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
MEGF6	1953	hgsc.bcm.edu	hg19	1	3511980	3511980	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MEGF6	NM_001409	exon3	c.T298C	p.Y100H	TGGTATACACCTG	.	117.0	41.0	105.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
TCEB3	6924	hgsc.bcm.edu	hg19	1	24080614	24080614	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	TCEB3	NM_003198	exon6	c.A1640C	p.E547A	AAGAAGAAGAAGC	.	120.0	42.0	124.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
PUM1	9698	hgsc.bcm.edu	hg19	1	31479871	31479871	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PUM1	NM_014676	exon4	c.C511G	p.Q171E	GCCATTGATCACC	.	363.0	122.0	340.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
CDC20	991	hgsc.bcm.edu	hg19	1	43828621	43828621	+	Splice_Site	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CDC20	NM_001255	exon11	c.1322-1G>A	.	GCTCCAGGTCACA	.	146.0	61.0	112.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
DBT	1629	hgsc.bcm.edu	hg19	1	100680458	100680458	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	DBT	NM_001918	exon7	c.C854A	p.T285N	AGTTCAGTAAGGT	.	80.0	29.0	59.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	hg19	1	109807126	109807126	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CELSR2	NM_001408	exon11	c.C5340A	p.S1780R	TCCCAGCCATGGG	.	184.0	71.0	148.0	0.0	.	228	.	.	.	none	.	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	hg19	1	111862962	111862962	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CHIA	NM_201653	exon12	c.C1305T	p.N435N	AGCCAACGGCCTC	.	77.0	31.0	68.0	0.0	.	115	.	.	.	none	.	.	PASS	Atlas-SNP
RSBN1	54665	hgsc.bcm.edu	hg19	1	114308975	114308975	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RSBN1	NM_018364	exon7	c.C2036G	p.P679R	TTTCTAGGGATGA	.	177.0	70.0	114.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	hg19	1	152276023	152276023	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	FLG	NM_002016	exon3	c.G11339C	p.R3780T	CCAGACCTATCTA	.	744.0	264.0	567.0	0.0	.	900	.	.	.	none	.	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	hg19	1	171527271	171527271	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	.	NM_015172	exon19	c.T6014C	p.I2005T	ATGATATCTCTAA	.	85.0	34.0	77.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MRPS14	63931	hgsc.bcm.edu	hg19	1	174987712	174987712	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MRPS14	NM_022100	exon2	c.A46G	p.M16V	GAACCATCTGAAA	.	88.0	35.0	72.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	hg19	1	175355248	175355248	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	TNR	NM_003285	exon8	c.C1697G	p.P566R	GAGCCAGGCCGCA	.	105.0	31.0	91.0	0.0	.	399	.	.	.	none	.	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	hg19	1	182856426	182856426	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	DHX9	NM_001357	exon28	c.G3670C	p.G1224R	TCCCGAGGTGGCT	.	136.0	58.0	103.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
RGS18	64407	hgsc.bcm.edu	hg19	1	192128419	192128419	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RGS18	NM_130782	exon2	c.C189T	p.S63S	CCGCTCCAGTAGA	.	83.0	21.0	64.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	hg19	1	232649814	232649814	+	Silent	SNP	A	A	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SIPA1L2	NM_020808	exon1	c.T1272A	p.I424I	GAGCGCAATCCGC	.	251.0	101.0	170.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
RASGRP3	25780	hgsc.bcm.edu	hg19	2	33768640	33768640	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RASGRP3	NM_170672	exon14	c.G1340C	p.S447T	TTGAAAGTATAGC	.	39.0	18.0	39.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
STRN	6801	hgsc.bcm.edu	hg19	2	37129786	37129786	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	STRN	NM_003162	exon5	c.A600C	p.K200N	CTGATTTTTGTCA	.	224.0	92.0	224.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
CNNM4	26504	hgsc.bcm.edu	hg19	2	97428005	97428005	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CNNM4	NM_020184	exon1	c.C1269A	p.Y423X	TCTCTACGTCAAA	.	209.0	74.0	217.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179599140	179599140	+	Silent	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	TTN	NM_001267550	exon52	c.T15411C	p.F5137F	ACTATTAAACGAA	.	232.0	81.0	185.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD44	91526	hgsc.bcm.edu	hg19	2	197889959	197889959	+	Silent	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ANKRD44	NM_001195144	exon17	c.A1683G	p.E561E	ATCTGATTCTTCA	.	107.0	39.0	118.0	0.0	.	281	.	.	.	none	.	.	PASS	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	hg19	2	203848266	203848266	+	Silent	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ALS2CR8	NM_024744	exon17	c.A2097G	p.Q699Q	GAGCCAAGTTAAA	.	93.0	33.0	111.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
CAMP	820	hgsc.bcm.edu	hg19	3	48266893	48266893	+	Silent	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CAMP	NM_004345	exon4	c.T501C	p.L167L	GAATCTTGTACCC	.	225.0	83.0	164.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
IQCF2	389123	hgsc.bcm.edu	hg19	3	51897303	51897303	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	IQCF2	NM_203424	exon3	c.T412C	p.C138R	CACAACTGCCAGA	.	180.0	12.0	204.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGEF3	50650	hgsc.bcm.edu	hg19	3	56779418	56779418	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ARHGEF3	NM_001128615	exon10	c.A781C	p.K261Q	CTTGCTTTTTGTG	.	238.0	82.0	229.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
C3orf14	57415	hgsc.bcm.edu	hg19	3	62317065	62317065	+	Silent	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	C3orf14	NM_020685	exon4	c.T243A	p.V81V	GGTGGTTTCTCTT	.	147.0	57.0	112.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
CPOX	1371	hgsc.bcm.edu	hg19	3	98309567	98309567	+	Silent	SNP	A	A	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CPOX	NM_000097	exon3	c.T720A	p.A240A	GCCCATAGCACAA	.	88.0	22.0	99.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
MCM2	4171	hgsc.bcm.edu	hg19	3	127340566	127340566	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MCM2	NM_004526	exon16	c.A2665G	p.N889D	AGGATGAACAAGT	.	82.0	4.0	77.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
PLSCR2	57047	hgsc.bcm.edu	hg19	3	146167110	146167110	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PLSCR2	NM_001199978	exon8	c.G747A	p.K249K	CCAGTGCTTAGAA	.	228.0	90.0	164.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
MCCC1	56922	hgsc.bcm.edu	hg19	3	182789038	182789038	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MCCC1	NM_020166	exon6	c.A599G	p.Y200C	ACAGGATAGCCAA	.	129.0	30.0	103.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
CDKL2	8999	hgsc.bcm.edu	hg19	4	76529105	76529105	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CDKL2	NM_003948	exon6	c.A691T	p.K231X	GATTTTTATTAAA	.	113.0	46.0	127.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	hg19	4	123202841	123202841	+	Missense_Mutation	SNP	G	G	C	rs115036597	byfrequency;by1000genomes;alternate_allele	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	KIAA1109	NM_015312	exon50	c.G8949C	p.M2983I	TGCCATGTTAGAT	.	160.0	57.0	124.0	0.0	.	424	.	.	.	alt	G|0.999;T|0.001	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	hg19	5	7878202	7878202	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MTRR	NM_024010	exon5	c.G628T	p.E210X	AAGTCAGAGCTGC	.	57.0	19.0	64.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	hg19	5	31515239	31515239	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	DROSHA,colon,carcinoma,0,1	DROSHA	NM_013235	exon7	c.G1146C	p.K382N	ATAGTTCTTGTCT	.	178.0	63.0	148.0	0.0	.	130	.	.	.	none	.	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	hg19	5	98192299	98192299	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CHD1	NM_001270	exon35	c.C4918T	p.H1640Y	CTGAATGTAACCG	.	45.0	29.0	68.0	0.0	.	137	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHGB2	56103	hgsc.bcm.edu	hg19	5	140741729	140741729	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PCDHGB2	NM_018923	exon1	c.G2027A	p.S676N	ACCTCAGCGACCG	.	68.0	44.0	67.0	0.0	.	196	.	.	.	none	.	.	PASS	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	hg19	5	180030377	180030377	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	FLT4	NM_182925	exon30	c.G3907A	p.G1303S	TCTGGCCAGGTCC	.	47.0	17.0	27.0	0.0	.	356	.	.	.	none	.	.	PASS	Atlas-SNP
CDKAL1	54901	hgsc.bcm.edu	hg19	6	20548882	20548882	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CDKAL1	NM_017774	exon4	c.T232G	p.S78A	AATAATTCAGATG	.	171.0	68.0	127.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
COL9A1	1297	hgsc.bcm.edu	hg19	6	71003975	71003975	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	COL9A1	NM_001851	exon5	c.C591T	p.D197D	GTTGCAGTCAACA	.	215.0	73.0	135.0	0.0	.	228	.	.	.	none	.	.	PASS	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	hg19	6	90660214	90660214	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	BACH2	NM_021813	exon7	c.C1611T	p.P537P	GCTGCAGGGTGAG	.	102.0	40.0	68.0	0.0	.	224	.	.	.	none	.	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	hg19	6	105776878	105776878	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PREP	NM_002726	exon9	c.A1039T	p.N347Y	AGAAGTTGGACCT	.	91.0	35.0	67.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA3A	10371	hgsc.bcm.edu	hg19	7	83631283	83631283	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	SEMA3A,NS,carcinoma,0,1	SEMA3A	NM_006080	exon12	c.G1440T	p.M480I	AACTGTCATTTCT	.	79.0	22.0	73.0	0.0	.	121	.	.	.	none	.	.	PASS	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	hg19	7	95818645	95818645	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SLC25A13	NM_001160210	exon9	c.G894A	p.E298E	AGTTCCCTCTTCC	.	54.0	23.0	48.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	hg19	8	10466983	10466983	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RP1L1	NM_178857	exon4	c.G4625T	p.R1542L	CGTGCTCGGAGCT	.	62.0	19.0	47.0	0.0	.	453	.	.	.	none	.	.	PASS	Atlas-SNP
CA13	377677	hgsc.bcm.edu	hg19	8	86180770	86180770	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CA13	NM_198584	exon6	c.T583G	p.Y195D	TGGACATATCCTG	.	166.0	64.0	145.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
EFR3A	23167	hgsc.bcm.edu	hg19	8	132982859	132982859	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	EFR3A	NM_015137	exon10	c.G1128T	p.K376N	TGAGAAGATTGTG	.	182.0	56.0	141.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA0020	9933	hgsc.bcm.edu	hg19	9	2810352	2810352	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	KIAA0020	NM_014878	exon16	c.G1715C	p.G572A	TCTCTCCCATTTT	.	91.0	21.0	65.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	hg19	9	33798069	33798069	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PRSS3	NM_007343	exon3	c.T614C	p.L205P	ACACTCTGAGCTT	.	174.0	52.0	129.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	hg19	9	92007357	92007357	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SEMA4D	NM_006378	exon10	c.T603A	p.Y201X	GATTGCATATTCT	.	139.0	40.0	138.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
NUP214	8021	hgsc.bcm.edu	hg19	9	134019822	134019822	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	NUP214	NM_005085	exon12	c.T1450A	p.F484I	TTCTCCTTTGGTT	.	479.0	161.0	413.0	0.0	.	166	.	.	.	none	.	.	PASS	Atlas-SNP
PFKFB3	5209	hgsc.bcm.edu	hg19	10	6258717	6258717	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PFKFB3	NM_004566	exon5	c.C415A	p.H139N	ATCCTTCATTTTG	.	206.0	49.0	254.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
PFKFB3	5209	hgsc.bcm.edu	hg19	10	6258719	6258719	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PFKFB3	NM_004566	exon5	c.T417A	p.H139Q	CCTTCATTTTGCC	.	201.0	47.0	244.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
PRPF18	8559	hgsc.bcm.edu	hg19	10	13653627	13653627	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PRPF18	NM_003675	exon6	c.T523A	p.S175T	GGAGAGTCCTTAG	.	105.0	39.0	119.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	hg19	10	16941136	16941136	+	Silent	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CUBN	NM_001081	exon54	c.T8457C	p.P2819P	CCAGTGAGGGGAT	.	103.0	44.0	111.0	0.0	.	515	.	.	.	none	.	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	hg19	10	115365937	115365937	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	NRAP	NM_001261463	exon33	c.C3807A	p.D1269E	GCTTACGTCACTC	.	82.0	24.0	63.0	0.0	.	208	.	.	.	none	.	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	hg19	10	115365938	115365938	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	NRAP	NM_001261463	exon33	c.A3806T	p.D1269V	CTTACGTCACTCA	.	84.0	24.0	63.0	0.0	.	208	.	.	.	none	.	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	hg19	10	115365939	115365939	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	NRAP	NM_001261463	exon33	c.G3805T	p.D1269Y	TTACGTCACTCAG	.	84.0	25.0	63.0	0.0	.	208	.	.	.	none	.	.	PASS	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	hg19	11	58978386	58978386	+	Silent	SNP	A	A	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MPEG1	NM_001039396	exon1	c.T1953A	p.G651G	TGACAGACCACCA	.	180.0	58.0	174.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	hg19	11	63885635	63885635	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	FLRT1	NM_013280	exon2	c.G1896A	p.E632E	AGAAGAGTACGTG	.	139.0	58.0	126.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PC	5091	hgsc.bcm.edu	hg19	11	66617172	66617172	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PC	NM_000920	exon20	c.C3057G	p.H1019Q	CTTGAAGTGGGCA	.	97.0	26.0	81.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
DRD2	1813	hgsc.bcm.edu	hg19	11	113288847	113288847	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	DRD2	NM_016574	exon3	c.G297A	p.E99E	TTTCCACTCACCT	.	65.0	18.0	65.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	hg19	11	133816079	133816079	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	IGSF9B	NM_014987	exon2	c.G139A	p.V47M	GGATCACGTCGCA	.	46.0	12.0	38.0	0.0	.	290	.	.	.	none	.	.	PASS	Atlas-SNP
KLRC4-KLRK1	0	hgsc.bcm.edu	hg19	12	10541382	10541382	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	.	NM_001199805	exon7	c.C28T	p.R10X	TGTGTCGAGACCT	.	111.0	47.0	98.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
LRP6	4040	hgsc.bcm.edu	hg19	12	12318144	12318144	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	LRP6	NM_002336	exon8	c.A1631T	p.Y544F	TAAACATAGTCAC	.	215.0	83.0	195.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
FAR2	55711	hgsc.bcm.edu	hg19	12	29469910	29469910	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	FAR2	NM_018099	exon9	c.T1092A	p.Y364X	TATCTATGACTGC	.	358.0	142.0	325.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	hg19	12	40758851	40758851	+	Silent	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	LRRK2	NM_198578	exon49	c.A7389G	p.L2463L	ACAGCTAGGCAAG	.	96.0	34.0	73.0	0.0	.	763	.	.	.	none	.	.	PASS	Atlas-SNP
ANO6	196527	hgsc.bcm.edu	hg19	12	45803213	45803213	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ANO6	NM_001204803	exon17	c.G2017T	p.D673Y	GAACAGGACTACC	.	168.0	58.0	161.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN11	5781	hgsc.bcm.edu	hg19	12	112892458	112892458	+	Silent	SNP	T	T	C	rs78376169	bycluster	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	PTPN11,NS,carcinoma,0,2	PTPN11	NM_080601	exon5	c.T616C	p.L206L	GAAACATTGGGTA	.	70.0	4.0	67.0	1.0	.	623	.	.	.	weak	.	.	PASS	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	hg19	13	52548876	52548876	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ATP7B	NM_001243182	exon2	c.C480T	p.S160S	TTCAATGGAGCTG	.	72.0	23.0	71.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	hg19	13	115022697	115022697	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CDC16	NM_003903	exon13	c.G1242T	p.Q414H	ATTTCAGAATGGA	.	166.0	53.0	142.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
TINF2	26277	hgsc.bcm.edu	hg19	14	24709984	24709984	+	Silent	SNP	G	G	C	rs201135568	by1000genomes;alternate_allele	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	TINF2	NM_001099274	exon6	c.C702G	p.A234A	AGGCTTGGCTTTT	.	143.0	35.0	150.0	0.0	.	61	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	hg19	14	65008125	65008125	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	HSPA2	NM_021979	exon1	c.G558A	p.L186L	CGGCCTGGACAAG	.	154.0	45.0	160.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	hg19	14	65008173	65008173	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	HSPA2	NM_021979	exon1	c.C606A	p.D202E	CTTTGACCTGGGC	.	200.0	58.0	169.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ADAM20	8748	hgsc.bcm.edu	hg19	14	70991146	70991146	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ADAM20	NM_003814	exon2	c.A479G	p.Y160C	TGGTAGTAGCAGT	.	161.0	71.0	123.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
SAMD15	161394	hgsc.bcm.edu	hg19	14	77844646	77844646	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SAMD15	NM_001010860	exon1	c.G885A	p.K295K	AAGAAAGGCAACT	.	123.0	47.0	126.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
NRXN3	9369	hgsc.bcm.edu	hg19	14	79423648	79423648	+	Missense_Mutation	SNP	G	G	A	rs367857290		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	NRXN3,NS,carcinoma,0,1	NRXN3	NM_004796	exon8	c.G1220A	p.R407Q	CCGTTCGGGTGGT	.	172.0	65.0	150.0	0.0	.	342	.	.	.	weak	.	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	hg19	14	95903278	95903278	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SYNE3	NM_152592	exon14	c.T2417C	p.F806S	TGGGAGAAATCTT	.	145.0	68.0	135.0	0.0	.	130	.	.	.	none	.	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	hg19	14	101012903	101012903	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	BEGAIN	NM_020836	exon3	c.C111T	p.H37H	CAGGTAGTGGCGC	.	124.0	44.0	127.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	hg19	15	28431846	28431846	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	HERC2	NM_004667	exon56	c.A8702T	p.D2901V	TTACAATCGATTC	.	71.0	27.0	54.0	0.0	.	501	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF770	54989	hgsc.bcm.edu	hg19	15	35274327	35274327	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ZNF770	NM_014106	exon3	c.A1309G	p.K437E	CTTTCTTATTCAC	.	167.0	65.0	117.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
BAHD1	22893	hgsc.bcm.edu	hg19	15	40758294	40758294	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	BAHD1	NM_014952	exon7	c.T2308C	p.F770L	TATGACTTCCGCC	.	249.0	103.0	200.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	hg19	15	52498142	52498142	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MYO5C	NM_018728	exon37	c.C4408A	p.P1470T	GCTGTGGACTATT	.	47.0	19.0	47.0	0.0	.	162	.	.	.	none	.	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	hg19	15	74327953	74327953	+	Silent	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PML	NM_033239	exon8	c.G2151A	p.R717R	GCAAAGGGGCATC	.	128.0	39.0	119.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	hg19	16	338194	338194	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	AXIN1	NM_003502	exon11	c.G2517T	p.E839D	TCGAACCTCCTCA	.	170.0	47.0	166.0	0.0	.	290	.	.	.	none	.	.	PASS	Atlas-SNP
GLYR1	84656	hgsc.bcm.edu	hg19	16	4864623	4864623	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	GLYR1	NM_032569	exon11	c.C932G	p.A311G	AGACGGGCCCCCT	.	61.0	17.0	43.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	hg19	16	15133833	15133833	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	NTAN1	NM_173474	exon8	c.G632C	p.G211A	GGTCCTCCTGCTA	.	286.0	106.0	277.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
XPO6	23214	hgsc.bcm.edu	hg19	16	28181133	28181133	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	XPO6_ENST00000304658,NS,carcinoma,0,2	XPO6	NM_015171	exon5	c.G503T	p.R168L	TCCTTCCGAGCCA	.	149.0	8.0	95.0	1.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
SH2B1	25970	hgsc.bcm.edu	hg19	16	28880661	28880661	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SH2B1	NM_001145796	exon5	c.C1266A	p.D422E	CCAGGACCTGCTG	.	96.0	35.0	96.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
RABEP2	79874	hgsc.bcm.edu	hg19	16	28925762	28925762	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RABEP2	NM_024816	exon5	c.A689T	p.D230V	GCGCTGTCATCGC	.	48.0	11.0	46.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
RNF40	9810	hgsc.bcm.edu	hg19	16	30775599	30775599	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RNF40	NM_014771	exon5	c.T542C	p.L181P	TGGAGCTGCAAGG	.	36.0	11.0	20.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	hg19	16	31340556	31340556	+	Missense_Mutation	SNP	G	G	T	rs199790913	bycluster	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ITGAM	NM_001145808	exon24	c.G2803T	p.V935F	CATGGGGTCTCCA	.	28.0	10.0	31.0	0.0	.	137	.	.	.	weak	.	.	PASS	Atlas-SNP
PHKB	5257	hgsc.bcm.edu	hg19	16	47684490	47684490	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PHKB	NM_000293	exon19	c.G1833T	p.M611I	GAAAATGCATGGA	.	120.0	40.0	140.0	0.0	.	298	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	hg19	17	65134124	65134124	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	HELZ	NM_014877	exon22	c.A2876C	p.Q959P	AACACTTGATCAG	.	203.0	74.0	174.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	hg19	17	65134125	65134125	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	HELZ	NM_014877	exon22	c.C2875T	p.Q959X	ACACTTGATCAGC	.	197.0	74.0	173.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
COG1	9382	hgsc.bcm.edu	hg19	17	71197359	71197359	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	COG1	NM_018714	exon7	c.A1393G	p.I465V	AAGCACATCCACT	.	195.0	69.0	187.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	hg19	18	8813135	8813135	+	Silent	SNP	C	C	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	.	NM_015210	exon12	c.C2763T	p.N921N	GAAGAACTGGAAC	.	26.0	14.0	36.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF599	148103	hgsc.bcm.edu	hg19	19	35250173	35250173	+	Missense_Mutation	SNP	T	T	A	rs375598988	alternate_allele	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ZNF599	NM_001007248	exon4	c.A1533T	p.E511D	TCCACATTCTCTA	.	173.0	71.0	136.0	0.0	.	72	.	.	.	alt	.	.	PASS	Atlas-SNP
ZNF599	148103	hgsc.bcm.edu	hg19	19	35250175	35250175	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ZNF599	NM_001007248	exon4	c.G1531T	p.E511X	CACATTCTCTACA	.	176.0	71.0	142.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	hg19	20	50407897	50407897	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SALL4	NM_020436	exon2	c.C1125G	p.D375E	CGCCTCGTCTTTG	.	128.0	45.0	134.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
RGL4	266747	hgsc.bcm.edu	hg19	22	24034222	24034222	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	RGL4	NM_153615	exon1	c.G5A	p.R2K	TGATGAGGAAGCT	.	88.0	5.0	109.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
MICALL1	85377	hgsc.bcm.edu	hg19	22	38328888	38328888	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MICALL1	NM_033386	exon12	c.A2227G	p.I743V	GAGCTCATCTATG	.	77.0	31.0	67.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
MKL1	57591	hgsc.bcm.edu	hg19	22	40816901	40816901	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	MKL1	NM_020831	exon10	c.G831C	p.Q277H	CTGCTGCTGGTTG	.	72.0	4.0	59.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
PLS3	5358	hgsc.bcm.edu	hg19	X	114883786	114883786	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PLS3	NM_005032	exon16	c.G1798C	p.V600L	GCCAGAGTGTATG	.	183.0	72.0	156.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	hg19	X	117526750	117526750	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	WDR44	NM_001184965	exon4	c.T342G	p.D114E	CATAGATCAAGTA	.	190.0	78.0	159.0	0.0	.	188	.	.	.	none	.	.	PASS	Atlas-SNP
THOC2	57187	hgsc.bcm.edu	hg19	X	122801090	122801090	+	Silent	SNP	A	A	G	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	THOC2	NM_001081550	exon11	c.T1057C	p.L353L	TCTTTAATAAGGC	.	171.0	64.0	155.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
ATP2B3	492	hgsc.bcm.edu	hg19	X	152826336	152826336	+	Silent	SNP	C	C	T	rs181539158	by1000genomes;alternate_allele	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ATP2B3	NM_001001344	exon17	c.C3042T	p.F1014F	CACTTTCGGGATT	.	106.0	50.0	114.0	0.0	.	552	.	.	.	alt	C|1.000;A|0.000	.	PASS	Atlas-SNP
F12	2161	hgsc.bcm.edu	hg19	5	176829362	176829363	+	Frame_Shift_Del	DEL	GC	GC	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	F12	NM_000505	exon14	c.1779_1780del	p.593_594del	.	.	44.0	13.0	41.0	0.0	.	35	.	0.295455	0	none	.	.	PASS	Atlas-INDEL
CHL1	10752	hgsc.bcm.edu	hg19	3	407694	407695	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CHL1	NM_001253388	exon13	c.1647_1648insT	p.E549fs	.	.	87.0	36.0	71.0	0.0	.	242	.	0.413793	0	none	.	.	PASS	Atlas-INDEL
SOGA2	23255	hgsc.bcm.edu	hg19	18	8813134	8813135	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	.	NM_015210	exon12	c.2762_2763insT	p.N921fs	.	.	26.0	14.0	37.0	0.0	.	.	.	0.538462	0	none	.	.	PASS	Atlas-INDEL
SKAP1	8631	hgsc.bcm.edu	hg19	17	46423341	46423341	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	SKAP1	NM_001075099	exon4	c.207delT	p.D69fs	.	.	67.0	30.0	55.0	0.0	.	41	.	0.447761	0	none	.	.	PASS	Atlas-INDEL
ARMCX1	51309	hgsc.bcm.edu	hg19	X	100808732	100808733	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ARMCX1	NM_016608	exon4	c.819_820insT	p.N273fs	.	.	103.0	44.0	96.0	0.0	.	67	.	0.427184	0	none	.	.	PASS	Atlas-INDEL
AHNAK2	113146	hgsc.bcm.edu	hg19	14	105408067	105408067	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	AHNAK2	NM_138420	exon7	c.13722delC	p.D4574fs	.	.	302.0	94.0	307.0	0.0	.	719	.	0.311258	0	none	.	.	PASS	Atlas-INDEL
FUT4	2526	hgsc.bcm.edu	hg19	11	94278647	94278649	+	In_Frame_Del	DEL	TTT	TTT	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	FUT4	NM_002033	exon1	c.1347_1349del	p.449_450del	.	.	73.0	25.0	58.0	0.0	.	17	.	0.342466	0	none	.	.	PASS	Atlas-INDEL
ZBTB20	26137	hgsc.bcm.edu	hg19	3	114057877	114057878	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	ZBTB20	NM_001164342	exon5	c.2201_2202del	p.734_734del	.	.	141.0	56.0	124.0	0.0	.	157	.	0.397163	0	none	.	.	PASS	Atlas-INDEL
CLEC1B	51266	hgsc.bcm.edu	hg19	12	10145838	10145838	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	CLEC1B	NM_016509	exon6	c.595delC	p.H199fs	.	.	191.0	72.0	127.0	0.0	.	39	.	0.376963	0	none	.	.	PASS	Atlas-INDEL
PBX1	5087	hgsc.bcm.edu	hg19	1	164781319	164781320	+	Frame_Shift_Ins	INS	-	-	GTATA	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PBX1	NM_001204963	exon6	c.930_931insGTATA	p.A310fs	.	.	100.0	23.0	83.0	0.0	.	60	.	0.23	0	none	.	.	PASS	Atlas-INDEL
LRTM1	57408	hgsc.bcm.edu	hg19	3	54952818	54952823	+	In_Frame_Del	DEL	CAGGAA	CAGGAA	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	CAGGAA	CAGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	LRTM1	NM_020678	exon3	c.702_707del	p.234_236del	.	.	43.0	14.0	38.0	0.0	.	52	.	0.325581	0	none	.	.	PASS	Atlas-INDEL
STIL	6491	hgsc.bcm.edu	hg19	1	47717027	47717027	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	STIL	NM_001048166	exon17	c.3649delG	p.A1217fs	.	.	175.0	71.0	117.0	0.0	.	91	.	0.405714	0	none	.	.	PASS	Atlas-INDEL
PRPF38A	84950	hgsc.bcm.edu	hg19	1	52881045	52881046	+	In_Frame_Ins	INS	-	-	AGT	novel		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	.	PRPF38A	NM_032864	exon9	c.883_884insAGT	p.K295delinsKX	.	.	51.0	19.0	53.0	0.0	.	36	.	0.372549	0	none	.	.	PASS	Atlas-INDEL