
TXK	7294	hgsc.bcm.edu	37	4	48115254	48115254	+	Silent	SNP	C	C	T	rs200958317	by1000genomes	TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_003328	exon3	c.G144A	p.P48P	GAGCCACGGCCTG	.	56.0	22.0	89.0	0.0	0.000	.	.	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839493	27839493	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_182506	exon3	c.G70A	p.D24N	CTGGAAGATTTGA	.	159.0	50.0	154.0	0.0	.	.	.	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	37	9	20819865	20819865	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_017794	exon14	c.T1526C	p.I509T	ATGATATATTGTA	.	487.0	190.0	645.0	0.0	.	.	.	Atlas-SNP
FLJ31813	0	hgsc.bcm.edu	37	10	51814574	51814574	+	RNA	SNP	G	G	C	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	.	.	.	.	CATTTAGAAAACG	.	57.0	22.0	86.0	0.0	.	.	.	Atlas-SNP
FLJ39080	0	hgsc.bcm.edu	37	8	75516361	75516361	+	RNA	SNP	C	C	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	.	.	.	.	TCCTCGCGCATCT	.	58.0	13.0	55.0	0.0	.	.	.	Atlas-SNP
LOR	4014	hgsc.bcm.edu	37	1	153233506	153233506	+	Silent	SNP	C	C	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	LOR,caecum,carcinoma,0,1	LOR	NM_000427	exon2	c.C81T	p.G27G	TGGCGGCGGCAGC	.	72.0	5.0	98.0	1.0	.	0	1	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	37	1	153907297	153907297	+	Silent	SNP	C	C	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	DENND4B_ENST00000361217,NS,carcinoma,0,6	DENND4B_ENST00000361217	NM_014856	exon18	c.G2712A	p.Q904Q	CTGCTGCTGCTGC	.	40.0	11.0	63.0	0.0	.	0	6	Atlas-SNP
SOCS4	122809	hgsc.bcm.edu	37	14	55509766	55509766	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_080867	exon2	c.G7T	p.E3X	ATGGCAGAAAATA	.	58.0	27.0	107.0	0.0	.	.	.	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	37	X	65479954	65479954	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_138737	exon19	c.T3211A	p.Y1071N	GAGAACTACCGGG	.	97.0	38.0	93.0	0.0	.	.	.	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145619906	145619906	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_013291	exon31	c.G3520A	p.A1174T	ACAGGGCGGTCAC	.	86.0	26.0	93.0	0.0	.	.	.	Atlas-SNP
EID3	493861	hgsc.bcm.edu	37	12	104698695	104698695	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_001008394	exon1	c.T983A	p.I328N	CTATGATTACATA	.	87.0	46.0	184.0	0.0	.	.	.	Atlas-SNP
DCAF8L1	139425	hgsc.bcm.edu	37	X	27998407	27998407	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_001017930	exon1	c.C1045A	p.Q349K	CAAATTGGTAAAT	.	157.0	10.0	140.0	0.0	.	.	.	Atlas-SNP
NTHL1	4913	hgsc.bcm.edu	37	16	2094711	2094711	+	Missense_Mutation	SNP	G	G	A	rs376048896		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_002528	exon3	c.C469T	p.R157W	GGCCCCGCGCCCG	.	35.0	15.0	75.0	0.0	.	.	.	Atlas-SNP
TMEM182	130827	hgsc.bcm.edu	37	2	103380825	103380825	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-YU-A94D-01A-11D-A435-10	TCGA-YU-A94D-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	6cdf8e7a-91c2-467f-a970-16d9a85624d8	9c956f87-fd2f-4e2b-ab4e-777d60094e09	.	.	NM_144632	exon3	c.C270A	p.Y90X	TGCTTACCTGTCT	.	136.0	37.0	153.0	0.0	.	.	.	Atlas-SNP
