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
AGTRAP	57085	hgsc.bcm.edu	hg19	1	11808542	11808542	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	AGTRAP	NM_001040194	exon4	c.G239A	p.S80N	GGGTCAGCCTCAC	.	50.0	21.0	60.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
ALPL	249	hgsc.bcm.edu	hg19	1	21890580	21890580	+	Silent	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ALPL	NM_000478	exon6	c.C519A	p.T173T	TGCCACCCCCAGC	.	28.0	12.0	22.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
SZT2	23334	hgsc.bcm.edu	hg19	1	43893320	43893320	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SZT2	NM_015284	exon25	c.T3547C	p.Y1183H	CCTGTCTACATCT	.	41.0	14.0	41.0	0.0	.	383	.	.	.	none	.	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	hg19	1	57409426	57409426	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	C8B	NM_000066	exon8	c.T1177A	p.Y393N	TGACGTAGACCTC	.	126.0	54.0	122.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
CCBL2	56267	hgsc.bcm.edu	hg19	1	89409053	89409053	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CCBL2	NM_001008661	exon12	c.A1195T	p.K399X	TCCATTTCACAAA	.	193.0	69.0	197.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF644	84146	hgsc.bcm.edu	hg19	1	91405923	91405923	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ZNF644	NM_201269	exon3	c.G988A	p.E330K	GCTCTTCATTTTG	.	87.0	26.0	84.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	hg19	1	111957099	111957099	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	OVGP1	NM_002557	exon11	c.A2024G	p.D675G	TCTTCATCCACAG	.	47.0	14.0	48.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	hg19	1	112299304	112299304	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	DDX20	NM_007204	exon2	c.C338G	p.T113S	GGAAAACCTGTGT	.	85.0	21.0	95.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
S100A16	140576	hgsc.bcm.edu	hg19	1	153580138	153580138	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	S100A16	NM_080388	exon3	c.C184G	p.L62V	GGATGAGCTTATC	.	60.0	22.0	63.0	0.0	.	7	.	.	.	none	.	.	PASS	Atlas-SNP
SLC19A2	10560	hgsc.bcm.edu	hg19	1	169454887	169454887	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SLC19A2	NM_006996	exon1	c.T118C	p.Y40H	AGCCGTAGGCGCA	.	58.0	29.0	51.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ETNK2	55224	hgsc.bcm.edu	hg19	1	204118891	204118891	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ETNK2	NM_018208	exon2	c.A458G	p.Y153C	TACTCATAGCACA	.	38.0	12.0	29.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
ETNK2	55224	hgsc.bcm.edu	hg19	1	204118892	204118892	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ETNK2	NM_018208	exon2	c.T457C	p.Y153H	ACTCATAGCACAG	.	37.0	12.0	29.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	215807830	215807830	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	USH2A	NM_206933	exon70	c.A15268C	p.N5090H	AAACATTCAATGG	.	118.0	46.0	110.0	0.0	.	1168	.	.	.	none	.	.	PASS	Atlas-SNP
PARP1	142	hgsc.bcm.edu	hg19	1	226570809	226570809	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PARP1	NM_001618	exon8	c.G1087A	p.A363T	CGGAGGCGCTGGT	.	68.0	30.0	72.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	hg19	1	228461691	228461691	+	Silent	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	OBSCN	NM_001271223	exon22	c.C6483T	p.S2161S	GGACAGCGCCATC	.	56.0	20.0	76.0	0.0	.	2142	.	.	.	none	.	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	hg19	2	11751041	11751041	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	GREB1	NM_014668	exon18	c.A2894G	p.E965G	CCTATGAGCGGCT	.	72.0	19.0	87.0	0.0	.	308	.	.	.	none	.	.	PASS	Atlas-SNP
GKN1	56287	hgsc.bcm.edu	hg19	2	69207188	69207188	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	GKN1	NM_019617	exon5	c.G501A	p.M167I	GGAGATGCAAGGT	.	43.0	24.0	58.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	hg19	2	86709089	86709089	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KDM3A	NM_001146688	exon17	c.T2549G	p.I850S	ATGAAATCAAATG	.	108.0	44.0	126.0	0.0	.	179	.	.	.	none	.	.	PASS	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	hg19	2	170936421	170936421	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	UBR3	NM_172070	exon37	c.G5297A	p.C1766Y	AAACCTGTAGTGT	.	207.0	78.0	227.0	0.0	.	182	.	.	.	none	.	.	PASS	Atlas-SNP
ALS2	57679	hgsc.bcm.edu	hg19	2	202625787	202625787	+	Silent	SNP	A	A	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ALS2	NM_001135745	exon4	c.T930A	p.A310A	GATCTGAGCACTT	.	239.0	106.0	233.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	hg19	3	39226976	39226976	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	XIRP1	NM_194293	exon2	c.A3961C	p.K1321Q	TCTTCTTTGGGGG	.	36.0	16.0	62.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
CXCR6	10663	hgsc.bcm.edu	hg19	3	45988859	45988859	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CXCR6	NM_006564	exon2	c.C886G	p.R296G	AAGTTTCGAAAGA	.	74.0	38.0	81.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
SLC38A3	10991	hgsc.bcm.edu	hg19	3	50254733	50254733	+	Silent	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SLC38A3	NM_006841	exon8	c.G612C	p.L204L	GCCCCTGGCACTG	.	62.0	27.0	42.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA2D2	9254	hgsc.bcm.edu	hg19	3	50416403	50416403	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CACNA2D2	NM_001174051	exon13	c.G1282A	p.V428M	GCCCCACGGAGAA	.	32.0	12.0	37.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	hg19	3	52548199	52548199	+	Silent	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	STAB1	NM_015136	exon33	c.C3516T	p.S1172S	CCGCTCCCTGGAG	.	38.0	15.0	51.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
NIT2	56954	hgsc.bcm.edu	hg19	3	100074091	100074091	+	Silent	SNP	T	T	A	rs144496756	byfrequency;alternate_allele	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NIT2	NM_020202	exon10	c.T810A	p.A270A	CTATGCTGTGGAG	.	82.0	24.0	62.0	0.0	.	35	.	.	.	alt	T|0.999;C|0.001	.	PASS	Atlas-SNP
ADCY5	111	hgsc.bcm.edu	hg19	3	123038548	123038548	+	Silent	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ADCY5	NM_183357	exon10	c.C2229T	p.T743T	CCTGAAGGTCAGG	.	28.0	10.0	27.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF639	51193	hgsc.bcm.edu	hg19	3	179050906	179050906	+	Missense_Mutation	SNP	C	C	G	rs75079502	alternate_allele	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ZNF639	NM_016331	exon6	c.C299G	p.S100C	CCTTTTCTACAGG	.	56.0	13.0	75.0	0.0	.	45	.	.	.	alt	C|0.750;T|0.250	.	PASS	Atlas-SNP
PPP1R2	5504	hgsc.bcm.edu	hg19	3	195251642	195251642	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PPP1R2	NM_006241	exon3	c.A283G	p.M95V	GCGCCATGGCTTC	.	152.0	50.0	161.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	hg19	4	2910285	2910285	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ADD1	NM_176801	exon12	c.A1652T	p.Q551L	GCCCTCAGTCCCA	.	81.0	33.0	73.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
TRMT44	152992	hgsc.bcm.edu	hg19	4	8456486	8456486	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	TRMT44	NM_152544	exon6	c.T1149G	p.I383M	AGGGATTGATGTC	.	68.0	29.0	96.0	0.0	.	7	.	.	.	none	.	.	PASS	Atlas-SNP
NIPAL1	152519	hgsc.bcm.edu	hg19	4	48037631	48037631	+	Silent	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NIPAL1	NM_207330	exon6	c.G675A	p.L225L	GATTTTGATTGTG	.	139.0	45.0	148.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	hg19	4	66201790	66201790	+	Silent	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	EPHA5	NM_004439	exon16	c.T2712C	p.P904P	AGCAGCAGGACAA	.	70.0	31.0	84.0	0.0	.	315	.	.	.	none	.	.	PASS	Atlas-SNP
SH3TC2	79628	hgsc.bcm.edu	hg19	5	148407090	148407090	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SH3TC2	NM_024577	exon11	c.G2205T	p.L735F	GCAGGCCAAGGCA	.	50.0	22.0	51.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
MGAT4B	11282	hgsc.bcm.edu	hg19	5	179225417	179225417	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	MGAT4B	NM_054013	exon12	c.G1485T	p.K495N	GGCCTCCTTGTCT	.	32.0	14.0	45.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	hg19	6	30886640	30886640	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	VARS2	NM_001167734	exon11	c.C1112G	p.T371R	CAGAGACGCTGCC	.	40.0	19.0	31.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
BRPF3	27154	hgsc.bcm.edu	hg19	6	36181792	36181792	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	BRPF3	NM_015695	exon8	c.A2618G	p.K873R	TCCTAAAGCCCAG	.	41.0	18.0	44.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	hg19	6	36259229	36259229	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PNPLA1	NM_001145717	exon2	c.A338G	p.Y113C	ACTCCTACAAGGT	.	45.0	21.0	53.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC10	89845	hgsc.bcm.edu	hg19	6	43403598	43403598	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ABCC10	NM_001198934	exon5	c.T1718C	p.L573P	TCCAGCTTTTCCT	.	77.0	37.0	94.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	hg19	6	111680124	111680124	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	REV3L	NM_002912	exon17	c.T6973C	p.F2325L	AGTAGAACAGAGC	.	121.0	48.0	125.0	0.0	.	386	.	.	.	none	.	.	PASS	Atlas-SNP
KPNA5	3841	hgsc.bcm.edu	hg19	6	117023282	117023282	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KPNA5	NM_002269	exon6	c.T536C	p.L179P	AACTTCTTAATTC	.	100.0	39.0	113.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	hg19	6	117246661	117246661	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	RFX6	NM_173560	exon16	c.T1724C	p.L575P	GCTTTCTGGCCAA	.	73.0	21.0	71.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
EPB41L2	2037	hgsc.bcm.edu	hg19	6	131216219	131216219	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	EPB41L2	NM_001135554	exon9	c.A1277G	p.N426S	AGTCCATTAGCAC	.	57.0	27.0	69.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
EYA4	2070	hgsc.bcm.edu	hg19	6	133849906	133849906	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	EYA4	NM_172105	exon20	c.T1883C	p.L628P	ACCTCCTGGCTCT	.	137.0	47.0	164.0	0.0	.	196	.	.	.	none	.	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	hg19	7	11581118	11581118	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	THSD7A	NM_015204	exon6	c.T1750C	p.C584R	GCTCGCAGTTTCC	.	129.0	57.0	123.0	0.0	.	219	.	.	.	none	.	.	PASS	Atlas-SNP
LSM5	23658	hgsc.bcm.edu	hg19	7	32527353	32527353	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	LSM5	NM_012322	exon4	c.G187A	p.G63R	TTCTTCCTTCTGG	.	56.0	24.0	77.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	hg19	7	82784425	82784425	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PCLO	NM_014510	exon2	c.C1532T	p.P511L	TGTTGAGGTGGGG	.	61.0	20.0	66.0	0.0	.	1506	.	.	.	none	.	.	PASS	Atlas-SNP
DMTF1	9988	hgsc.bcm.edu	hg19	7	86808921	86808921	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	DMTF1	NM_001142327	exon8	c.G580C	p.D194H	AGAAAAGATTTCT	.	49.0	18.0	45.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
STEAP4	79689	hgsc.bcm.edu	hg19	7	87910335	87910335	+	Nonsense_Mutation	SNP	A	A	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	STEAP4	NM_001205315	exon5	c.T1044G	p.Y348X	AGCCACATATGAA	.	76.0	34.0	78.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
SLC12A9	56996	hgsc.bcm.edu	hg19	7	100463464	100463464	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SLC12A9	NM_020246	exon14	c.C1982T	p.A661V	CCCCAGCTCTGAG	.	58.0	18.0	77.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
PSMC2	5701	hgsc.bcm.edu	hg19	7	103008247	103008247	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PSMC2	NM_002803	exon11	c.A1135T	p.N379Y	TGTCCAAATAGCA	.	92.0	41.0	94.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
DNAJB6	10049	hgsc.bcm.edu	hg19	7	157178258	157178258	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	DNAJB6	NM_058246	exon8	c.G644T	p.R215I	AAGAAAGAGTAGA	.	96.0	40.0	99.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB10	65986	hgsc.bcm.edu	hg19	8	81399773	81399773	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ZBTB10	NM_023929	exon1	c.T728C	p.M243T	CTCTAATGCAGAA	.	60.0	24.0	33.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
SLC25A32	81034	hgsc.bcm.edu	hg19	8	104419932	104419932	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SLC25A32	NM_030780	exon2	c.C235T	p.R79W	GTCCCCGTAGTCC	.	75.0	24.0	62.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	hg19	9	6012658	6012658	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	RANBP6,bladder,carcinoma,0,7	RANBP6	NM_012416	exon1	c.A2950C	p.I984L	TCCCTATTGCTGA	.	133.0	6.0	130.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
AQP3	360	hgsc.bcm.edu	hg19	9	33447468	33447468	+	Silent	SNP	G	G	A	rs56131976		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	AQP3	NM_004925	exon1	c.C61T	p.L21L	GGAGCAGCCGGTA	.	91.0	37.0	84.0	0.0	.	18	.	.	.	weak	.	.	PASS	Atlas-SNP
SPTLC1	10558	hgsc.bcm.edu	hg19	9	94809499	94809499	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SPTLC1	NM_006415	exon11	c.G1036A	p.A346T	CAGCAGCTAACAG	.	43.0	10.0	43.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
KLF4	9314	hgsc.bcm.edu	hg19	9	110249965	110249965	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KLF4	NM_004235	exon3	c.C710T	p.A237V	CCAGGGGCGCTCA	.	27.0	11.0	27.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
RPL7A	6130	hgsc.bcm.edu	hg19	9	136216882	136216882	+	Silent	SNP	G	G	T	rs7700	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	RPL7A	NM_000972	exon4	c.G390T	p.T130T	CCCAACGAAGAGA	.	27.0	11.0	32.0	0.0	.	9	.	.	.	alt	G|0.942;A|0.058	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	hg19	9	137710604	137710604	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	COL5A1	NM_000093	exon55	c.C4333T	p.P1445S	CCTGGCCCTGTGG	.	28.0	10.0	41.0	0.0	.	323	.	.	.	none	.	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	hg19	10	61842390	61842390	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ANK3	NM_001204404	exon35	c.C4309G	p.L1437V	CTGGCAGAGTGAT	.	76.0	32.0	72.0	0.0	.	703	.	.	.	none	.	.	PASS	Atlas-SNP
GBF1	8729	hgsc.bcm.edu	hg19	10	104126202	104126202	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	GBF1	NM_001199378	exon19	c.G2372A	p.R791H	CCTTCCGTTTGCC	.	95.0	18.0	131.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
C10orf118	55088	hgsc.bcm.edu	hg19	10	115922488	115922488	+	Silent	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	C10orf118	NM_018017	exon2	c.A540C	p.V180V	ATTTGGTACTCGA	.	176.0	66.0	255.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
PSMC3	5702	hgsc.bcm.edu	hg19	11	47446781	47446781	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PSMC3	NM_002804	exon3	c.T176C	p.V59A	CTCAACACTTCAC	.	84.0	37.0	100.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
B3GAT3	26229	hgsc.bcm.edu	hg19	11	62388048	62388048	+	Missense_Mutation	SNP	G	G	A	rs374687580	alternate_allele	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	B3GAT3	NM_012200	exon2	c.C178T	p.R60W	GTGGCCGTCGGAG	.	49.0	18.0	39.0	0.0	.	24	.	.	.	alt	.	.	PASS	Atlas-SNP
LRRC32	2615	hgsc.bcm.edu	hg19	11	76371152	76371152	+	Silent	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	LRRC32	NM_005512	exon3	c.C1485T	p.V495V	TGCCAGGACCTCC	.	23.0	14.0	34.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	hg19	12	1993454	1993454	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CACNA2D4	NM_172364	exon12	c.G1306A	p.V436M	AAGACACTTCTCT	.	57.0	33.0	29.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	hg19	12	6639960	6639960	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NCAPD2	NM_014865	exon30	c.C3941A	p.P1314Q	GAGCGCCATCAGC	.	47.0	16.0	38.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	hg19	12	6933104	6933104	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	GPR162	NM_019858	exon2	c.C40T	p.R14C	TCCCTGCGCTCCA	.	24.0	17.0	19.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
KRAS	3845	hgsc.bcm.edu	hg19	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529	bycluster	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	NM_004985	exon2	c.G35T	p.G12V	ACGCCACCAGCTC	.	201.0	132.0	155.0	0.0	.	30930	.	.	.	weak	.	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	hg19	12	52710705	52710705	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KRT83	NM_002282	exon5	c.G853T	p.A285S	ACTGTGCCTTGAT	.	93.0	50.0	68.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	hg19	12	121881963	121881963	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KDM2B	NM_032590	exon16	c.G2303A	p.S768N	CACTCACTCCTCC	.	29.0	15.0	29.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
HCAR2	338442	hgsc.bcm.edu	hg19	12	123187139	123187139	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	HCAR2	NM_177551	exon1	c.C692A	p.T231N	ATGAAGGTGATGG	.	174.0	37.0	146.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
XPO4	64328	hgsc.bcm.edu	hg19	13	21370348	21370348	+	Silent	SNP	C	C	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	XPO4	NM_022459	exon18	c.G2664C	p.V888V	AGAATACACTTGC	.	62.0	29.0	46.0	0.0	.	153	.	.	.	none	.	.	PASS	Atlas-SNP
SMAD9	4093	hgsc.bcm.edu	hg19	13	37427774	37427774	+	Missense_Mutation	SNP	C	C	T	rs375386551		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SMAD9	NM_001127217	exon6	c.G1042A	p.E348K	CGCACTCGGCATA	.	54.0	23.0	52.0	0.0	.	91	.	.	.	weak	.	.	PASS	Atlas-SNP
FAM124A	220108	hgsc.bcm.edu	hg19	13	51825756	51825756	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	FAM124A	NM_145019	exon4	c.C361T	p.R121W	GAGAGGCGGGCGT	.	53.0	16.0	35.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
CARKD	55739	hgsc.bcm.edu	hg19	13	111279816	111279816	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CARKD	NM_018210	exon5	c.G417T	p.E139D	GGTGGAGAAGTGG	.	90.0	36.0	89.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
CHAMP1	283489	hgsc.bcm.edu	hg19	13	115089604	115089604	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	.	NM_001164144	exon3	c.A287G	p.K96R	AACCAAAAAATCA	.	72.0	28.0	97.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SPTLC2	9517	hgsc.bcm.edu	hg19	14	78021667	78021667	+	Silent	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SPTLC2	NM_004863	exon8	c.T1152C	p.S384S	TCCTCCAGAAGCA	.	23.0	17.0	52.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
TCF12	6938	hgsc.bcm.edu	hg19	15	57484401	57484401	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	TCF12	NM_207036	exon7	c.C436A	p.L146I	GCACAGCTATCTT	.	35.0	13.0	47.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	hg19	16	1507707	1507707	+	Silent	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CLCN7	NM_001287	exon8	c.G726A	p.L242L	CACGGCCAGGCCC	.	26.0	19.0	21.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	hg19	16	2098730	2098730	+	Silent	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	TSC2	NM_001114382	exon2	c.T114C	p.F38F	GGAGTTTATCATC	.	77.0	18.0	76.0	0.0	.	364	.	.	.	none	.	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	hg19	16	2814755	2814755	+	Missense_Mutation	SNP	C	C	T	rs141353583	alternate_allele	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SRRM2	NM_016333	exon11	c.C4226T	p.A1409V	TTGATGCTGTACC	.	42.0	10.0	30.0	0.0	.	263	.	.	.	alt	C|1.000;A|0.000	.	PASS	Atlas-SNP
GTF3C1	2975	hgsc.bcm.edu	hg19	16	27480845	27480845	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	GTF3C1	NM_001520	exon32	c.A4841G	p.D1614G	TCGTCATCCTCCA	.	111.0	33.0	92.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
NLGN2	57555	hgsc.bcm.edu	hg19	17	7317791	7317791	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NLGN2	NM_020795	exon3	c.A637C	p.N213H	ACGCTCAACTACC	.	39.0	17.0	44.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
NEUROD2	4761	hgsc.bcm.edu	hg19	17	37762540	37762540	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NEUROD2	NM_006160	exon2	c.G313T	p.G105W	TGGGCCCGCGCTT	.	43.0	17.0	38.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
UBTF	7343	hgsc.bcm.edu	hg19	17	42288679	42288679	+	Silent	SNP	C	C	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	UBTF	NM_014233	exon11	c.G1068T	p.V356V	CAGCTCCACCTCG	.	32.0	12.0	40.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
C17orf104	284071	hgsc.bcm.edu	hg19	17	42750780	42750780	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	C17orf104	NM_001145080	exon7	c.T2504G	p.L835R	CTCTTCTTCATGC	.	93.0	37.0	109.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9074934	9074934	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	MUC16	NM_024690	exon3	c.C12512G	p.P4171R	TTGGAAGGCGAGG	.	96.0	35.0	97.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
ANO8	57719	hgsc.bcm.edu	hg19	19	17438617	17438617	+	Silent	SNP	G	G	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ANO8	NM_020959	exon14	c.C2299T	p.L767L	CCGCCAGGGGGAA	.	86.0	34.0	98.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
HNRNPUL1	11100	hgsc.bcm.edu	hg19	19	41774184	41774184	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	HNRNPUL1	NM_007040	exon2	c.C352T	p.Q118X	ATCAAACAAGAAA	.	52.0	24.0	64.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	hg19	19	44117767	44117767	+	Silent	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SRRM5	NM_001145641	exon1	c.A1494G	p.R498R	TCACAGACGATCT	.	17.0	7.0	19.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
FKRP	79147	hgsc.bcm.edu	hg19	19	47260096	47260096	+	Silent	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	FKRP	NM_024301	exon4	c.C1389T	p.N463N	GCCTAACAACTAC	.	26.0	15.0	33.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
DBP	1628	hgsc.bcm.edu	hg19	19	49136867	49136867	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	DBP	NM_001352	exon3	c.T596C	p.V199A	ACCTCCACGGTGT	.	51.0	19.0	73.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
FITM2	128486	hgsc.bcm.edu	hg19	20	42935653	42935653	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	FITM2	NM_001080472	exon2	c.A401T	p.H134L	CTCTGGTGTTCCT	.	44.0	13.0	46.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	hg19	20	47568002	47568002	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ARFGEF2	NM_006420	exon4	c.T419G	p.I140S	AAATAATTAAGGT	.	86.0	22.0	58.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
HSPA13	6782	hgsc.bcm.edu	hg19	21	15746414	15746414	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	HSPA13	NM_006948	exon5	c.G940A	p.E314K	GCTCCTCCACCGT	.	71.0	27.0	88.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
CABIN1	23523	hgsc.bcm.edu	hg19	22	24480737	24480737	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CABIN1	NM_001199281	exon21	c.A3116T	p.E1039V	CAACTGAGGTGGG	.	64.0	29.0	72.0	0.0	.	153	.	.	.	none	.	.	PASS	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	hg19	22	31487406	31487406	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	SMTN	NM_001207018	exon9	c.A1565C	p.K522T	AGATCAAGGACGG	.	21.0	9.0	20.0	0.0	.	219	.	.	.	none	.	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	hg19	X	70355044	70355044	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	MED12	NM_005120	exon36	c.T4966G	p.S1656A	CAGGGCTCCCTTA	.	119.0	47.0	143.0	0.0	.	984	.	.	.	none	.	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	hg19	X	117526785	117526785	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	WDR44	NM_001184965	exon4	c.G377C	p.S126T	CAGAGAGTCAGAA	.	154.0	73.0	124.0	0.0	.	188	.	.	.	none	.	.	PASS	Atlas-SNP
IKBKG	8517	hgsc.bcm.edu	hg19	X	153770658	153770658	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	IKBKG	NM_001099856	exon1	c.G180T	p.W60C	TTTCTGGAAGGGG	.	44.0	21.0	53.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6685	6685	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	.	ENST00000361624	exon1	c.A782G	p.Y261C	CTTACTACTCCGG	.	188.0	12.0	4.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	11869	11869	+	Silent	SNP	C	C	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	.	ENST00000361381	exon1	c.C1110T	p.P370P	CTTACCCCCCACT	.	204.0	138.0	3.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CLIC6	54102	hgsc.bcm.edu	hg19	21	36080328	36080329	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CLIC6	NM_053277	exon3	c.1570_1571del	p.524_524del	.	.	61.0	23.0	52.0	0.0	.	49	.	0.377049	0	none	.	.	PASS	Atlas-Indel,Pindel
TFR2	7036	hgsc.bcm.edu	hg19	7	100238810	100238819	+	Frame_Shift_Del	DEL	ACGCTGGTAG	ACGCTGGTAG	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	ACGCTGGTAG	ACGCTGGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	TFR2	NM_003227	exon2	c.67_76del	p.23_26del	.	.	28.0	10.0	28.0	0.0	.	53	.	0.357143	0	none	.	.	PASS	Atlas-Indel,Pindel
CCBL2	56267	hgsc.bcm.edu	hg19	1	89409051	89409051	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CCBL2	NM_001008661	exon12	c.1198delT	p.W400fs	.	.	196.0	69.0	195.0	0.0	.	138	.	0.352041	0	none	.	.	PASS	Atlas-INDEL
MT1H	4496	hgsc.bcm.edu	hg19	16	56704825	56704826	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	MT1H	NM_005951	exon3	c.110_111insC	p.C37fs	.	.	119.0	53.0	101.0	0.0	.	19	.	0.445378	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF749	388567	hgsc.bcm.edu	hg19	19	57956719	57956719	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	ZNF749	NM_001023561	exon3	c.2202delC	p.N734fs	.	.	59.0	27.0	67.0	0.0	.	75	.	0.457627	0	none	.	.	PASS	Atlas-Indel,Pindel
TAF3	83860	hgsc.bcm.edu	hg19	10	8006138	8006138	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	TAF3	NM_031923	exon3	c.664delC	p.Q222fs	.	.	95.0	43.0	74.0	0.0	.	93	.	0.452632	0	none	.	.	PASS	Atlas-Indel,Pindel
MYF6	4618	hgsc.bcm.edu	hg19	12	81102003	81102003	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	MYF6	NM_002469	exon1	c.504delA	p.R168fs	.	.	19.0	12.0	19.0	0.0	.	74	.	0.631579	0	none	.	.	PASS	Atlas-Indel,Pindel
WDR44	54521	hgsc.bcm.edu	hg19	X	117526809	117526809	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	WDR44	NM_001184965	exon4	c.400delG	p.E134fs	.	.	131.0	64.0	118.0	0.0	.	188	.	0.48855	0	none	.	.	PASS	Atlas-Indel,Pindel
NOX3	50508	hgsc.bcm.edu	hg19	6	155776915	155776915	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	NOX3	NM_015718	exon1	c.21delG	p.L7fs	.	.	134.0	74.0	175.0	0.0	.	93	.	0.552239	0	none	.	.	PASS	Atlas-Indel,Pindel
PAPSS2	9060	hgsc.bcm.edu	hg19	10	89474565	89474566	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	PAPSS2	NM_001015880	exon5	c.584_585insT	p.N195fs	.	.	96.0	31.0	100.0	0.0	.	46	.	0.322917	0	none	.	.	PASS	Atlas-Indel,Pindel
AGPAT5	55326	hgsc.bcm.edu	hg19	8	6590118	6590118	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	AGPAT5	NM_018361	exon4	c.441delT	p.F147fs	.	.	280.0	128.0	271.0	0.0	.	31	.	0.457143	0	none	.	.	PASS	Atlas-Indel,Pindel
KIAA1009	22832	hgsc.bcm.edu	hg19	6	84936099	84936099	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	KIAA1009	NM_014895	exon2	c.14delC	p.S5fs	.	.	71.0	34.0	71.0	0.0	.	119	.	0.478873	0	none	.	.	PASS	Atlas-Indel,Pindel
CCBL2	56267	hgsc.bcm.edu	hg19	1	89409052	89409053	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	.	CCBL2	NM_001008661	exon12	c.1196_1197del	p.399_399del	.	.	196.0	51.0	200.0	0.0	.	138	.	0.260	.	none	.	.	PASS	Pindel