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
SCAF4	57466	hgsc.bcm.edu	37	21	33044299	33044310	+	In_Frame_Del	DEL	GCTGTGGCTGCT	GCTGTGGCTGCT	-	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	GCTGTGGCTGCT	GCTGTGGCTGCT	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	SCAF4	NM_020706	exon20	c.2847_2858del	p.949_953del	.	.	89.0	17.0	47.0	0.0	.	142	.	Pindel,Atlas-Indel
LRRC7	57554	hgsc.bcm.edu	37	1	70504317	70504317	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	LRRC7	NM_020794	exon19	c.2695delT	p.S899fs	.	.	147.0	29.0	141.0	0.0	.	400	.	Pindel,Atlas-Indel
EVPLL	645027	hgsc.bcm.edu	37	17	18286644	18286644	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001145127	exon8	c.C732A	p.D244E	GGAGGACGGCAAG	.	32.0	12.0	57.0	0.0	.	.	.	Atlas-SNP
MEPCE	56257	hgsc.bcm.edu	37	7	100028454	100028454	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	MEPCE,NS,carcinoma,0,1	MEPCE	NM_019606	exon1	c.G813C	p.Q271H	CCACCAGCAGCAG	.	39.0	2.0	46.0	1.0	.	0	1	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54668249	54668249	+	Silent	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001145303	exon7	c.G1050A	p.L350L	GTTGAGCAGCACC	.	62.0	20.0	68.0	0.0	.	.	.	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84852104	84852104	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001370	exon29	c.A4432C	p.K1478Q	ACTGGGAAAACAG	.	174.0	53.0	170.0	0.0	.	.	.	Atlas-SNP
MTMR3	8897	hgsc.bcm.edu	37	22	30416250	30416250	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_153050	exon17	c.C2602T	p.L868F	TCTTGCCTTGTAA	.	96.0	38.0	68.0	0.0	.	.	.	Atlas-SNP
PDHA2	5161	hgsc.bcm.edu	37	4	96761797	96761797	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	PDHA2,NS,carcinoma,0,1	PDHA2	NM_005390	exon1	c.G496A	p.G166S	ATCGTCGGTGCAC	.	31.0	12.0	57.0	0.0	.	0	1	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	37	13	52518252	52518252	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_000053	exon14	c.G3236A	p.C1079Y	TCTTTACAGTATT	.	35.0	22.0	58.0	0.0	.	.	.	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14760	14760	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	ENST00000361789	exon1	c.G14A	p.R5H	CAATACGCAAAAC	.	44.0	39.0	111.0	0.0	.	.	.	Atlas-SNP
HAPLN2	60484	hgsc.bcm.edu	37	1	156595122	156595122	+	Silent	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_021817	exon7	c.C969T	p.G323G	TTTCGGCTTCCCC	.	111.0	43.0	116.0	0.0	.	.	.	Atlas-SNP
CBS	875	hgsc.bcm.edu	37	21	44479351	44479351	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_000071	exon13	c.C1208A	p.T403K	TTCTCCGTGAGGT	.	76.0	4.0	48.0	0.0	.	.	.	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57970760	57970760	+	Missense_Mutation	SNP	C	C	T	rs200054918		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	OR1S2,NS,carcinoma,0,3	OR1S2	NM_001004459	exon1	c.G894A	p.M298I	GGGGTTCATCATG	.	96.0	5.0	79.0	2.0	.	0	3	Atlas-SNP
SLC26A6	65010	hgsc.bcm.edu	37	3	48663665	48663665	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_022911	exon20	c.G2251A	p.D751N	GGCTGTCGGGGAC	.	118.0	37.0	100.0	0.0	.	.	.	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146059041	146059041	+	Silent	SNP	A	A	G	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	OTUD4,bladder,carcinoma,0,2	OTUD4	NM_001102653	exon21	c.T2691C	p.H897H	GGGAGGATGAGCC	.	122.0	5.0	88.0	1.0	.	0	2	Atlas-SNP
IL17RA	23765	hgsc.bcm.edu	37	22	17584446	17584446	+	Silent	SNP	G	G	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_014339	exon8	c.G825T	p.G275G	TAAAGGGTGCTGT	.	83.0	6.0	63.0	0.0	.	.	.	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48654898	48654898	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_152701	exon59	c.C14762G	p.A4921G	GTGAGGCTCTTTG	.	129.0	42.0	171.0	0.0	.	.	.	Atlas-SNP
FAM98B	283742	hgsc.bcm.edu	37	15	38776833	38776833	+	Silent	SNP	T	T	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	FAM98B_ENST00000397609,NS,carcinoma,0,2	FAM98B_ENST00000397609	NM_173611	exon8	c.T1275A	p.G425G	TGGTGGTGGAGGA	.	76.0	4.0	82.0	1.0	.	0	2	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52199327	52199327	+	Silent	SNP	G	G	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_006526	exon1	c.C39A	p.S13S	TAAGAGGGATTGA	.	91.0	4.0	56.0	0.0	.	.	.	Atlas-SNP
REEP6	92840	hgsc.bcm.edu	37	19	1496340	1496340	+	Silent	SNP	G	G	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_138393	exon4	c.G405A	p.L135L	CATGCTGTATCAG	.	50.0	12.0	47.0	0.0	.	.	.	Atlas-SNP
PRR4	11272	hgsc.bcm.edu	37	12	10999711	10999711	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_007244	exon3	c.T356C	p.F119S	CTCTGGAAGAATG	.	276.0	28.0	100.0	0.0	.	.	.	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842333	154842333	+	Silent	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001204087	exon1	c.G108A	p.Q36Q	CTGTTGCTGCTGC	.	79.0	4.0	75.0	0.0	.	.	.	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32476309	32476309	+	Silent	SNP	G	G	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001199138	exon4	c.C624A	p.A208A	ACCCTGGGCCCTG	.	113.0	35.0	92.0	0.0	.	.	.	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62979205	62979205	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001271999	exon33	c.G4192T	p.E1398X	TAGCTTCTTCAAG	.	113.0	33.0	126.0	0.0	.	.	.	Atlas-SNP
CLP1	10978	hgsc.bcm.edu	37	11	57427264	57427264	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001142597	exon2	c.C316T	p.Q106X	CGGAGGCAAGCGG	.	101.0	29.0	94.0	0.0	.	.	.	Atlas-SNP
A2M	2	hgsc.bcm.edu	37	12	9258885	9258885	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_000014	exon10	c.T1051G	p.S351A	CAAATGAGAGTTT	.	292.0	19.0	118.0	0.0	.	.	.	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579329	55579329	+	Silent	SNP	T	T	C	rs148925009	byfrequency	TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	.	.	NM_001004738	exon1	c.T387C	p.P129P	TAACCCTTTGCTA	.	102.0	5.0	74.0	0.0	0.000	.	.	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579330	55579330	+	Silent	SNP	T	T	C	rs143718494		TCGA-XE-AAOJ-01A-12D-A435-10	TCGA-XE-AAOJ-10A-01D-A438-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	88e1b406-efd2-4cb8-b0e6-9c731cb5bb8d	2c753e80-371a-4046-a18c-d1f470e43b3d	OR5L1,NS,carcinoma,-1,1	OR5L1	NM_001004738	exon1	c.T388C	p.L130L	AACCCTTTGCTAT	.	100.0	5.0	74.0	0.0	0.000	-1	1	Atlas-SNP
