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	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
MECR	51102	hgsc.bcm.edu	hg19	1	29557328	29557328	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	MECR	NM_016011	exon1	c.G91A	p.A31T	AGGAGGCGGCAGG	.	30.0	20.0	44.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
AGO3	192669	hgsc.bcm.edu	hg19	1	36475164	36475164	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	.	NM_024852	exon9	c.C1118T	p.A373V	GATCTGCACCAGA	.	254.0	99.0	309.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	hg19	1	153740253	153740253	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	INTS3	NM_023015	exon21	c.G2194T	p.E732X	TGCCAGGAGGACG	.	95.0	33.0	78.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
CFH	3075	hgsc.bcm.edu	hg19	1	196654324	196654324	+	Silent	SNP	A	A	G	rs1061147	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes;alternate_allele	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CFH	NM_001014975	exon7	c.A921G	p.A307A	TACAGCAAAATGC	.	239.0	84.0	292.0	0.0	.	251	.	.	.	alt	A|0.352;C|0.648	.	PASS	Atlas-SNP
PTPRC	5788	hgsc.bcm.edu	hg19	1	198678922	198678922	+	Silent	SNP	C	C	T	rs200643724	bycluster	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	PTPRC	NM_002838	exon11	c.C1140T	p.N380N	TACTAACGCAAGT	.	149.0	40.0	222.0	0.0	.	229	.	.	.	weak	C|0.999;T|0.001	0.001	PASS	Atlas-SNP
GPR37L1	9283	hgsc.bcm.edu	hg19	1	202097357	202097357	+	Silent	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	GPR37L1	NM_004767	exon2	c.C1119T	p.L373L	CACCCTCCCAGAG	.	108.0	8.0	124.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
RCOR3	55758	hgsc.bcm.edu	hg19	1	211449723	211449723	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	RCOR3	NM_001136223	exon5	c.G479C	p.S160T	CCTTTAGTTTTCA	.	104.0	9.0	105.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	hg19	1	214815375	214815375	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	CENPF,NS,carcinoma,0,1	CENPF	NM_016343	exon12	c.G3694T	p.E1232X	GAGAAGGAGTGCC	.	118.0	33.0	187.0	1.0	.	321	.	.	.	none	.	.	PASS	Atlas-SNP
SNAP47	116841	hgsc.bcm.edu	hg19	1	227946738	227946738	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SNAP47	NM_053052	exon3	c.C675A	p.S225R	CTTTAGCTCCAAG	.	73.0	4.0	91.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
SDCCAG8	10806	hgsc.bcm.edu	hg19	1	243419490	243419490	+	Silent	SNP	G	G	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SDCCAG8	NM_006642	exon1	c.G15A	p.P5P	GTCCCCGGAGAAC	.	123.0	7.0	146.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
MOGS	7841	hgsc.bcm.edu	hg19	2	74688599	74688599	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	MOGS	NM_006302	exon4	c.G2317A	p.E773K	GACCCTCCAGATG	.	197.0	56.0	248.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
ACMSD	130013	hgsc.bcm.edu	hg19	2	135621133	135621133	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	ACMSD	NM_138326	exon5	c.G418A	p.G140R	TTTCCCGGGGTCC	.	98.0	6.0	116.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
SSFA2	6744	hgsc.bcm.edu	hg19	2	182774650	182774650	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SSFA2	NM_001130445	exon9	c.C1438G	p.P480A	GAAGCTCCTCATG	.	92.0	39.0	120.0	0.0	.	130	.	.	.	none	.	.	PASS	Atlas-SNP
KCNH8	131096	hgsc.bcm.edu	hg19	3	19554559	19554559	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	KCNH8,NS,malignant_melanoma,0,1	KCNH8	NM_144633	exon13	c.C2177T	p.S726F	CAGTCTCCCTCTC	.	265.0	13.0	248.0	0.0	.	189	.	.	.	none	.	.	PASS	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	hg19	3	36874430	36874430	+	Missense_Mutation	SNP	C	C	T	rs370553712		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	TRANK1	NM_014831	exon21	c.G6512A	p.R2171H	TCACAACGCCGCA	.	22.0	10.0	42.0	0.0	.	398	.	.	.	weak	.	.	PASS	Atlas-SNP
BAP1	8314	hgsc.bcm.edu	hg19	3	52439275	52439275	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	BAP1	NM_004656	exon11	c.G967T	p.A323S	ATGGGGCTTGTGC	.	84.0	65.0	99.0	0.0	.	371	.	.	.	none	.	.	PASS	Atlas-SNP
OSBPL11	114885	hgsc.bcm.edu	hg19	3	125250787	125250787	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	OSBPL11	NM_022776	exon12	c.C2096T	p.T699I	TCCAGGGTATGCT	.	102.0	5.0	118.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
CLDN11	5010	hgsc.bcm.edu	hg19	3	170141043	170141043	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CLDN11	NM_005602	exon2	c.C319T	p.R107W	TGCATCCGGATGG	.	174.0	15.0	210.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
MFN1	55669	hgsc.bcm.edu	hg19	3	179082985	179082985	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	MFN1	NM_033540	exon7	c.C725G	p.S242C	ATGCCTCTGCATC	.	86.0	66.0	120.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
FGG	2266	hgsc.bcm.edu	hg19	4	155526043	155526043	+	Silent	SNP	T	T	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	FGG	NM_021870	exon9	c.A1305G	p.R435R	CTCTGGTCTGACC	.	93.0	37.0	66.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
PAPD4	167153	hgsc.bcm.edu	hg19	5	78941013	78941013	+	Silent	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	PAPD4	NM_173797	exon9	c.C819T	p.V273V	TAAAGTCAGGTAA	.	100.0	4.0	121.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	hg19	7	11675888	11675888	+	Silent	SNP	G	G	A	rs375820480		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	THSD7A	NM_015204	exon2	c.C891T	p.R297R	AAGCTCGCGGGCT	.	46.0	21.0	80.0	0.0	.	219	.	.	.	weak	.	.	PASS	Atlas-SNP
IMMP2L	83943	hgsc.bcm.edu	hg19	7	111161447	111161447	+	Silent	SNP	G	G	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	IMMP2L	NM_032549	exon2	c.C57T	p.F19F	CACAAAGAAGCCT	.	58.0	17.0	86.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1147	57189	hgsc.bcm.edu	hg19	7	141365048	141365048	+	Silent	SNP	A	A	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	KIAA1147	NM_001080392	exon6	c.T891A	p.P297P	GAAGAAAGGTTTG	.	190.0	65.0	250.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
CUL1	8454	hgsc.bcm.edu	hg19	7	148496376	148496376	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CUL1	NM_003592	exon21	c.G2146A	p.V716M	GCCATCGTGAGAA	.	114.0	42.0	181.0	0.0	.	80	.	.	.	none	.	.	PASS	Atlas-SNP
DEFA6	1671	hgsc.bcm.edu	hg19	8	6783427	6783427	+	Missense_Mutation	SNP	G	G	A	rs371286175		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	DEFA6	NM_001926	exon1	c.C131T	p.A44V	TCATTTGCCCCAC	.	65.0	25.0	101.0	0.0	.	9	.	.	.	weak	.	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	hg19	8	8655002	8655002	+	Splice_Site	SNP	C	C	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	MFHAS1	NM_004225	exon3	c.2999-1G>T	.	ACTCCCCTGTAGG	.	116.0	47.0	120.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	hg19	9	135163729	135163729	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SETX	NM_015046	exon17	c.T6218C	p.L2073S	GAAGGTAACTCTT	.	63.0	25.0	78.0	0.0	.	234	.	.	.	none	.	.	PASS	Atlas-SNP
TAF3	83860	hgsc.bcm.edu	hg19	10	8007636	8007636	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	TAF3	NM_031923	exon3	c.G2163C	p.K721N	GGAGAAGGAAAGA	.	82.0	21.0	66.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
DHTKD1	55526	hgsc.bcm.edu	hg19	10	12139749	12139749	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	DHTKD1	NM_018706	exon8	c.G1425C	p.E475D	GCAGGAGGAGGTG	.	125.0	53.0	116.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	hg19	10	70182074	70182074	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	DNA2	NM_001080449	exon17	c.G2605A	p.E869K	CCAGTTCCAGCTT	.	167.0	58.0	156.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
HPSE2	60495	hgsc.bcm.edu	hg19	10	100481443	100481443	+	Silent	SNP	C	C	T	rs200916817		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	HPSE2	NM_001166246	exon5	c.G927A	p.P309P	CTTCCTCGGCCGC	.	64.0	7.0	59.0	0.0	.	203	.	.	.	weak	C|0.999;T|0.001	0.001	PASS	Atlas-SNP
CARNS1	57571	hgsc.bcm.edu	hg19	11	67186592	67186592	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CARNS1	NM_001166222	exon5	c.G730C	p.G244R	CTGCGGGGAGGGG	.	37.0	20.0	46.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
C11orf53	341032	hgsc.bcm.edu	hg19	11	111156468	111156468	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	C11orf53	NM_198498	exon4	c.A400C	p.S134R	AGCACGAGTTGCC	.	50.0	16.0	101.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	hg19	11	117789342	117789342	+	Missense_Mutation	SNP	T	T	C	rs75037497	bycluster	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.,4	TMPRSS13	NM_001206790	exon2	c.A233G	p.Q78R	GATGCCTGGGCTG	.	52.0	7.0	73.0	0.0	.	75	.	.	.	weak	T|0.500;C|0.500	0.500	PASS	Atlas-SNP
C14orf39	317761	hgsc.bcm.edu	hg19	14	60921717	60921717	+	Splice_Site	SNP	A	A	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	C14orf39	NM_174978	exon17	c.1503+2T>A	.	CATATTACCTGAT	.	15.0	8.0	24.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
FAM98B	283742	hgsc.bcm.edu	hg19	15	38776827	38776827	+	Silent	SNP	T	T	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	FAM98B_ENST00000397609,NS,carcinoma,0,1	FAM98B	NM_173611	exon8	c.T1269A	p.G423G	TGGTGGTGGTGGT	.	18.0	4.0	17.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	hg19	17	29162089	29162089	+	Silent	SNP	T	T	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	ATAD5	NM_024857	exon2	c.T990A	p.P330P	TCACCCTATTCCG	.	167.0	75.0	189.0	0.0	.	150	.	.	.	none	.	.	PASS	Atlas-SNP
ORMDL3	94103	hgsc.bcm.edu	hg19	17	38078866	38078866	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	ORMDL3	NM_139280	exon4	c.C399G	p.S133R	AAGCACGCTCATC	.	141.0	29.0	159.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	hg19	17	65110487	65110487	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	HELZ	NM_014877	exon28	c.A3871C	p.I1291L	TATTAATTTCAGG	.	47.0	31.0	21.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	hg19	17	73831821	73831821	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	UNC13D	NM_199242	exon19	c.G1634A	p.G545D	ACATCACCCACAA	.	123.0	5.0	129.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
CREB3L3	84699	hgsc.bcm.edu	hg19	19	4171149	4171149	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CREB3L3	NM_032607	exon8	c.G952T	p.A318S	AAGTCAGCCCAGA	.	115.0	42.0	147.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	hg19	19	44739325	44739325	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	ZNF227	NM_182490	exon6	c.A742T	p.K248X	GGAGAGAAACCCC	.	73.0	29.0	99.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	hg19	19	52131213	52131213	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SIGLEC5	NM_003830	exon5	c.A871T	p.T291S	TGGGGGTGGCGTT	.	93.0	37.0	82.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
TGIF2	60436	hgsc.bcm.edu	hg19	20	35219589	35219589	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	TGIF2	NM_021809	exon3	c.C469A	p.L157M	AAGCCCCTGGTGA	.	53.0	30.0	89.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
SUSD2	56241	hgsc.bcm.edu	hg19	22	24583996	24583996	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	SUSD2	NM_019601	exon13	c.C2234A	p.S745Y	CGGGTTCCACCAT	.	357.0	138.0	472.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
CACNG2	10369	hgsc.bcm.edu	hg19	22	37098581	37098581	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	CACNG2	NM_006078	exon1	c.C41A	p.T14N	CCAACGGTGGTTA	.	149.0	56.0	104.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
FAM47A	158724	hgsc.bcm.edu	hg19	X	34148936	34148936	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	FAM47A	NM_203408	exon1	c.G1460A	p.R487Q	GACCTCCGACGTG	.	70.0	4.0	91.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF233	353355	hgsc.bcm.edu	hg19	19	44778797	44778797	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.,8	ZNF233	NM_001207005	exon5	c.1983delG	p.S661fs	.	.	56.0	20.0	61.0	0.0	.	73	.	0.357143	0	none	.	.	PASS	Atlas-INDEL
HNF4A	3172	hgsc.bcm.edu	hg19	20	43052875	43052876	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	HNF4A	NM_178849	exon8	c.1110_1111insC	p.L370fs	.	.	148.0	50.0	185.0	0.0	.	150	.	0.337838	0	none	.	.	PASS	Atlas-Indel,Pindel
LAMA3	3909	hgsc.bcm.edu	hg19	18	21511118	21511118	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	LAMA3	NM_198129	exon65	c.8528delA	p.Y2843fs	.	.	57.0	13.0	54.0	0.0	.	397	.	0.22807	0	none	.	.	PASS	Atlas-INDEL
GBF1	8729	hgsc.bcm.edu	hg19	10	104123472	104123472	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	GBF1	NM_001199378	exon17	c.2022delC	p.D674fs	.	.	69.0	19.0	76.0	0.0	.	142	.	0.275362	0	none	.	.	PASS	Atlas-Indel,Pindel
LAMA3	3909	hgsc.bcm.edu	hg19	18	21511115	21511115	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	LAMA3	NM_198129	exon65	c.8525delC	p.T2842fs	.	.	49.0	13.0	52.0	0.0	.	397	.	0.265306	0	none	.	.	PASS	Atlas-INDEL
BAP1	8314	hgsc.bcm.edu	hg19	3	52439271	52439271	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	BAP1	NM_004656	exon11	c.972delA	p.P324fs	.	.	81.0	60.0	100.0	0.0	.	371	.	0.740741	0	none	.	.	PASS	Atlas-Indel,Pindel
LAMA3	3909	hgsc.bcm.edu	hg19	18	21511115	21511118	+	Frame_Shift_Del	DEL	GTAT	GTAT	-	novel		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	.	LAMA3	NM_198129	exon65	c.8525_8528del	p.2842_2843del	.	.	54.0	14.0	51.0	0.0	.	397	.	0.259	.	none	.	.	PASS	Pindel