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	TTotCov	TVarCov	NTotCov	NVarCov	TVarRat	NVarRat	dbSNP_AF	dbSNP_PopFreq	dbSNP_Strength	COSMIC_Codon	COSMIC_Gene	COSMIC_Gene_Freq	COSMIC_Site_Freq	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	Confidence	Algorithm
PPFIBP2	8495	hgsc.bcm.edu	37	11	7661048	7661050	+	In_Frame_Del	DEL	CTC	CTC	-	rs143023559	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	52	152	.	0.299	.	CTC|0.944;-|0.056	0.056	strong	.	PPFIBP2	87	.	NM_003621	exon15	c.1321_1323del	p.441_441del	.	.	PASS	Pindel,Atlas-Indel
OVGP1	5016	hgsc.bcm.edu	37	1	111957502	111957525	+	In_Frame_Del	DEL	TCACAGACTGATGACTCACAGGGG	TCACAGACTGATGACTCACAGGGG	-	rs201350653		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCACAGACTGATGACTCACAGGGG	TCACAGACTGATGACTCACAGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	35	155	.	0.224	.	.	.	weak	.	OVGP1	177	.	NM_002557	exon11	c.1599_1622del	p.533_541del	.	.	PASS	Pindel,Atlas-Indel
ORM1	5004	hgsc.bcm.edu	37	9	117088618	117088620	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	979	178	915	0	0.181818	0	.	.	none	.	ORM1	20	.	NM_000607	exon6	c.586_588del	p.196_196del	.	.	PASS	Atlas-Indel
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382374	24382385	+	In_Frame_Del	DEL	TGCTGCTGCTGC	TGCTGCTGCTGC	-	rs371342199	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGCTGCTGC	TGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	418	131	393	0	0.313397	0	.	.	alt	.	.	.	.	NM_001136234	exon1	c.1496_1507del	p.499_503del	.	.	PASS	Atlas-Indel
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31913982	31913982	+	Frame_Shift_Del	DEL	G	G	-	rs5843453	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	43	65	.	0.614	.	-|0.758;G|0.242	0.758	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.172delT	p.Y58fs	.	.	PASS	Pindel,Atlas-Indel
LRRC37A2	474170	hgsc.bcm.edu	37	17	44590963	44590965	+	In_Frame_Del	DEL	CAA	CAA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	20	238	0	0.0655738	0	.	.	none	.	LRRC37A2	37	.	NM_001006607	exon1	c.884_886del	p.295_296del	.	.	PASS	Atlas-Indel
AKD1	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	51	.	0.450	.	CTT|0.626;-|0.374	0.374	strong	.	AKD1	223	.	NM_001145128	exon19	c.2109_2111del	p.703_704del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L6	653404	hgsc.bcm.edu	37	9	69201361	69201362	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	547	86	354	0	0.157221	0	.	.	none	.	.	.	.	NM_001085476	exon1	c.252_253del	p.84_85del	.	.	PASS	Atlas-Indel
TTN	7273	hgsc.bcm.edu	37	2	179514942	179514959	+	In_Frame_Del	DEL	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	-	rs139512154	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	39	220	.	0.198	.	TTTCCTCTTCAGGAGCAA|0.972;-|0.028	0.028	strong	.	TTN	18412	.	NM_001267550	exon210	c.39750_39767del	p.13250_13256del	.	.	PASS	Pindel,Atlas-Indel
SPAG8	26206	hgsc.bcm.edu	37	9	35811486	35811497	+	In_Frame_Del	DEL	CCAGGACCAGAG	CCAGGACCAGAG	-	rs113712230		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCAGGACCAGAG	CCAGGACCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	29	53	.	0.630	.	CCAGGACCAGAG|0.500;-|0.500	0.500	weak	.	SPAG8	67	.	NM_172312	exon2	c.547_558del	p.183_186del	.	.	PASS	Pindel,Atlas-Indel
LCNL1	401562	hgsc.bcm.edu	37	9	139879429	139879429	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	15	315	0	0.0717703	0	.	.	none	.	LCNL1	4	.	NM_207510	exon3	c.460delC	p.L154fs	.	.	PASS	Atlas-Indel
MIR520H	574493	hgsc.bcm.edu	37	19	54245839	54245840	+	RNA	INS	-	-	GT	rs111745142	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	21	172	.	0.163	.	-|0.978;GT|0.022	0.022	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
C6orf48	50854	hgsc.bcm.edu	37	6	31807372	31807373	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	41	119	.	0.342	.	.	.	none	.	C6orf48	8	.	NM_001040437	exon5	c.160_161insA	p.Y54_N55delinsX	.	.	PASS	Pindel,Atlas-Indel
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	48	110	.	0.366	.	-|0.492;CTC|0.508	0.508	strong	.	PRDM2	147	.	NM_015866	exon8	c.2104_2105insCTC	p.T702delinsTP	.	.	PASS	Pindel,Atlas-Indel
ZNF717	100131827	hgsc.bcm.edu	37	3	75786761	75786761	+	Frame_Shift_Del	DEL	C	C	-	rs145576551	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	16	22	.	0.281	.	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.2014delA	p.K672fs	.	.	PASS	Pindel,Atlas-Indel
OR6C4	341418	hgsc.bcm.edu	37	12	55945585	55945588	+	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs59693527	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTT	TCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	72	249	.	0.306	.	TCTT|0.950;-|0.050	0.050	strong	.	OR6C4	34	.	NM_001005494	exon1	c.574_577del	p.192_193del	.	.	PASS	Pindel,Atlas-Indel
TIGD6	81789	hgsc.bcm.edu	37	5	149374880	149374880	+	Frame_Shift_Del	DEL	T	T	-	rs3832324	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	73	226	.	0.264	.	T|0.470;-|0.530	0.530	strong	.	TIGD6	29	.	NM_030953	exon2	c.1033delG	p.E345fs	.	.	PASS	Pindel,Atlas-Indel
NAP1L5	266812	hgsc.bcm.edu	37	4	89618415	89618426	+	In_Frame_Del	DEL	GCAGCCTCTGCC	GCAGCCTCTGCC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCCTCTGCC	GCAGCCTCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	66	279	.	0.232	.	.	.	none	.	NAP1L5	23	.	NM_153757	exon1	c.481_492del	p.161_164del	.	.	PASS	Pindel,Atlas-Indel
LRRC37A	9884	hgsc.bcm.edu	37	17	44373384	44373386	+	In_Frame_Del	DEL	CAA	CAA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	21	235	0	0.0688525	0	.	.	none	.	LRRC37A	19	.	NM_014834	exon1	c.884_886del	p.295_296del	.	.	PASS	Atlas-Indel
GIGYF2	26058	hgsc.bcm.edu	37	2	233712227	233712229	+	In_Frame_Del	DEL	ACA	ACA	-	rs10555297	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	28	50	0	0.474576	0	ACA|0.358;-|0.642	0.642	strong	.	GIGYF2	288	.	NM_001103147	exon29	c.3692_3694del	p.1231_1232del	.	.	PASS	Atlas-Indel
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643073	1643073	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	23	225	0	0.0809859	0	.	.	none	KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	NM_001012709	exon1	c.252delT	p.C84fs	.	.	PASS	Atlas-Indel
FANCE	2178	hgsc.bcm.edu	37	6	35424008	35424010	+	In_Frame_Del	DEL	GGA	GGA	-	rs45451605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	42	138	.	0.296	.	GGA|0.979;-|0.021	0.021	strong	.	FANCE	45	.	NM_021922	exon2	c.732_734del	p.244_245del	.	.	PASS	Pindel,Atlas-Indel
FERMT1	55612	hgsc.bcm.edu	37	20	6091083	6091085	+	In_Frame_Del	DEL	ATG	ATG	-	rs150175364	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	68	221	.	0.325	.	.	.	strong	.	FERMT1	106	.	NM_017671	exon5	c.607_609del	p.203_203del	.	.	PASS	Pindel,Atlas-Indel
HYDIN	54768	hgsc.bcm.edu	37	16	71007312	71007312	+	Frame_Shift_Del	DEL	G	G	-	rs373616607		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	25	101	.	0.179	.	.	.	weak	.	HYDIN	788	.	NM_001270974	exon35	c.5314delA	p.I1772fs	.	.	PASS	Pindel,Atlas-Indel
CTU2	348180	hgsc.bcm.edu	37	16	88780635	88780636	+	Frame_Shift_Ins	INS	-	-	GTGT	rs149847195		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	10	115	.	0.161	.	.	.	weak	.	CTU2	66	.	NM_001012759	exon10	c.1097_1098insGTGT	p.R366fs	.	.	PASS	Pindel,Atlas-Indel
SSPO	23145	hgsc.bcm.edu	37	7	149480091	149480092	+	Frame_Shift_Ins	INS	-	-	C	rs144883973	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	71	217	.	0.327	.	-|0.979;C|0.021	0.021	strong	.	.	.	.	NM_198455	exon15	c.2057_2058insC	p.D686fs	.	.	PASS	Pindel,Atlas-Indel
TIGD6	81789	hgsc.bcm.edu	37	5	149375721	149375721	+	Frame_Shift_Del	DEL	C	C	-	rs33910807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	32	66	.	0.390	.	C|0.913;-|0.087	0.087	strong	.	TIGD6	29	.	NM_030953	exon2	c.192delA	p.G64fs	.	.	PASS	Pindel,Atlas-Indel
SHROOM4	57477	hgsc.bcm.edu	37	X	50350728	50350729	+	In_Frame_Ins	INS	-	-	TCC	rs143151534	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	12	82	0	0.169014	0	-|0.700;TCC|0.300	0.300	strong	.	SHROOM4	171	.	NM_020717	exon6	c.3414_3415insGGA	p.E1138delinsEE	.	.	PASS	Atlas-Indel
SCARA5	286133	hgsc.bcm.edu	37	8	27779652	27779672	+	In_Frame_Del	DEL	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	97	.	0.491	.	.	.	none	.	SCARA5	53	.	NM_173833	exon4	c.333_353del	p.111_118del	.	.	PASS	Pindel,Atlas-Indel
DEFB126	81623	hgsc.bcm.edu	37	20	126156	126159	+	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs11467497	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAAA	CAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	44	152	.	0.400	.	CAAA|0.834;-|0.166	0.166	strong	.	DEFB126	52	.	NM_030931	exon2	c.158_161del	p.53_54del	.	.	PASS	Pindel,Atlas-Indel
SLC39A8	64116	hgsc.bcm.edu	37	4	103188834	103188836	+	Splice_Site	DEL	AGA	AGA	-	rs71813938	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	55	166	0	0.34375	0	AGA|0.950;-|0.050	0.050	strong	SLC39A8,NS,carcinoma,0,1	SLC39A8	24	1	.	.	.	.	.	.	PASS	Atlas-Indel
NBPF3	84224	hgsc.bcm.edu	37	1	21801436	21801444	+	In_Frame_Del	DEL	GTCTCCCAG	GTCTCCCAG	-	rs139002241	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTCTCCCAG	GTCTCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	17	85	.	0.193	.	GTCTCCCAG|0.948;-|0.052	0.052	strong	.	NBPF3	55	.	NM_032264	exon8	c.983_991del	p.328_331del	.	.	PASS	Pindel,Atlas-Indel
PHRF1	57661	hgsc.bcm.edu	37	11	608503	608514	+	In_Frame_Del	DEL	GGACGCGCTCTG	GGACGCGCTCTG	-	rs113708663		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGACGCGCTCTG	GGACGCGCTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	31	100	.	0.290	.	-|1.000;|0.000	1.000	weak	.	PHRF1	188	.	NM_020901	exon14	c.3043_3054del	p.1015_1018del	.	.	PASS	Pindel,Atlas-Indel
REXO1	57455	hgsc.bcm.edu	37	19	1825928	1825930	+	In_Frame_Del	DEL	CTC	CTC	-	rs149465929	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	56	162	.	0.301	.	CTC|0.704;-|0.296	0.296	strong	.	REXO1	55	.	NM_020695	exon3	c.1925_1927del	p.642_643del	.	.	PASS	Pindel,Atlas-Indel
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	46	95	.	0.390	.	GTT|0.969;-|0.031	0.031	strong	.	THAP2	29	.	NM_031435	exon3	c.304_306del	p.102_102del	.	.	PASS	Pindel,Atlas-Indel
ING3	54556	hgsc.bcm.edu	37	7	120610847	120610849	+	In_Frame_Del	DEL	AAC	AAC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	37	112	.	0.402	.	.	.	none	.	ING3	36	.	NM_019071	exon10	c.1013_1015del	p.338_339del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	56	322	0	0.162791	0	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1216delT	p.W406fs	.	.	PASS	Atlas-Indel
NAIP	4671	hgsc.bcm.edu	37	5	70281620	70281621	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	32	214	0	0.156098	0	.	.	none	.	NAIP	38	.	NM_004536	exon12	c.1256_1257del	p.419_419del	.	.	PASS	Atlas-Indel
PIEZO1	9780	hgsc.bcm.edu	37	16	88800373	88800375	+	In_Frame_Del	DEL	TCC	TCC	-	rs59446030		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	12	68	0	0.2	0	.	.	weak	.	PIEZO1	79	.	NM_001142864	exon17	c.2269_2271del	p.757_757del	.	.	PASS	Atlas-Indel
MYO5B	4645	hgsc.bcm.edu	37	18	47405425	47405426	+	In_Frame_Ins	INS	-	-	GAG	rs3841750	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	88	173	.	0.500	.	-|0.623;GAG|0.377	0.377	strong	MYO5B,NS,carcinoma,0,1	MYO5B	178	1	NM_001080467	exon24	c.3166_3167insCTC	p.M1056delinsLM	.	.	PASS	Pindel,Atlas-Indel
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	356	48	352	0	0.134831	0	.	.	weak	.	FOXD4L5	27	.	NM_001126334	exon1	c.1216delT	p.W406fs	.	.	PASS	Atlas-Indel
CHDC2	286464	hgsc.bcm.edu	37	X	36162684	36162685	+	Frame_Shift_Ins	INS	-	-	TG	rs112700338	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	54	106	.	0.621	.	TG|1.000;|0.000	1.000	weak	.	.	.	.	NM_173695	exon11	c.1267_1268insTG	p.L423fs	.	.	PASS	Pindel,Atlas-Indel
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778796	+	Frame_Shift_Del	DEL	G	G	-	rs59660444	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	51	56	0	0.894737	0	G|0.700;-|0.300	0.300	strong	.	ZNF233	73	.	NM_001207005	exon5	c.1982delC	p.S661fs	.	.	PASS	Atlas-Indel
ARID4B	51742	hgsc.bcm.edu	37	1	235377279	235377281	+	In_Frame_Del	DEL	TCC	TCC	-	rs113458177	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	28	137	.	0.159	.	TCC|0.967;-|0.033	0.033	strong	.	ARID4B	142	.	NM_016374	exon17	c.1645_1647del	p.549_549del	.	.	PASS	Pindel,Atlas-Indel
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	42	470	0	0.149466	0	.	.	strong	SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	NM_001040022	exon3	c.386_388del	p.129_130del	.	.	PASS	Atlas-Indel
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	32	121	.	0.381	.	-|0.664;TGCTGCTGCTGT|0.336	0.336	strong	.	SHROOM4	171	.	NM_020717	exon6	c.3384_3385insACAGCAGCAGCA	p.Q1128delinsQQQQQ	.	.	PASS	Pindel,Atlas-Indel
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Frame_Shift_Del	DEL	GGATGCATC	GGATGCATC	-	rs139827156	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGATGCATC	GGATGCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	20	78	.	0.294	.	GGATGCATC|0.963;-|0.037	0.037	strong	.	C14orf177	37	.	NM_182560	wholegene	.	.	.	.	PASS	Pindel,Atlas-Indel
CACNA1B	774	hgsc.bcm.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	27	108	.	0.659	.	GGAGAAGGAGACCAC|0.621;-|0.379	0.379	strong	.	CACNA1B	266	.	NM_001243812	exon19	c.2975_2989del	p.992_997del	.	.	PASS	Pindel,Atlas-Indel
CMA1	1215	hgsc.bcm.edu	37	14	24976605	24976605	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	39	147	.	0.325	.	.	.	none	.	CMA1	21	.	NM_001836	exon2	c.167delT	p.I56fs	.	.	PASS	Pindel,Atlas-Indel
SSPO	23145	hgsc.bcm.edu	37	7	149516839	149516839	+	Frame_Shift_Del	DEL	C	C	-	rs145311298	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	34	61	.	0.680	.	C|0.933;-|0.067	0.067	strong	.	.	.	.	NM_198455	exon85	c.12040delT	p.S4014fs	.	.	PASS	Pindel,Atlas-Indel
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs200434923	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	16	84	.	0.213	.	TGGGG|0.528;-|0.472	0.472	strong	.	TMPRSS6	99	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
FAM45B	55855	hgsc.bcm.edu	37	X	129630968	129630969	+	RNA	DEL	GT	GT	-	rs372692629		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	82	383	.	0.200	.	.	.	weak	.	FAM45B	26	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
MTFP1	51537	hgsc.bcm.edu	37	22	30824659	30824660	+	Frame_Shift_Ins	INS	-	-	A	rs149958301	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	27	72	.	0.360	.	-|0.993;A|0.007	0.007	strong	.	MTFP1	7	.	NM_001003704	exon3	c.406_407insA	p.X136delinsX	.	.	PASS	Pindel,Atlas-Indel
SSPO	23145	hgsc.bcm.edu	37	7	149484830	149484830	+	Frame_Shift_Del	DEL	G	G	-	rs137977793	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	11	52	.	0.239	.	G|0.985;-|0.015	0.015	strong	.	.	.	.	NM_198455	exon25	c.3651delC	p.H1217fs	.	.	PASS	Pindel,Atlas-Indel
OR8B12	219858	hgsc.bcm.edu	37	11	124413049	124413051	+	In_Frame_Del	DEL	AGA	AGA	-	rs201026337	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	45	125	.	0.417	.	AGA|0.983;-|0.017	0.017	strong	.	OR8B12	66	.	NM_001005195	exon1	c.501_503del	p.167_168del	.	.	PASS	Pindel,Atlas-Indel
SLC38A10	124565	hgsc.bcm.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	68	252	.	0.304	.	ATG|0.576;-|0.424	0.424	strong	.	SLC38A10	133	.	NM_001037984	exon16	c.3214_3216del	p.1072_1072del	.	.	PASS	Pindel,Atlas-Indel
WDR81	124997	hgsc.bcm.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs35048651	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	13	54	.	0.200	.	-|0.172;GAG|0.828	0.172	strong	.	WDR81	180	.	NM_001163809	exon1	c.3087_3089del	p.1029_1030del	.	.	PASS	Pindel,Atlas-Indel
KRTAP6-2	337967	hgsc.bcm.edu	37	21	31971075	31971076	+	Frame_Shift_Ins	INS	-	-	A	rs113674499	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	60	206	.	0.300	.	-|0.990;A|0.010	0.010	strong	.	KRTAP6-2	24	.	NM_181604	exon1	c.119_120insT	p.Y40fs	.	.	PASS	Pindel,Atlas-Indel
ZSCAN29	146050	hgsc.bcm.edu	37	15	43658416	43658418	+	In_Frame_Del	DEL	CCT	CCT	-	rs151154169	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	25	61	.	0.338	.	CCT|0.977;-|0.023	0.023	strong	.	ZSCAN29	57	.	NM_152455	exon3	c.1113_1115del	p.371_372del	.	.	PASS	Pindel,Atlas-Indel
OR4C46	119749	hgsc.bcm.edu	37	11	51515413	51515441	+	Frame_Shift_Del	DEL	GGTCACCATCACTGCCAGCCCATCACTGG	GGTCACCATCACTGCCAGCCCATCACTGG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGTCACCATCACTGCCAGCCCATCACTGG	GGTCACCATCACTGCCAGCCCATCACTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	74	212	.	0.632	.	.	.	none	OR4C46,colon,carcinoma,0,1	OR4C46	96	1	NM_001004703	exon1	c.131_159del	p.44_53del	.	.	PASS	Pindel,Atlas-Indel
UPP2	151531	hgsc.bcm.edu	37	2	158958551	158958552	+	Splice_Site	INS	-	-	A	rs11368509	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	36	92	.	0.356	.	-|0.862;A|0.138	0.138	strong	.	UPP2	60	.	NM_001135098	exon3	c.148-1->A	.	.	.	PASS	Pindel,Atlas-Indel
TP53TG5	27296	hgsc.bcm.edu	37	20	44004156	44004158	+	In_Frame_Del	DEL	ATT	ATT	-	rs10546815	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	39	59	.	0.696	.	ATT|0.574;-|0.426	0.426	strong	.	TP53TG5	36	.	NM_014477	exon4	c.290_292del	p.97_98del	.	.	PASS	Pindel,Atlas-Indel
DCHS2	54798	hgsc.bcm.edu	37	4	155158259	155158260	+	In_Frame_Ins	INS	-	-	GTT	rs138652483	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	40	140	.	0.317	.	-|0.988;GTT|0.012	0.012	strong	.	DCHS2	594	.	NM_017639	exon25	c.6180_6181insAAC	p.T2060delinsTT	.	.	PASS	Pindel,Atlas-Indel
LCNL1	401562	hgsc.bcm.edu	37	9	139879427	139879428	+	Frame_Shift_Ins	INS	-	-	GG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	14	314	0	0.0645161	0	.	.	none	.	LCNL1	4	.	NM_207510	exon3	c.459_460insGG	p.S153fs	.	.	PASS	Atlas-Indel
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548788	+	In_Frame_Ins	INS	-	-	GTGAAT	rs34870944	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	35	193	.	0.215	.	-|0.604;GTGAAT|0.396	0.396	strong	.	ACIN1	147	.	NM_001164814	exon6	c.1931_1932insATTCAC	p.R644delinsHSR	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057775	46057804	+	In_Frame_Del	DEL	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	45	151	0	0.269461	0	.	.	none	.	KRTAP10-10	37	.	NM_181688	exon1	c.440_469del	p.147_157del	.	.	PASS	Atlas-Indel
RNU6-81	100873780	hgsc.bcm.edu	37	2	132248330	132248331	+	RNA	INS	-	-	GT	rs111311763	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	63	266	.	0.232	.	-|0.500;GC|0.500	.	alt	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
MN1	4330	hgsc.bcm.edu	37	22	28194912	28194913	+	In_Frame_Ins	INS	-	-	TGC	rs75719175		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	42	0	0.482143	0	.	.	weak	MN1,NS,carcinoma,0,1	MN1	122	1	NM_002430	exon1	c.1620_1621insGCA	p.Q540delinsQQ	.	.	PASS	Atlas-Indel
CLCA4	22802	hgsc.bcm.edu	37	1	87045903	87045908	+	In_Frame_Del	DEL	CCTACT	CCTACT	-	rs56040873	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTACT	CCTACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	46	146	.	0.254	.	.	.	weak	.	CLCA4	131	.	NM_012128	exon14	c.2634_2639del	p.878_880del	.	.	PASS	Pindel,Atlas-Indel
SEC63	11231	hgsc.bcm.edu	37	6	108214734	108214735	+	In_Frame_Ins	INS	-	-	GTA	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	39	104	.	0.355	.	.	.	none	.	SEC63	79	.	NM_007214	exon16	c.1626_1627insTAC	p.P542delinsPT	.	.	PASS	Pindel,Atlas-Indel
MICA	100507436	hgsc.bcm.edu	37	6	31380161	31380161	+	Frame_Shift_Del	DEL	G	G	-	rs67841474	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	17	128	0	0.186813	0	.	.	strong	.	MICA	21	.	NM_001177519	exon5	c.951delT	p.A317fs	.	.	PASS	Atlas-Indel
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937852	88937854	+	In_Frame_Del	DEL	TTT	TTT	-	rs34431437	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	62	230	.	0.295	.	.	.	weak	.	ZCCHC6	105	.	NM_024617	exon13	c.2812_2814del	p.938_938del	.	.	PASS	Pindel,Atlas-Indel
MAGI1	9223	hgsc.bcm.edu	37	3	65425560	65425561	+	In_Frame_Ins	INS	-	-	CTG	rs142043619	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	23	52	.	0.404	.	.	.	strong	.	MAGI1	481	.	NM_001033057	exon9	c.1264_1265insCAG	p.T422delinsQT	.	.	PASS	Pindel,Atlas-Indel
RNF34	80196	hgsc.bcm.edu	37	12	121858078	121858080	+	In_Frame_Del	DEL	GAT	GAT	-	rs72059744	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	35	66	.	0.380	.	GAT|0.969;-|0.031	0.031	strong	.	RNF34	54	.	NM_194271	exon5	c.669_671del	p.223_224del	.	.	PASS	Pindel,Atlas-Indel
KLF17	128209	hgsc.bcm.edu	37	1	44596380	44596382	+	In_Frame_Del	DEL	CAA	CAA	-	rs34057178	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	37	109	.	0.381	.	CAA|0.811;-|0.189	0.189	strong	.	KLF17	92	.	NM_173484	exon3	c.1121_1123del	p.374_375del	.	.	PASS	Pindel,Atlas-Indel
TBC1D5	9779	hgsc.bcm.edu	37	3	17208285	17208286	+	Frame_Shift_Del	DEL	CG	CG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	46	165	.	0.256	.	.	.	none	.	TBC1D5	69	.	NM_001134381	exon23	c.2134_2135del	p.712_712del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L4	349334	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-	rs59364037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	49	332	0	0.14497	0	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1214delG	p.C405fs	.	.	PASS	Atlas-Indel
SERPINB3	6317	hgsc.bcm.edu	37	18	61323014	61323014	+	Frame_Shift_Del	DEL	T	T	-	rs201374310	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	49	209	0	0.269231	0	T|0.960;-|0.040	0.040	strong	.	SERPINB3	90	.	NM_006919	exon8	c.1051delG	p.G351fs	.	.	PASS	Atlas-Indel
RTKN2	219790	hgsc.bcm.edu	37	10	63976913	63976918	+	In_Frame_Del	DEL	AGCTTC	AGCTTC	-	rs149331212	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGCTTC	AGCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	10	55	.	0.714	.	AGCTTC|0.861;-|0.139	0.139	strong	.	RTKN2	68	.	NM_145307	exon9	c.980_985del	p.327_329del	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959341	45959343	+	In_Frame_Del	DEL	GGA	GGA	-	rs150327748	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	23	106	.	0.221	.	GGA|0.975;-|0.025	0.025	strong	.	KRTAP10-1	34	.	NM_198691	exon1	c.692_694del	p.231_232del	.	.	PASS	Pindel,Atlas-Indel
MIR943	100126332	hgsc.bcm.edu	37	4	1988188	1988189	+	RNA	INS	-	-	CT	rs3034718	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	52	155	.	0.254	.	CT|1.000;|0.000	1.000	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
PABPC3	5042	hgsc.bcm.edu	37	13	25671097	25671098	+	Frame_Shift_Ins	INS	-	-	T	rs140090397	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	14	150	0	0.079096	0	.	.	strong	.	PABPC3	129	.	NM_030979	exon1	c.761_762insT	p.K254fs	.	.	PASS	Atlas-Indel
OR52D1	390066	hgsc.bcm.edu	37	11	5510540	5510541	+	Frame_Shift_Ins	INS	-	-	GGCT	rs146317894	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	21	135	.	0.157	.	.	.	strong	.	OR52D1	66	.	NM_001005163	exon1	c.604_605insGGCT	p.G202fs	.	.	PASS	Pindel,Atlas-Indel
ORM2	5005	hgsc.bcm.edu	37	9	117095395	117095397	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	888	290	871	0	0.326577	0	.	.	none	.	ORM2	13	.	NM_000608	exon6	c.586_588del	p.196_196del	.	.	PASS	Atlas-Indel
NEDD8-MDP1	100528064	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	46	90	.	0.338	.	A|0.812;-|0.188	0.188	strong	.	.	.	.	NM_001199823	exon7	c.546delG	p.L182fs	.	.	PASS	Pindel,Atlas-Indel
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650055	+	In_Frame_Ins	INS	-	-	CTC	rs112267342	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	27	88	.	0.318	.	CTC|0.250;CTT|0.750	0.250	strong	CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	NM_001141947	exon13	c.1816_1817insCTC	p.S606delinsSP	.	.	PASS	Pindel,Atlas-Indel
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs61179824	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	35	109	.	0.273	.	T|0.888;-|0.112	0.112	strong	.	SLC3A1	62	.	NM_000341	exon6	c.1136+1T>-	.	.	.	PASS	Pindel,Atlas-Indel
FRG2C	100288801	hgsc.bcm.edu	37	3	75713659	75713660	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	427	50	406	0	0.117096	0	.	.	none	.	FRG2C	16	.	NM_001124759	exon1	c.128_129del	p.43_43del	.	.	PASS	Atlas-Indel
SPATA21	374955	hgsc.bcm.edu	37	1	16727305	16727306	+	In_Frame_Ins	INS	-	-	CTT	rs139527123	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	95	192	.	0.519	.	-|0.888;CTT|0.112	0.112	strong	SPATA21,NS,carcinoma,+1,1	SPATA21	47	1	NM_198546	exon11	c.1084_1085insAAG	p.L362delinsKL	.	.	PASS	Pindel,Atlas-Indel
TRIM16	10626	hgsc.bcm.edu	37	17	15546132	15546133	+	Splice_Site	INS	-	-	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	402	88	335	0	0.218905	0	.	.	none	.	TRIM16	45	.	NM_006470	exon6	c.520-2->T	.	.	.	PASS	Atlas-Indel
LTF	4057	hgsc.bcm.edu	37	3	46496843	46496843	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	43	128	.	0.301	.	.	.	none	.	LTF	98	.	NM_002343	exon5	c.590delA	p.E197fs	.	.	PASS	Pindel,Atlas-Indel
ANKRD36B	57730	hgsc.bcm.edu	37	2	98129757	98129758	+	Frame_Shift_Ins	INS	-	-	T	rs367988895		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	678	61	1139	0	0.0899705	0	.	.	weak	.	.	.	.	NM_025190	exon38	c.2691_2692insA	p.K897fs	.	.	PASS	Atlas-Indel
FAM157A	728262	hgsc.bcm.edu	37	3	197880131	197880139	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	rs3061423	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	74	344	0	0.354067	0	.	.	alt	.	FAM157A	4	.	NM_001145248	exon2	c.209_217del	p.70_73del	.	.	PASS	Atlas-Indel
DPP7	29952	hgsc.bcm.edu	37	9	140005117	140005118	+	Frame_Shift_Ins	INS	-	-	C	rs11391519	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	18	42	.	0.419	.	-|0.973;C|0.027	0.027	strong	.	DPP7	22	.	NM_013379	exon13	c.1462_1463insG	p.P488fs	.	.	PASS	Pindel,Atlas-Indel
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Frame_Shift_Del	DEL	G	G	-	rs56086318	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	101	202	0	0.429787	0	.	.	strong	.	CLDN16	59	.	NM_006580	exon1	c.163delA	p.R55fs	.	.	PASS	Atlas-Indel
OR6Q1	219952	hgsc.bcm.edu	37	11	57799109	57799109	+	Frame_Shift_Del	DEL	C	C	-	rs34846253	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	65	205	.	0.298	.	C|0.867;-|0.133	0.133	strong	.	OR6Q1	58	.	NM_001005186	exon1	c.684delA	p.T228fs	.	.	PASS	Pindel,Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887092	1887092	+	Frame_Shift_Del	DEL	G	G	-	rs139735565	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	36	102	0	0.346154	0	G|0.777;-|0.223	0.223	strong	.	KIAA1751	92	.	NM_001080484	exon18	c.2215delG	p.G739fs	.	.	PASS	Atlas-Indel
PROL1	58503	hgsc.bcm.edu	37	4	71275631	71275632	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	65	167	.	0.330	.	.	.	none	.	PROL1	46	.	NM_021225	exon3	c.586_587insC	p.T196fs	.	.	PASS	Pindel,Atlas-Indel
TNS1	7145	hgsc.bcm.edu	37	2	218762663	218762665	+	In_Frame_Del	DEL	TCC	TCC	-	rs200962764	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	47	112	.	0.367	.	TCC|0.989;-|0.011	0.011	strong	.	TNS1	251	.	NM_022648	exon6	c.25_27del	p.9_9del	.	.	PASS	Pindel,Atlas-Indel
ZNF717	100131827	hgsc.bcm.edu	37	3	75786895	75786895	+	Frame_Shift_Del	DEL	T	T	-	rs144168413	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	30	54	.	0.240	.	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.1880delC	p.T627fs	.	.	PASS	Pindel,Atlas-Indel
LINC00471	151477	hgsc.bcm.edu	37	2	232373857	232373860	+	RNA	DEL	TTCT	TTCT	-	rs150545131	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	69	237	.	0.275	.	TTCT|0.994;-|0.006	0.006	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249117	71249118	+	In_Frame_Ins	INS	-	-	CCG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	18	337	0	0.0789474	0	.	.	none	.	KRTAP5-8	28	.	NM_021046	exon1	c.16_17insCCG	p.C6delinsSG	.	.	PASS	Atlas-Indel
HCLS1	3059	hgsc.bcm.edu	37	3	121351315	121351316	+	In_Frame_Ins	INS	-	-	GGCTCAGGCTCA	rs150627065	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	26	122	.	0.190	.	-|0.731;GGCTCAGGCTCA|0.269	0.269	strong	HCLS1,caecum,carcinoma,0,1	HCLS1	78	1	NM_005335	exon12	c.1104_1105insTGAGCCTGAGCC	p.P368delinsPEPEP	.	.	PASS	Pindel,Atlas-Indel
SALL1	6299	hgsc.bcm.edu	37	16	51175655	51175656	+	In_Frame_Ins	INS	-	-	GCT	rs113614842	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	32	145	0	0.217687	0	-|0.500;GCC|0.250;GCT|0.250	0.250	strong	.	SALL1	301	.	NM_002968	exon2	c.478_479insAGC	p.G160delinsSG	.	.	PASS	Atlas-Indel
OR5L2	26338	hgsc.bcm.edu	37	11	55594980	55594980	+	Frame_Shift_Del	DEL	G	G	-	rs144106069	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	37	201	.	0.262	.	G|0.995;-|0.005	0.005	strong	OR5L2,NS,carcinoma,+2,2	OR5L2	135	2	NM_001004739	exon1	c.285delA	p.L95fs	.	.	PASS	Pindel,Atlas-Indel
CA9	768	hgsc.bcm.edu	37	9	35674191	35674208	+	In_Frame_Del	DEL	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	-	rs201260414	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	18	103	.	0.151	.	GGAGAGGAGGATCTACCT|0.933;-|0.067	0.067	strong	.	CA9	48	.	NM_001216	exon1	c.234_251del	p.78_84del	.	.	PASS	Pindel,Atlas-Indel
KIR2DL4	3805	hgsc.bcm.edu	37	19	55324675	55324675	+	Frame_Shift_Del	DEL	A	A	-	rs11371265	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	10	17	0	0.108696	0	A|1.000;|0.000	.	weak	.	KIR2DL4	62	.	NM_001080772	exon6	c.801delC	p.S267fs	.	.	PASS	Atlas-Indel
CEP85L	387119	hgsc.bcm.edu	37	6	118812811	118812813	+	In_Frame_Del	DEL	TGT	TGT	-	rs71866282	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	77	.	0.429	.	TGT|0.979;-|0.021	0.021	strong	.	CEP85L	26	.	NM_206921	exon6	c.1474_1476del	p.492_492del	.	.	PASS	Pindel,Atlas-Indel
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346446	140346451	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs148181752	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	17	90	.	0.213	.	TGCTGC|0.974;-|0.026	0.026	strong	.	PCDHAC2	142	.	NM_031883	exon1	c.94_99del	p.32_33del	.	.	PASS	Pindel,Atlas-Indel
ZNF594	84622	hgsc.bcm.edu	37	17	5085878	5085879	+	Frame_Shift_Del	DEL	CT	CT	-	rs146837771	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	33	120	.	0.282	.	CT|0.987;-|0.013	0.013	strong	.	ZNF594	89	.	NM_032530	exon2	c.1674_1675del	p.558_559del	.	.	PASS	Pindel,Atlas-Indel
CYP3A43	64816	hgsc.bcm.edu	37	7	99434078	99434078	+	Frame_Shift_Del	DEL	A	A	-	rs61469810	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	32	109	.	0.327	.	A|0.903;-|0.097	0.097	strong	.	CYP3A43	52	.	NM_057095	exon2	c.73delT	p.Y25fs	.	.	PASS	Pindel,Atlas-Indel
TNRC6A	27327	hgsc.bcm.edu	37	16	24788401	24788402	+	In_Frame_Ins	INS	-	-	GCA	rs112426081		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	11	48	0	0.2	0	-|0.500;GCA|0.500	0.500	weak	TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	NM_014494	exon5	c.311_312insGCA	p.P104delinsPQ	.	.	PASS	Atlas-Indel
CBLC	23624	hgsc.bcm.edu	37	19	45296846	45296847	+	Frame_Shift_Ins	INS	-	-	C	rs66944506	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	28	52	.	0.431	.	-|0.926;C|0.074	0.074	strong	.	CBLC	41	.	NM_012116	exon8	c.1253_1254insC	p.D418fs	.	.	PASS	Pindel,Atlas-Indel
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772899	140772899	+	Frame_Shift_Del	DEL	C	C	-	rs3214276	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	53	121	.	0.346	.	C|0.882;-|0.118	0.118	strong	.	PCDHGA8	146	.	NM_014004	exon1	c.518delG	p.S173fs	.	.	PASS	Pindel,Atlas-Indel
OR2W3	343171	hgsc.bcm.edu	37	1	248059779	248059780	+	Frame_Shift_Ins	INS	-	-	A	rs112696640	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	60	128	.	0.469	.	-|0.876;A|0.124	0.124	strong	.	OR2W3	113	.	NM_001001957	exon1	c.891_892insA	p.V297fs	.	.	PASS	Pindel,Atlas-Indel
ETFB	2109	hgsc.bcm.edu	37	19	51857874	51857875	+	In_Frame_Ins	INS	-	-	CCACAG	rs61361626	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	20	79	.	0.222	.	-|0.937;CCACAG|0.063	0.063	strong	.	ETFB	46	.	NM_001014763	exon1	c.19_20insCTGTGG	p.V7delinsLWV	.	.	PASS	Pindel,Atlas-Indel
SLC4A2	6522	hgsc.bcm.edu	37	7	150763616	150763621	+	In_Frame_Del	DEL	GGAGGC	GGAGGC	-	rs150330052	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGGC	GGAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	12	56	.	0.245	.	GGAGGC|0.962;-|0.038	0.038	strong	.	SLC4A2	98	.	NM_001199692	exon6	c.590_595del	p.197_199del	.	.	PASS	Pindel,Atlas-Indel
TICAM1	148022	hgsc.bcm.edu	37	19	4817288	4817289	+	In_Frame_Ins	INS	-	-	AGG	rs144100421	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	48	248	.	0.208	.	.	.	strong	.	TICAM1	69	.	NM_182919	exon2	c.1102_1103insCCT	p.S368delinsPS	.	.	PASS	Pindel,Atlas-Indel
C8orf82	414919	hgsc.bcm.edu	37	8	145753431	145753431	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	28	51	.	0.491	.	.	.	none	C8orf82,bladder,carcinoma,0,1	C8orf82	7	1	NM_001001795	exon2	c.183delG	p.K61fs	.	.	PASS	Pindel,Atlas-Indel
OR52D1	390066	hgsc.bcm.edu	37	11	5510498	5510499	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	54	121	0	0.402985	0	.	.	none	.	OR52D1	66	.	NM_001005163	exon1	c.562_563insC	p.A188fs	.	.	PASS	Atlas-Indel
BDNF	627	hgsc.bcm.edu	37	11	27680797	27680806	+	RNA	DEL	GAAGACTTGC	GAAGACTTGC	-	rs57127302	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGACTTGC	GAAGACTTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	33	158	.	0.306	.	GAAGACTTGC|0.962;-|0.038	0.038	strong	.	BDNF	63	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
RBPJL	11317	hgsc.bcm.edu	37	20	43940531	43940542	+	In_Frame_Del	DEL	CAGCGCGTCCGG	CAGCGCGTCCGG	-	rs142744285	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCGCGTCCGG	CAGCGCGTCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	45	127	.	0.381	.	CAGCGCGTCCGG|0.987;-|0.013	0.013	strong	.	RBPJL	67	.	NM_014276	exon5	c.380_391del	p.127_131del	.	.	PASS	Pindel,Atlas-Indel
RPGR	6103	hgsc.bcm.edu	37	X	38145916	38145918	+	In_Frame_Del	DEL	TCC	TCC	-	rs201730068	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	486	107	462	.	0.220	.	TCC|0.991;-|0.009	0.009	strong	.	RPGR	175	.	NM_001034853	exon15	c.2335_2337del	p.779_779del	.	.	PASS	Pindel,Atlas-Indel
LGR6	59352	hgsc.bcm.edu	37	1	202183358	202183358	+	Frame_Shift_Del	DEL	G	G	-	rs74355478	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	79	235	.	0.293	.	G|0.905;-|0.095	0.095	strong	.	LGR6	102	.	NM_001017404	exon1	c.75delT	p.G25fs	.	.	PASS	Pindel,Atlas-Indel
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	34	122	.	0.288	.	ACTCAA|0.643;-|0.357	0.357	strong	.	GFM2	38	.	NM_032380	exon18	c.1827_1832del	p.609_611del	.	.	PASS	Pindel,Atlas-Indel
ATP2C2	9914	hgsc.bcm.edu	37	16	84497336	84497337	+	In_Frame_Ins	INS	-	-	AGTGGA	rs149491518	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	26	146	.	0.217	.	-|0.987;AGTGGA|0.013	0.013	strong	.	ATP2C2	75	.	NM_014861	exon27	c.2839_2840insAGTGGA	p.X947delinsX	.	.	PASS	Pindel,Atlas-Indel
LRRC46	90506	hgsc.bcm.edu	37	17	45914125	45914136	+	In_Frame_Del	DEL	AGGAGCTGGAGC	AGGAGCTGGAGC	-	rs142960476	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGGAGCTGGAGC	AGGAGCTGGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	35	184	.	0.267	.	AGGAGCTGGAGC|0.978;-|0.022	0.022	strong	.	LRRC46	25	.	NM_033413	exon8	c.604_615del	p.202_205del	.	.	PASS	Pindel,Atlas-Indel
UPK3BL	100134938	hgsc.bcm.edu	37	7	102281151	102281152	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	27	134	0	0.346154	0	.	.	none	.	UPK3BL	6	.	NM_001114403	exon2	c.182_183insT	p.S61fs	.	.	PASS	Atlas-Indel
MTERFD2	130916	hgsc.bcm.edu	37	2	242035516	242035518	+	In_Frame_Del	DEL	TCA	TCA	-	rs142629642	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	44	219	.	0.196	.	.	.	strong	.	MTERFD2	33	.	NM_182501	exon4	c.1042_1044del	p.348_348del	.	.	PASS	Pindel,Atlas-Indel
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609296	32609297	+	Frame_Shift_Ins	INS	-	-	G	rs9282026	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	14	73	0	0.7	0	-|0.857;G|0.143	0.143	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.292_293insG	p.I98fs	.	.	PASS	Atlas-Indel
AMBN	258	hgsc.bcm.edu	37	4	71468346	71468348	+	In_Frame_Del	DEL	AGG	AGG	-	rs141384720	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	55	285	.	0.250	.	AGG|0.889;-|0.111	0.111	strong	.	AMBN	73	.	NM_016519	exon7	c.536_538del	p.179_180del	.	.	PASS	Pindel,Atlas-Indel
ADAM33	80332	hgsc.bcm.edu	37	20	3652979	3652983	+	Splice_Site	DEL	GCGCA	GCGCA	-	rs143884879	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCGCA	GCGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	26	86	.	0.366	.	GCGCA|0.958;-|0.042	0.042	strong	.	ADAM33	76	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
KGFLP1	0	hgsc.bcm.edu	37	9	46687757	46687757	+	RNA	DEL	G	G	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	35	203	0	0.166667	0	.	.	none	.	.	.	.	.	.	.	.	.	.	PASS	Atlas-Indel
ZNF107	51427	hgsc.bcm.edu	37	7	64169017	64169018	+	Frame_Shift_Ins	INS	-	-	A	rs375319415	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	15	44	0	0.340909	0	.	.	weak	.	ZNF107	107	.	NM_016220	exon7	c.2335_2336insA	p.E779fs	.	.	PASS	Atlas-Indel
ARID1A	8289	hgsc.bcm.edu	37	1	27097616	27097618	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	16	81	.	0.203	.	.	.	none	.	ARID1A	842	.	NM_139135	exon12	c.3204_3206del	p.1068_1069del	.	.	PASS	Pindel,Atlas-Indel
ROBO3	64221	hgsc.bcm.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	CGGAGT	-	rs71859853	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CGGAGT	CGGAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	31	90	.	0.326	.	CGGAGT|0.626;-|0.374	0.374	strong	.	ROBO3	199	.	NM_022370	exon27	c.4092_4097del	p.1364_1366del	.	.	PASS	Pindel,Atlas-Indel
RSPH10B	222967	hgsc.bcm.edu	37	7	6838173	6838176	+	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	379	34	497	0	0.0897098	0	.	.	none	.	RSPH10B	28	.	NM_173565	exon21	c.2611_2884del	p.871_871del	.	.	PASS	Atlas-Indel
ANKRD40	91369	hgsc.bcm.edu	37	17	48777220	48777221	+	In_Frame_Ins	INS	-	-	TCA	rs138572332	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	15	40	0	0.294118	0	-|0.957;TCA|0.043	0.043	strong	.	ANKRD40	35	.	NM_052855	exon3	c.318_319insTGA	p.D106delinsDD	.	.	PASS	Atlas-Indel
C11orf16	56673	hgsc.bcm.edu	37	11	8942889	8942890	+	Frame_Shift_Del	DEL	AT	AT	-	rs10583719	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	52	174	.	0.291	.	AT|0.978;-|0.022	0.022	strong	.	C11orf16	43	.	NM_020643	exon6	c.1378_1379del	p.460_460del	.	.	PASS	Pindel,Atlas-Indel
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327916	+	In_Frame_Ins	INS	-	-	TGC	rs71806515		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	14	69	.	0.206	.	.	.	weak	ATXN1,colon,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.627_628insGCA	p.H209delinsQH	.	.	PASS	Pindel,Atlas-Indel
CHD1	1105	hgsc.bcm.edu	37	5	98192165	98192167	+	In_Frame_Del	DEL	AGG	AGG	-	rs138635992	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	113	231	.	0.489	.	AGG|0.775;-|0.225	0.225	strong	.	CHD1	137	.	NM_001270	exon35	c.5051_5053del	p.1684_1685del	.	.	PASS	Pindel,Atlas-Indel
KIAA1609	57707	hgsc.bcm.edu	37	16	84529358	84529360	+	In_Frame_Del	DEL	CTC	CTC	-	rs200260198	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	53	226	.	0.288	.	CTC|0.994;-|0.006	0.006	strong	.	KIAA1609	39	.	NM_020947	exon3	c.314_316del	p.105_106del	.	.	PASS	Pindel,Atlas-Indel
SLC39A14	23516	hgsc.bcm.edu	37	8	22262229	22262234	+	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs111662782	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCTGCT	GCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	62	165	.	0.681	.	GCTGCT|0.701;-|0.299	0.299	strong	.	SLC39A14	59	.	NM_001135154	exon2	c.5_10del	p.2_4del	.	.	PASS	Pindel,Atlas-Indel
HCG9	10255	hgsc.bcm.edu	37	6	29943255	29943259	+	RNA	DEL	GGGCT	GGGCT	-	rs150979551	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGGCT	GGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	26	175	.	0.208	.	GGGCT|0.787;-|0.213	0.213	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
PACS2	23241	hgsc.bcm.edu	37	14	105848398	105848398	+	Splice_Site	DEL	G	G	-	rs112632153	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	14	40	.	0.359	.	G|0.920;-|0.080	0.080	strong	.	PACS2	75	.	NM_001100913	exon13	c.1413+2G>-	.	.	.	PASS	Pindel,Atlas-Indel
OR6P1	128366	hgsc.bcm.edu	37	1	158533298	158533299	+	Frame_Shift_Ins	INS	-	-	A	rs201077183	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	28	94	.	0.295	.	-|0.995;A|0.005	0.005	strong	.	OR6P1	47	.	NM_001160325	exon1	c.97_98insT	p.A33fs	.	.	PASS	Pindel,Atlas-Indel
BORA	79866	hgsc.bcm.edu	37	13	73317740	73317741	+	Frame_Shift_Ins	INS	-	-	GTGA	rs10648315	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	58	217	.	0.283	.	.	.	strong	.	.	.	.	NM_024808	exon6	c.454_455insGTGA	p.A152fs	.	.	PASS	Pindel,Atlas-Indel
FAM83G	644815	hgsc.bcm.edu	37	17	18874685	18874686	+	In_Frame_Ins	INS	-	-	GGT	rs3071666	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	33	74	.	0.702	.	-|0.250;GGT|0.750	0.750	strong	.	FAM83G	51	.	NM_001039999	exon6	c.2459_2460insACC	p.R820delinsHR	.	.	PASS	Pindel,Atlas-Indel
FOXD4L3	286380	hgsc.bcm.edu	37	9	70919085	70919085	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	931	76	668	0	0.0816327	0	.	.	none	.	FOXD4L3	7	.	NM_199135	exon1	c.1217delG	p.C406fs	.	.	PASS	Atlas-Indel
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs111905975	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	30	85	.	0.341	.	TCC|0.852;-|0.148	0.148	strong	.	KANK3	35	.	NM_198471	exon8	c.2023_2025del	p.675_675del	.	.	PASS	Pindel,Atlas-Indel
PODXL2	50512	hgsc.bcm.edu	37	3	127379364	127379369	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-	rs200281996	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	29	95	.	0.367	.	GAAGAG|0.992;-|0.008	0.008	strong	.	PODXL2	53	.	NM_015720	exon3	c.492_497del	p.164_166del	.	.	PASS	Pindel,Atlas-Indel
HRC	3270	hgsc.bcm.edu	37	19	49657594	49657595	+	In_Frame_Ins	INS	-	-	TTCTTCTTT	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	28	180	0	0.131455	0	.	.	none	.	HRC	85	.	NM_002152	exon1	c.901_902insAAAGAAGAA	p.E301delinsKEEE	.	.	PASS	Atlas-Indel
C14orf23	387978	hgsc.bcm.edu	37	14	29261307	29261308	+	RNA	INS	-	-	C	rs56363493	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	32	110	0	0.344086	0	-|0.736;C|0.264	0.264	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Atlas-Indel
OR2T27	403239	hgsc.bcm.edu	37	1	248813309	248813310	+	Frame_Shift_Ins	INS	-	-	A	rs141113411	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	39	280	0	0.155378	0	-|0.960;A|0.040	0.040	strong	.	OR2T27	52	.	NM_001001824	exon1	c.877_878insT	p.R293_N294delinsX	.	.	PASS	Atlas-Indel
CIC	23152	hgsc.bcm.edu	37	19	42794829	42794831	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	33	87	.	0.308	.	.	.	none	.	CIC	249	.	NM_015125	exon10	c.1908_1910del	p.636_637del	.	.	PASS	Pindel,Atlas-Indel
SMPD2	6610	hgsc.bcm.edu	37	6	109764875	109764877	+	In_Frame_Del	DEL	GGA	GGA	-	rs142982624	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	34	123	.	0.333	.	GGA|0.957;-|0.043	0.043	strong	.	SMPD2	25	.	NM_003080	exon10	c.1038_1040del	p.346_347del	.	.	PASS	Pindel,Atlas-Indel
OR2A14	135941	hgsc.bcm.edu	37	7	143826730	143826732	+	In_Frame_Del	DEL	CTT	CTT	-	rs66549240	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	61	353	.	0.195	.	CTT|0.441;-|0.559	0.559	strong	.	OR2A14	66	.	NM_001001659	exon1	c.524_526del	p.175_176del	.	.	PASS	Pindel,Atlas-Indel
NCOA3	8202	hgsc.bcm.edu	37	20	46279864	46279866	+	In_Frame_Del	DEL	CAA	CAA	-	rs67218125		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	16	97	.	0.151	.	.	.	weak	NCOA3,colon,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.3789_3791del	p.1263_1264del	.	.	PASS	Pindel,Atlas-Indel
MPRIP	23164	hgsc.bcm.edu	37	17	17075181	17075181	+	Splice_Site	DEL	T	T	-	rs3215213	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	36	79	.	0.404	.	T|0.807;-|0.193	0.193	strong	.	MPRIP	87	.	NM_015134	exon16	c.2311+1T>-	.	.	.	PASS	Pindel,Atlas-Indel
USP34	9736	hgsc.bcm.edu	37	2	61575022	61575023	+	In_Frame_Ins	INS	-	-	TGG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	17	41	.	0.315	.	.	.	none	.	USP34	334	.	NM_014709	exon15	c.2268_2269insCCA	p.H756delinsHH	.	.	PASS	Pindel,Atlas-Indel
DMXL1	1657	hgsc.bcm.edu	37	5	118529595	118529597	+	In_Frame_Del	DEL	AAT	AAT	-	rs374810198		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	10	52	.	0.182	.	.	.	weak	.	DMXL1	268	.	NM_005509	exon30	c.7386_7388del	p.2462_2463del	.	.	PASS	Pindel,Atlas-Indel
BMP15	9210	hgsc.bcm.edu	37	X	50659210	50659211	+	In_Frame_Ins	INS	-	-	TCT	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	83	221	.	0.336	.	.	.	none	.	BMP15	62	.	NM_005448	exon2	c.782_783insTCT	p.S261delinsSL	.	.	PASS	Pindel,Atlas-Indel
FOXD4L6	653404	hgsc.bcm.edu	37	9	69200395	69200395	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1099	96	643	0	0.0873521	0	.	.	none	.	.	.	.	NM_001085476	exon1	c.1219delT	p.W407fs	.	.	PASS	Atlas-Indel
ZNF107	51427	hgsc.bcm.edu	37	7	64169019	64169020	+	Frame_Shift_Ins	INS	-	-	AA	rs201020174	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	13	43	0	0.317073	0	-|0.838;AA|0.162	0.162	strong	.	ZNF107	107	.	NM_016220	exon7	c.2337_2338insAA	p.E779fs	.	.	PASS	Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	In_Frame_Ins	INS	-	-	CTC	rs145742571	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	42	176	.	0.256	.	.	.	strong	.	KIAA1751	92	.	NM_001080484	exon11	c.1213_1214insGAG	p.K405delinsEK	.	.	PASS	Pindel,Atlas-Indel
HLA-L	3139	hgsc.bcm.edu	37	6	30229034	30229035	+	RNA	INS	-	-	T	rs111358359	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	58	248	.	0.218	.	-|0.500;T|0.500	0.500	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
SLC22A25	387601	hgsc.bcm.edu	37	11	62996774	62996775	+	Frame_Shift_Ins	INS	-	-	A	rs112260121	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	57	235	.	0.285	.	-|0.990;A|0.010	0.010	strong	.	SLC22A25	87	.	NM_199352	exon1	c.351_352insT	p.V117fs	.	.	PASS	Pindel,Atlas-Indel
OR9K2	441639	hgsc.bcm.edu	37	12	55523587	55523587	+	Frame_Shift_Del	DEL	T	T	-	rs58036029	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	40	131	.	0.385	.	T|0.711;-|0.289	0.289	strong	.	OR9K2	63	.	NM_001005243	exon1	c.34delA	p.I12fs	.	.	PASS	Pindel,Atlas-Indel
ADRM1	11047	hgsc.bcm.edu	37	20	60883770	60883778	+	In_Frame_Del	DEL	GACACGAAG	GACACGAAG	-	rs202079747	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GACACGAAG	GACACGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	56	250	.	0.230	.	GACACGAAG|0.012;-|0.988	0.988	strong	.	ADRM1	28	.	NM_007002	exon10	c.1176_1184del	p.392_395del	.	.	PASS	Pindel,Atlas-Indel
KRTAP2-3	730755	hgsc.bcm.edu	37	17	39216302	39216303	+	Frame_Shift_Ins	INS	-	-	G	rs113441706	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	28	38	.	0.596	.	-|0.804;G|0.196	0.196	strong	.	.	.	.	NM_001165252	exon1	c.1_2insC	p.M1fs	.	.	PASS	Pindel,Atlas-Indel
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324139	39324140	+	In_Frame_Ins	INS	-	-	GCAGCAGGTGGTCTG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	159	427	0	0.554007	0	.	.	none	.	KRTAP4-3	40	.	NM_033187	exon1	c.286_287insCAGACCACCTGCTGC	p.R96delinsQTTCCR	.	.	PASS	Atlas-Indel
HRC	3270	hgsc.bcm.edu	37	19	49657889	49657890	+	In_Frame_Ins	INS	-	-	TCCTCCTCC	rs147238387	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	31	165	0	0.182353	0	.	.	alt	.	HRC	85	.	NM_002152	exon1	c.606_607insGGAGGAGGA	p.E202delinsEEEE	.	.	PASS	Atlas-Indel
UGDH	7358	hgsc.bcm.edu	37	4	39515807	39515813	+	Splice_Site	DEL	AAAAAGA	AAAAAGA	-	rs151116497	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAAAAGA	AAAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	33	116	.	0.393	.	.	.	strong	.	UGDH	52	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
ONECUT2	9480	hgsc.bcm.edu	37	18	55103476	55103477	+	In_Frame_Ins	INS	-	-	CAC	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	11	63	.	0.167	.	.	.	none	.	ONECUT2	42	.	NM_004852	exon1	c.528_529insCAC	p.P176delinsPH	.	.	PASS	Pindel,Atlas-Indel
CABYR	26256	hgsc.bcm.edu	37	18	21740032	21740033	+	Frame_Shift_Del	DEL	TG	TG	-	rs149126027	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	26	57	.	0.338	.	TG|0.978;-|0.022	0.022	strong	.	CABYR	51	.	NM_153769	exon5	c.1137_1138del	p.379_380del	.	.	PASS	Pindel,Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887112	1887112	+	Frame_Shift_Del	DEL	C	C	-	rs3838975	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	40	109	0	0.392157	0	C|0.783;-|0.217	0.217	strong	.	KIAA1751	92	.	NM_001080484	exon18	c.2195delC	p.A732fs	.	.	PASS	Atlas-Indel
SERPINB3	6317	hgsc.bcm.edu	37	18	61323011	61323012	+	Frame_Shift_Ins	INS	-	-	GCCA	rs60533853	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	49	212	0	0.255208	0	.	.	alt	.	SERPINB3	90	.	NM_006919	exon8	c.1053_1054insTGGC	p.G351fs	.	.	PASS	Atlas-Indel
DUPD1	338599	hgsc.bcm.edu	37	10	76803600	76803602	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	18	44	.	0.321	.	.	.	none	.	DUPD1	30	.	NM_001003892	exon2	c.375_377del	p.125_126del	.	.	PASS	Pindel,Atlas-Indel
DEFB119	245932	hgsc.bcm.edu	37	20	29965208	29965211	+	Frame_Shift_Del	DEL	ACTG	ACTG	-	rs374993061	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTG	ACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	36	110	.	0.409	.	.	.	weak	DEFB119_ENST00000376321,NS,malignant_melanoma,+1,2	DEFB119	37	2	NM_153289	exon2	c.94_97del	p.32_33del	.	.	PASS	Pindel,Atlas-Indel
NRAP	4892	hgsc.bcm.edu	37	10	115348749	115348751	+	In_Frame_Del	DEL	CTT	CTT	-	rs11575787	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	61	144	.	0.326	.	CTT|0.992;-|0.008	0.008	strong	.	NRAP	208	.	NM_001261463	exon42	c.5180_5182del	p.1727_1728del	.	.	PASS	Pindel,Atlas-Indel
APOL1	8542	hgsc.bcm.edu	37	22	36662042	36662047	+	In_Frame_Del	DEL	ATAATT	ATAATT	-	rs143830837	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATAATT	ATAATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	53	198	.	0.276	.	ATAATT|0.979;-|0.021	0.021	strong	.	APOL1	35	.	NM_145343	exon7	c.1207_1212del	p.403_404del	.	.	PASS	Pindel,Atlas-Indel
HACE1	57531	hgsc.bcm.edu	37	6	105192108	105192110	+	Splice_Site	DEL	AAC	AAC	-	rs72218235	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	34	122	.	0.281	.	AAC|0.835;-|0.165	0.165	strong	.	HACE1	96	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
FMO2	2327	hgsc.bcm.edu	37	1	171162551	171162552	+	In_Frame_Ins	INS	-	-	GAC	rs2020868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	19	76	.	0.328	.	-|0.904;GAC|0.096	0.096	strong	.	FMO2	66	.	NM_001460	exon3	c.210_211insGAC	p.S70delinsSD	.	.	PASS	Pindel,Atlas-Indel
OR2A1	346528	hgsc.bcm.edu	37	7	144015524	144015527	+	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1136	133	626	0	0.117077	0	.	.	none	.	OR2A1	10	.	NM_001005287	exon1	c.306_309del	p.102_103del	.	.	PASS	Atlas-Indel
QRICH2	84074	hgsc.bcm.edu	37	17	74288565	74288567	+	In_Frame_Del	DEL	TGA	TGA	-	rs35035566	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	27	155	.	0.186	.	TGA|0.548;-|0.452	0.452	strong	QRICH2,NS,carcinoma,-1,1	QRICH2	143	1	NM_032134	exon4	c.1744_1746del	p.582_582del	.	.	PASS	Pindel,Atlas-Indel
LIPM	340654	hgsc.bcm.edu	37	10	90562801	90562802	+	Splice_Site	INS	-	-	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	35	129	.	0.337	.	.	.	none	.	LIPM	17	.	NM_001128215	exon1	c.147+1->T	.	.	.	PASS	Pindel,Atlas-Indel
TRPM3	80036	hgsc.bcm.edu	37	9	73151130	73151133	+	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	453	86	439	.	0.190	.	.	.	none	.	TRPM3	700	.	NM_001007471	exon25	c.4861_4864del	p.1621_1622del	.	.	PASS	Pindel,Atlas-Indel
PLIN5	440503	hgsc.bcm.edu	37	19	4529255	4529257	+	In_Frame_Del	DEL	GAG	GAG	-	rs140507757	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	36	143	.	0.305	.	GAG|0.986;-|0.014	0.014	strong	.	PLIN5	27	.	NM_001013706	exon5	c.349_351del	p.117_117del	.	.	PASS	Pindel,Atlas-Indel
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	19	77	.	0.275	.	.	.	strong	.	C2orf71	146	.	NM_001029883	exon2	c.3676_3677insAGC	p.E1226delinsSE	.	.	PASS	Pindel,Atlas-Indel
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	28	68	.	0.368	.	GGGCCC|0.831;-|0.169	0.169	strong	.	TSPYL6	54	.	NM_001003937	exon1	c.581_586del	p.194_196del	.	.	PASS	Pindel,Atlas-Indel
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609299	32609299	+	Frame_Shift_Del	DEL	A	A	-	rs199556640	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	72	0	1	0	A|0.857;-|0.143	0.143	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.294delC	p.I98fs	.	.	PASS	Atlas-Indel
ADAM28	10863	hgsc.bcm.edu	37	8	24184128	24184129	+	In_Frame_Ins	INS	-	-	ATC	rs111491080		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	83	269	.	0.294	.	-|0.500;ATC|0.500	0.500	weak	.	ADAM28	100	.	NM_014265	exon10	c.952_953insATC	p.Y318delinsYH	.	.	PASS	Pindel,Atlas-Indel
ARID1B	57492	hgsc.bcm.edu	37	6	157099402	157099403	+	In_Frame_Ins	INS	-	-	CAGCAG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	30	0	0.444444	0	.	.	none	.	ARID1B	320	.	NM_020732	exon1	c.339_340insCAGCAG	p.F113delinsFQQ	.	.	PASS	Atlas-Indel
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262109	39262138	+	In_Frame_Del	DEL	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	22	124	0	0.118919	0	.	.	none	.	KRTAP4-9	110	.	NM_001146041	exon1	c.468_497del	p.156_166del	.	.	PASS	Atlas-Indel
ANO7	50636	hgsc.bcm.edu	37	2	242163366	242163367	+	Frame_Shift_Del	DEL	CA	CA	-	rs60985508	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	16	92	.	0.184	.	CA|0.917;-|0.083	0.083	strong	.	ANO7	136	.	NM_001001891	exon24	c.2740_2741del	p.914_914del	.	.	PASS	Pindel,Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs139041445	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	517	78	424	.	0.151	.	.	.	strong	.	HAVCR1	84	.	NM_001099414	exon4	c.477_478insAAC	p.T159delinsTT	.	.	PASS	Pindel,Atlas-Indel
MUC20	200958	hgsc.bcm.edu	37	3	195447912	195447914	+	In_Frame_Del	DEL	TTC	TTC	-	rs201907823	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	62	268	0	0.168478	0	TTC|0.981;-|0.019	0.019	strong	.	MUC20	84	.	NM_152673	exon1	c.33_35del	p.11_12del	.	.	PASS	Atlas-Indel
FMO2	2327	hgsc.bcm.edu	37	1	171165803	171165803	+	Frame_Shift_Del	DEL	G	G	-	rs199532864		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	43	184	.	0.277	.	.	.	weak	.	FMO2	66	.	NM_001460	exon4	c.336delT	p.S112fs	.	.	PASS	Pindel,Atlas-Indel
KCNA7	3743	hgsc.bcm.edu	37	19	49573363	49573365	+	In_Frame_Del	DEL	GGA	GGA	-	rs10535426	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	27	64	.	0.360	.	GGA|0.851;-|0.149	0.149	strong	.	KCNA7	30	.	NM_031886	exon2	c.1327_1329del	p.443_443del	.	.	PASS	Pindel,Atlas-Indel
OR4L1	122742	hgsc.bcm.edu	37	14	20528449	20528467	+	Frame_Shift_Del	DEL	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	-	rs112192573	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	59	243	.	0.307	.	CATAGATTTGCTCACTGAC|0.504;-|0.496	0.496	strong	.	OR4L1	98	.	NM_001004717	exon1	c.245_263del	p.82_88del	.	.	PASS	Pindel,Atlas-Indel
SSPO	23145	hgsc.bcm.edu	37	7	149519007	149519007	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	54	181	.	0.273	.	.	.	none	.	.	.	.	NM_198455	exon90	c.12810delA	p.G4270fs	.	.	PASS	Pindel,Atlas-Indel
YWHAE	7531	hgsc.bcm.edu	37	17	1265304	1265305	+	Splice_Site	INS	-	-	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	15	53	0	0.220588	0	.	.	none	.	YWHAE	50	.	NM_006761	exon4	c.265-2->T	.	.	.	PASS	Atlas-Indel
CDCP2	200008	hgsc.bcm.edu	37	1	54610404	54610405	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	33	138	.	0.277	.	.	.	none	.	CDCP2	52	.	NM_201546	exon2	c.162_163del	p.54_55del	.	.	PASS	Pindel,Atlas-Indel
APLP2	334	hgsc.bcm.edu	37	11	129991653	129991658	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-	rs71750553	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	19	115	.	0.194	.	GAAGAG|0.892;-|0.108	0.108	strong	.	APLP2	71	.	NM_001243299	exon5	c.690_695del	p.230_232del	.	.	PASS	Pindel,Atlas-Indel
SSPO	23145	hgsc.bcm.edu	37	7	149503917	149503920	+	Frame_Shift_Del	DEL	GATA	GATA	-	rs72359812	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GATA	GATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	75	136	.	0.605	.	GATA|0.750;-|0.250	0.250	strong	.	.	.	.	NM_198455	exon59	c.8744_8745del	p.2915_2915del	.	.	PASS	Pindel,Atlas-Indel
NOTCH1	4851	hgsc.bcm.edu	37	9	139390649	139390650	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	38	113	.	0.322	.	.	.	none	.	NOTCH1	1980	.	NM_017617	exon34	c.7542_7543del	p.2514_2515del	.	.	PASS	Pindel,Atlas-Indel
MRM1	79922	hgsc.bcm.edu	37	17	34958760	34958761	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	12	29	.	0.364	.	.	.	none	.	MRM1	19	.	NM_024864	exon1	c.521_522insG	p.V174fs	.	.	PASS	Pindel,Atlas-Indel
IFNE	338376	hgsc.bcm.edu	37	9	21482239	21482241	+	RNA	DEL	AAT	AAT	-	rs34533918	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	11	37	.	0.262	.	AAT|0.882;-|0.118	0.118	strong	.	IFNE	16	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
CACNA1F	778	hgsc.bcm.edu	37	X	49076224	49076225	+	In_Frame_Ins	INS	-	-	TCC	rs112450928	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	24	84	.	0.214	.	-|0.908;TCC|0.092	0.092	strong	.	CACNA1F	218	.	NM_005183	exon20	c.2445_2446insGGA	p.E815delinsEE	.	.	PASS	Pindel,Atlas-Indel
TPSD1	23430	hgsc.bcm.edu	37	16	1306560	1306560	+	Frame_Shift_Del	DEL	G	G	-	rs3830782	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	105	199	0	0.530303	0	G|0.731;-|0.269	0.269	strong	.	TPSD1	47	.	NM_012217	exon2	c.125delA	p.Q42fs	.	.	PASS	Atlas-Indel
SSC5D	284297	hgsc.bcm.edu	37	19	56029616	56029617	+	In_Frame_Ins	INS	-	-	CCA	rs150781976	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	50	165	0	0.331126	0	.	.	strong	.	SSC5D	65	.	NM_001144950	exon14	c.3973_3974insCCA	p.P1325delinsPT	.	.	PASS	Atlas-Indel
CCDC34	91057	hgsc.bcm.edu	37	11	27384449	27384466	+	In_Frame_Del	DEL	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	-	rs138931796	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	39	294	.	0.181	.	TCATCCACGTCTTCCTCA|0.966;-|0.034	0.034	strong	.	CCDC34	48	.	NM_030771	exon1	c.277_294del	p.93_98del	.	.	PASS	Pindel,Atlas-Indel
ZNF717	100131827	hgsc.bcm.edu	37	3	75790810	75790811	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	12	7	0	0.15	0	.	.	none	.	ZNF717	160	.	NM_001128223	exon3	c.135_136insA	p.T45fs	.	.	PASS	Atlas-Indel
PEBP4	157310	hgsc.bcm.edu	37	8	22570908	22570908	+	Frame_Shift_Del	DEL	T	T	-	rs35121552	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	38	158	.	0.260	.	T|0.680;-|0.320	0.320	strong	.	PEBP4	23	.	NM_144962	exon7	c.660delC	p.N220fs	.	.	PASS	Pindel,Atlas-Indel
ZFHX3	463	hgsc.bcm.edu	37	16	72831357	72831358	+	In_Frame_Ins	INS	-	-	TTG	rs372909378	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	51	198	0	0.277174	0	.	.	weak	.	ZFHX3	404	.	NM_006885	exon9	c.5224_5225insCAA	p.A1742delinsQA	.	.	PASS	Atlas-Indel
PDE6H	5149	hgsc.bcm.edu	37	12	15134337	15134337	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	33	110	.	0.311	.	.	.	none	.	PDE6H	13	.	NM_006205	exon4	c.178delA	p.I60fs	.	.	PASS	Pindel,Atlas-Indel
ZNF474	133923	hgsc.bcm.edu	37	5	121488636	121488636	+	Frame_Shift_Del	DEL	T	T	-	rs3217313	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	12	21	0	0.315789	0	T|0.822;-|0.178	0.178	strong	.	ZNF474	43	.	NM_207317	exon2	c.950delA	p.N317fs	.	.	PASS	Atlas-Indel
CLECL1	160365	hgsc.bcm.edu	37	12	9885707	9885708	+	Frame_Shift_Ins	INS	-	-	TAAGT	rs71045297	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	44	110	.	0.376	.	-|0.485;TAAGT|0.515	0.515	strong	.	CLECL1	18	.	NM_001267701	exon1	c.154_155insACTTA	p.S52fs	.	.	PASS	Pindel,Atlas-Indel
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77334292	77334293	+	In_Frame_Ins	INS	-	-	CAGCAA	rs201548881	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	63	93	0	0.463235	0	-|0.929;CAGCAA|0.071	0.071	strong	.	ST6GALNAC5	59	.	NM_030965	exon2	c.126_127insCAGCAA	p.Q42delinsQQQ	.	.	PASS	Atlas-Indel
NUP155	9631	hgsc.bcm.edu	37	5	37309372	37309374	+	Splice_Site	DEL	AGA	AGA	-	rs3835198	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	23	52	.	0.434	.	AGA|0.730;-|0.270	0.270	strong	.	NUP155	116	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
PABPC1	26986	hgsc.bcm.edu	37	8	101721933	101721933	+	Frame_Shift_Del	DEL	T	T	-	rs112966887	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	39	112	0	0.207447	0	T|0.500;-|0.500	0.500	strong	.	PABPC1	76	.	NM_002568	exon8	c.1000delG	p.G334fs	.	.	PASS	Atlas-Indel
FOXD4L3	286380	hgsc.bcm.edu	37	9	70918118	70918119	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	469	74	316	0	0.157783	0	.	.	none	.	FOXD4L3	7	.	NM_199135	exon1	c.250_251del	p.84_84del	.	.	PASS	Atlas-Indel
C10orf113	387638	hgsc.bcm.edu	37	10	21435341	21435344	+	Frame_Shift_Del	DEL	CACT	CACT	-	rs72102767	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CACT	CACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	59	130	.	0.391	.	CACT|0.769;-|0.231	0.231	strong	.	C10orf113	32	.	NM_001177483	exon1	c.95_98del	p.32_33del	.	.	PASS	Pindel,Atlas-Indel
DEFB126	81623	hgsc.bcm.edu	37	20	126311	126312	+	Frame_Shift_Del	DEL	CC	CC	-	rs11467417	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	12	34	.	0.500	.	CC|0.459;-|0.541	0.541	strong	.	DEFB126	52	.	NM_030931	exon2	c.313_314del	p.105_105del	.	.	PASS	Pindel,Atlas-Indel
HSPBAP1	79663	hgsc.bcm.edu	37	3	122459290	122459291	+	In_Frame_Ins	INS	-	-	AGA	rs16338	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	71	296	.	0.240	.	-|0.847;AGA|0.153	0.153	strong	HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	NM_024610	exon8	c.1369_1370insTCT	p.Q457delinsSQ	.	.	PASS	Pindel,Atlas-Indel
ZNF717	100131827	hgsc.bcm.edu	37	3	75787812	75787813	+	Frame_Shift_Ins	INS	-	-	T	rs138918118		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	10	31	0	0.142857	0	.	.	weak	ZNF717,rectum,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.962_963insA	p.S321fs	.	.	PASS	Atlas-Indel
AXDND1	126859	hgsc.bcm.edu	37	1	179504026	179504028	+	In_Frame_Del	DEL	AAG	AAG	-	rs141228272	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	53	219	.	0.261	.	AAG|0.640;-|0.360	0.360	strong	.	AXDND1	142	.	NM_144696	exon25	c.2959_2961del	p.987_987del	.	.	PASS	Pindel,Atlas-Indel
C14orf23	387978	hgsc.bcm.edu	37	14	29261309	29261310	+	RNA	INS	-	-	AAC	rs56025822	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	29	111	.	0.315	.	AAC|1.000	.	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
SUMF2	25870	hgsc.bcm.edu	37	7	56140760	56140761	+	Frame_Shift_Del	DEL	TT	TT	-	rs146946713	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	43	105	.	0.426	.	TT|0.993;-|0.007	0.007	strong	.	SUMF2	56	.	NM_001130069	exon3	c.351_352del	p.117_118del	.	.	PASS	Pindel,Atlas-Indel
ATG2B	55102	hgsc.bcm.edu	37	14	96790337	96790338	+	Splice_Site	INS	-	-	A	rs34296665	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	17	24	.	0.607	.	-|0.648;A|0.352	0.352	strong	.	ATG2B	169	.	NM_018036	exon17	c.2438-2->T	.	.	.	PASS	Pindel
RBM12B	389677	hgsc.bcm.edu	37	8	94747893	94747895	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	45	151	.	0.336	.	.	.	none	.	RBM12B	78	.	NM_203390	exon3	c.745_747del	p.249_249del	.	.	PASS	Pindel
RPGR	6103	hgsc.bcm.edu	37	X	38145694	38145717	+	In_Frame_Del	DEL	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	24	100	.	0.200	.	.	.	none	.	RPGR	175	.	NM_001034853	exon15	c.2536_2559del	p.846_853del	.	.	PASS	Pindel
RELN	5649	hgsc.bcm.edu	37	7	103301976	103301977	+	Splice_Site	INS	-	-	A	rs146986040	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	14	81	.	0.206	.	.	.	strong	.	RELN	593	.	NM_005045	exon13	c.1290-2->T	.	.	.	PASS	Pindel
NADK	65220	hgsc.bcm.edu	37	1	1684348	1684350	+	In_Frame_Del	DEL	CCT	CCT	-	rs150880809	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	29	82	.	0.225	.	.	.	strong	.	NADK	79	.	NM_001198994	exon14	c.1770_1772del	p.590_591del	.	.	PASS	Pindel
ZNF271	10778	hgsc.bcm.edu	37	18	32889822	32889823	+	RNA	INS	-	-	ATTGGTGTCCAAAACTGACACA	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	16	43	.	0.364	.	.	.	none	.	ZNF271	16	.	.	.	.	.	.	.	PASS	Pindel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	In_Frame_Del	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs139735565	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	23	108	.	0.219	.	-|0.223;G|0.777	0.223	alt	.	KIAA1751	92	.	NM_001080484	exon18	c.2195_2215del	p.732_739del	.	.	PASS	Pindel
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs200486992	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	369	59	349	.	0.160	.	.	.	alt	.	DSPP	174	.	NM_014208	exon5	c.2018_2019insTAGCAGTGACAGCAGCAG	p.D673delinsDSSDSSS	.	.	PASS	Pindel
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778799	+	Frame_Shift_Del	DEL	GTTG	GTTG	-	rs59660444	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTTG	GTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	36	55	.	0.621	.	-|0.300;G|0.700	0.300	alt	.	ZNF233	73	.	NM_001207005	exon5	c.1982_1985del	p.661_662del	.	.	PASS	Pindel
ODF1	4956	hgsc.bcm.edu	37	8	103573020	103573037	+	In_Frame_Del	DEL	TGCAGCCCCTGCAACCCG	TGCAGCCCCTGCAACCCG	-	rs143802899	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCAGCCCCTGCAACCCG	TGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	16	142	.	0.160	.	.	.	strong	.	ODF1	55	.	NM_024410	exon2	c.660_677del	p.220_226del	.	.	PASS	Pindel
KRT3	3850	hgsc.bcm.edu	37	12	53189414	53189431	+	In_Frame_Del	DEL	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	35	162	.	0.210	.	.	.	none	.	KRT3	65	.	NM_057088	exon1	c.397_414del	p.133_138del	.	.	PASS	Pindel
TMEM87B	84910	hgsc.bcm.edu	37	2	112832536	112832538	+	In_Frame_Del	DEL	AAT	AAT	-	rs71385858	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	53	263	.	0.229	.	AAT|0.722;-|0.278	0.278	strong	.	TMEM87B	52	.	NM_032824	exon5	c.497_499del	p.166_167del	.	.	PASS	Pindel
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503916	+	Frame_Shift_Del	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	25	199	.	0.181	.	.	.	none	.	.	.	.	NM_182614	exon6	c.499_509del	p.167_170del	.	.	PASS	Pindel
HNRNPU-AS1	284702	hgsc.bcm.edu	37	1	245008378	245008380	+	RNA	DEL	TTG	TTG	-	rs147190115	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	10	25	.	0.323	.	TTG|0.891;-|0.109	0.109	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
ZNF107	51427	hgsc.bcm.edu	37	7	64169019	64169019	+	Frame_Shift_Del	DEL	G	G	-	rs199594424	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	13	43	.	0.310	.	.	.	alt	.	ZNF107	107	.	NM_016220	exon7	c.2336delA	p.E779fs	.	.	PASS	Pindel
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	48	305	.	0.172	.	.	.	none	.	SELPLG	138	.	NM_001206609	exon2	c.453_482del	p.151_161del	.	.	PASS	Pindel
GPSM2	29899	hgsc.bcm.edu	37	1	109465166	109465168	+	In_Frame_Del	DEL	CTT	CTT	-	rs35029887	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	40	196	.	0.274	.	CTT|0.700;-|0.300	0.300	strong	.	GPSM2	56	.	NM_013296	exon13	c.1567_1569del	p.523_523del	.	.	PASS	Pindel
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	26	137	.	0.289	.	.	.	none	KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	NM_033188	exon1	c.245_246insGCCCCAGCTGCTGCC	p.Q82delinsRPSCCQ	.	.	PASS	Pindel
ABCF1	23	hgsc.bcm.edu	37	6	30545854	30545854	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	10	65	.	0.161	.	.	.	none	.	ABCF1	61	.	NM_001090	exon4	c.217delC	p.Q73fs	.	.	PASS	Pindel
PRKCSH	5589	hgsc.bcm.edu	37	19	11558341	11558343	+	In_Frame_Del	DEL	GAG	GAG	-	rs3217229	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	55	150	.	0.314	.	GAG|0.500;-|0.500	0.500	strong	.	PRKCSH	55	.	NM_001001329	exon11	c.936_938del	p.312_313del	.	.	PASS	Pindel
CALHM3	119395	hgsc.bcm.edu	37	10	105233174	105233175	+	In_Frame_Ins	INS	-	-	GGGGGCTCAGGCACTGCG	rs143800079	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	11	102	.	0.157	.	-|0.871;GGGGGCTCAGGCACTGCG|0.129	0.129	strong	.	CALHM3	46	.	NM_001129742	exon3	c.831_832insCGCAGTGCCTGAGCCCCC	p.P277delinsPAVPEPP	.	.	PASS	Pindel
ACIN1	22985	hgsc.bcm.edu	37	14	23549879	23549881	+	In_Frame_Del	DEL	TCC	TCC	-	rs3841035	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	29	150	.	0.169	.	.	.	strong	.	ACIN1	147	.	NM_014977	exon6	c.838_840del	p.280_280del	.	.	PASS	Pindel
PCSK9	255738	hgsc.bcm.edu	37	1	55505552	55505553	+	In_Frame_Ins	INS	-	-	CTG	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	13	63	.	0.167	.	.	.	none	.	PCSK9	76	.	NM_174936	exon1	c.42_43insCTG	p.P14delinsPL	.	.	PASS	Pindel
C11orf40	143501	hgsc.bcm.edu	37	11	4592706	4592707	+	Frame_Shift_Ins	INS	-	-	AC	rs141600462	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	46	152	.	0.286	.	-|0.377;AC|0.623	0.623	strong	.	C11orf40	37	.	NM_144663	exon4	c.601_602insGT	p.M201fs	.	.	PASS	Pindel
ATR	545	hgsc.bcm.edu	37	3	142274740	142274740	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	17	60	.	0.230	.	.	.	none	.	ATR	285	.	NM_001184	exon10	c.2321delT	p.I774fs	.	.	PASS	Pindel
PA2G4	5036	hgsc.bcm.edu	37	12	56500502	56500503	+	Splice_Site	INS	-	-	A	rs34728522	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	12	32	.	0.343	.	-|0.250;A|0.750	0.750	weak	.	PA2G4	24	.	NM_006191	exon2	c.217+2->A	.	.	.	PASS	Pindel
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	In_Frame_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs372974824	byfrequency;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	19	161	.	0.154	.	-|0.574;CACCAGGAAGCG|0.426	0.574	alt	.	CELA1	39	.	NM_001971	exon1	c.8_16del	p.3_6del	.	.	PASS	Pindel
CRELD2	79174	hgsc.bcm.edu	37	22	50315936	50315973	+	Frame_Shift_Del	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	29	50	.	0.935	.	.	.	none	.	CRELD2	57	.	NM_001135101	exon6	c.593_620del	p.198_207del	.	.	PASS	Pindel
NFKB1	4790	hgsc.bcm.edu	37	4	103534740	103534741	+	Splice_Site	INS	-	-	A	rs148268461	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	17	82	.	0.270	.	-|0.899;A|0.101	0.101	strong	.	NFKB1	78	.	NM_001165412	exon23	c.2746+2->A	.	.	.	PASS	Pindel
RPL14	9045	hgsc.bcm.edu	37	3	40503521	40503529	+	In_Frame_Del	DEL	CTGCTGCTG	CTGCTGCTG	-	rs147295890	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTGCTGCTG	CTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	27	58	.	0.333	.	.	.	strong	.	RPL14	21	.	NM_001034996	exon6	c.445_453del	p.149_151del	.	.	PASS	Pindel
SERPINB3	6317	hgsc.bcm.edu	37	18	61323012	61323014	+	In_Frame_Del	DEL	CCT	CCT	-	rs60533853	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	42	211	.	0.221	.	.	.	alt	.	SERPINB3	90	.	NM_006919	exon8	c.1051_1053del	p.351_351del	.	.	PASS	Pindel
NKAP	79576	hgsc.bcm.edu	37	X	119070328	119070330	+	In_Frame_Del	DEL	GAT	GAT	-	rs10577974	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	366	93	447	.	0.254	.	.	.	weak	.	NKAP	53	.	NM_024528	exon4	c.604_606del	p.202_202del	.	.	PASS	Pindel
RPGR	6103	hgsc.bcm.edu	37	X	38145199	38145201	+	In_Frame_Del	DEL	TCC	TCC	-	rs200955614	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	10	29	.	0.182	.	TCC|0.992;-|0.008	0.008	strong	.	RPGR	175	.	NM_001034853	exon15	c.3052_3054del	p.1018_1018del	.	.	PASS	Pindel
ZNF720	124411	hgsc.bcm.edu	37	16	31770696	31770697	+	Frame_Shift_Ins	INS	-	-	A	rs34487972	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	64	232	.	0.318	.	A|1.000;|0.000	1.000	strong	.	ZNF720	15	.	NM_001130913	exon5	c.380_381insA	p.X127delinsX	.	.	PASS	Pindel
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606121	1606150	+	In_Frame_Del	DEL	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	45	277	.	0.294	.	.	.	none	.	KRTAP5-1	74	.	NM_001005922	exon1	c.331_360del	p.111_120del	.	.	PASS	Pindel
CLDN16	10686	hgsc.bcm.edu	37	3	190106073	190106074	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	38	205	.	0.160	.	.	.	none	.	CLDN16	59	.	NM_006580	exon1	c.164_165del	p.55_55del	.	.	PASS	Pindel
CYP2F1	1572	hgsc.bcm.edu	37	19	41622107	41622108	+	Frame_Shift_Ins	INS	-	-	C	rs3833221	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	59	105	.	0.584	.	-|0.741;C|0.259	0.259	strong	.	CYP2F1	60	.	NM_000774	exon2	c.14_15insC	p.S5fs	.	.	PASS	Pindel
DMKN	93099	hgsc.bcm.edu	37	19	36002371	36002394	+	In_Frame_Del	DEL	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	25	91	.	0.278	.	.	.	none	.	DMKN	116	.	NM_033317	exon5	c.838_861del	p.280_287del	.	.	PASS	Pindel
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197501	39197638	+	In_Frame_Del	DEL	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	43	224	.	0.188	.	.	.	none	.	KRTAP1-1	23	.	NM_030967	exon1	c.13_150del	p.5_50del	.	.	PASS	Pindel
KAT6B	23522	hgsc.bcm.edu	37	10	76781906	76781908	+	In_Frame_Del	DEL	GAA	GAA	-	rs71929101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	59	162	.	0.396	.	GAA|0.500;-|0.500	0.500	strong	MYST4,colon,carcinoma,0,1	.	.	1	NM_012330	exon16	c.3288_3290del	p.1096_1097del	.	.	PASS	Pindel
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653375	121653377	+	In_Frame_Del	DEL	TGA	TGA	-	rs35947407	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	39	124	.	0.277	.	TGA|0.585;-|0.415	0.415	strong	PTPRZ1,leg,malignant_melanoma,-1,1	PTPRZ1	605	1	NM_002851	exon12	c.4274_4276del	p.1425_1426del	.	.	PASS	Pindel
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261306	+	RNA	INS	-	-	AAC	rs200251419	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	29	112	.	0.315	.	-|0.668;AAC|0.332	0.332	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Pindel
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012225	46012226	+	In_Frame_Ins	INS	-	-	CAGCAGCTGGGGGCA	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	14	93	.	0.241	.	.	.	none	.	KRTAP10-6	57	.	NM_198688	exon1	c.141_142insTGCCCCCAGCTGCTG	p.C47delinsCAPSCC	.	.	PASS	Pindel
ACTRT2	140625	hgsc.bcm.edu	37	1	2938408	2938410	+	In_Frame_Del	DEL	AGA	AGA	-	rs4013154	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	33	103	.	0.270	.	AGA|0.848;-|0.152	0.152	strong	ACTRT2,NS,carcinoma,-1,1	ACTRT2	69	1	NM_080431	exon1	c.157_159del	p.53_53del	.	.	PASS	Pindel
GPRASP2	114928	hgsc.bcm.edu	37	X	101970172	101970183	+	In_Frame_Del	DEL	GGCCCAGGCATG	GGCCCAGGCATG	-	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGCCCAGGCATG	GGCCCAGGCATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	38	90	.	0.463	.	.	.	none	.	GPRASP2	89	.	NM_138437	exon4	c.374_385del	p.125_129del	.	.	PASS	Pindel
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs10617561	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	21	79	.	0.273	.	GCA|0.779;-|0.221	0.221	strong	.	TNRC6B	195	.	NM_001162501	exon15	c.3959_3961del	p.1320_1321del	.	.	PASS	Pindel
GPR39	2863	hgsc.bcm.edu	37	2	133403034	133403036	+	In_Frame_Del	DEL	AGA	AGA	-	rs113224054	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	10	26	.	0.435	.	AGA|0.500;-|0.500	0.500	weak	.	GPR39	60	.	NM_001508	exon2	c.1216_1218del	p.406_406del	.	.	PASS	Pindel
PTTG2	10744	hgsc.bcm.edu	37	4	37962609	37962610	+	Frame_Shift_Del	DEL	AT	AT	-	rs200376306	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	43	113	.	0.406	.	AT|0.986;-|0.014	0.014	strong	.	PTTG2	15	.	NM_006607	exon1	c.553_554del	p.185_185del	.	.	PASS	Pindel
RPF2	84154	hgsc.bcm.edu	37	6	111310252	111310252	+	Missense_Mutation	SNP	G	G	A	rs6909298	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	66	113	0	0.496241	0	G|0.977;A|0.023	0.023	strong	.	RPF2	26	.	NM_032194	exon3	c.G178A	p.G60S	CCATACGGTGTAC	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139370829	139370829	+	Silent	SNP	G	G	A	rs114386206	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	45	89	0	0.371901	0	G|0.996;A|0.004	0.004	strong	.	SEC16A	249	.	NM_014866	exon3	c.C1239T	p.P413P	AGGTGCGGGCGGA	.	PASS	Atlas-SNP
CTBS	1486	hgsc.bcm.edu	37	1	85039955	85039955	+	Silent	SNP	G	G	A	rs2303307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	60	94	0	0.504202	0	G|0.741;A|0.259	0.259	strong	CTBS,rectum,carcinoma,0,1	CTBS	24	1	NM_004388	exon1	c.C144T	p.L48L	GCGGCAGAGCTCA	.	PASS	Atlas-SNP
ZNF700	90592	hgsc.bcm.edu	37	19	12059467	12059467	+	Missense_Mutation	SNP	C	C	G	rs73509026	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	65	128	0	0.560345	0	C|0.940;G|0.060	0.060	strong	ZNF700,NS,carcinoma,-1,1	ZNF700	81	1	NM_001271848	exon4	c.C637G	p.R213G	AGCATTCGAAGAC	.	PASS	Atlas-SNP
EIF2A	83939	hgsc.bcm.edu	37	3	150285535	150285535	+	Silent	SNP	T	T	C	rs376872417		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	95	174	0	0.508021	0	.	.	weak	.	EIF2A	59	.	NM_032025	exon7	c.T531C	p.P177P	ATCACCTGGACCC	.	PASS	Atlas-SNP
TNPO2	30000	hgsc.bcm.edu	37	19	12813683	12813683	+	Silent	SNP	T	T	C	rs16978630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	141	310	0	0.449045	0	T|0.866;C|0.134	0.134	strong	.	TNPO2	108	.	NM_013433	exon20	c.A2259G	p.E753E	AATGATTTCCACC	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280053	39280053	+	Missense_Mutation	SNP	T	T	A	rs622950	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	119	103	0	0.708333	0	T|0.831;A|0.169	0.169	strong	.	KRTAP4-12	32	.	NM_031854	exon1	c.A322T	p.T108S	AGGTGGTCTGACA	.	PASS	Atlas-SNP
PTPRA	5786	hgsc.bcm.edu	37	20	2945759	2945759	+	Missense_Mutation	SNP	C	C	T	rs1178027	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	44	83	0	0.52381	0	C|0.738;T|0.262	0.262	strong	PTPRA,NS,carcinoma,0,1	PTPRA	75	1	NM_002836	exon9	c.C326T	p.P109L	GGCTTCCAGATAA	.	PASS	Atlas-SNP
MBTPS2	51360	hgsc.bcm.edu	37	X	21861434	21861434	+	Silent	SNP	A	A	G	rs3213451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	71	154	0	0.427711	0	A|0.567;G|0.433	0.433	strong	.	MBTPS2	52	.	NM_015884	exon2	c.A222G	p.Q74Q	TTACCAATGGTAT	.	PASS	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46917868	46917868	+	Missense_Mutation	SNP	A	A	G	rs7926667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	7	28	0	0.318182	0	A|0.948;G|0.052	0.052	strong	.	LRP4	160	.	NM_002334	exon9	c.T941C	p.L314S	TGGTCCAAGGCAC	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77376633	77376633	+	Silent	SNP	A	A	G	rs2274925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	138	220	1	0.64486	0.00454545	A|0.851;G|0.149	0.149	strong	.	TRPM6	377	.	NM_017662	exon27	c.T4764C	p.N1588N	TTGAGTATTCTTC	.	PASS	Atlas-SNP
EHBP1L1	254102	hgsc.bcm.edu	37	11	65347723	65347723	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	3	78	0	0.0309278	0	.	.	none	EHBP1L1,colon,carcinoma,-1,1	EHBP1L1	64	1	NM_001099409	exon5	c.C484T	p.R162C	GAGGGCCGTGCCA	.	scavenged	Atlas-SNP
DTX4	23220	hgsc.bcm.edu	37	11	58949852	58949852	+	Silent	SNP	C	C	T	rs75403375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	25	45	0	0.510204	0	C|0.975;T|0.025	0.025	strong	.	DTX4	84	.	NM_015177	exon2	c.C852T	p.T284T	CAAGACCGGAAGG	.	PASS	Atlas-SNP
CDK11B	984	hgsc.bcm.edu	37	1	1571841	1571841	+	Missense_Mutation	SNP	A	A	C	rs150949339	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	47	166	1	0.21267	0.0060241	A|0.994;C|0.006	0.006	strong	CDK11A,rectum,carcinoma,0,5	CDK11B	37	5	NM_033486	exon18	c.T1914G	p.D638E	CCCCAGATCCTGA	.	scavenged	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26699159	26699159	+	Silent	SNP	C	C	T	rs4997760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	51	80	0	0.653846	0	C|0.956;T|0.044	0.044	strong	.	OTOF	524	.	NM_194248	exon23	c.G2703A	p.S901S	GCCTGCCGAGCCG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88965040	88965040	+	Missense_Mutation	SNP	C	C	T	rs56948780	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	65	135	0	0.5	0	C|0.964;T|0.036	0.036	strong	.	ZNF804B	322	.	NM_181646	exon4	c.C2744T	p.T915I	CAAACACTGCAGA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547162	132547162	+	Silent	SNP	G	G	A	rs55938102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	132	233	1	0.503817	0.00429185	G|0.890;A|0.110	0.110	strong	.	EP400	370	.	NM_015409	exon47	c.G8250A	p.T2750T	GACGACGACGACC	.	PASS	Atlas-SNP
IFNA13	3447	hgsc.bcm.edu	37	9	21367519	21367519	+	Missense_Mutation	SNP	G	G	C	rs28383794	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	592	229	569	1	0.386824	0.00175747	G|0.832;C|0.168	0.168	strong	.	IFNA13	19	.	NM_006900	exon1	c.C491G	p.A164G	TCCCAGGCACAAG	.	PASS	Atlas-SNP
ARAP2	116984	hgsc.bcm.edu	37	4	36152584	36152584	+	Silent	SNP	G	G	T	rs13148785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	52	92	0	0.477064	0	G|0.916;T|0.084	0.084	strong	.	ARAP2	210	.	NM_015230	exon16	c.C2835A	p.T945T	ATTAATGGTGCCA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	497	391	383	0	0.78672	0	G|0.837;A|0.163	0.163	strong	PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	NM_023014	exon4	c.G1124A	p.C375Y	TGAGCTGCTGCTC	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969501	49969501	+	Silent	SNP	G	G	A	rs61732839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	20	40	0	0.4	0	G|0.975;A|0.025	0.025	strong	.	ALDH16A1	54	.	NM_153329	exon14	c.G1899A	p.A633A	TCGGGCGTGGGGG	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22846962	22846962	+	Missense_Mutation	SNP	G	G	C	rs138844698	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	119	281	2	0.74375	0.00711744	G|0.957;C|0.043	0.043	strong	.	ZNF492	129	.	NM_020855	exon4	c.G491C	p.S164T	TTCATAGTGGAGA	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901109	52901109	+	Missense_Mutation	SNP	T	T	C	rs61731676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	38	55	0	0.457831	0	T|0.982;C|0.018	0.018	strong	.	.	.	.	NM_019600	exon6	c.A2002G	p.K668E	AGAATTTTGGATT	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	31946282	31946282	+	Silent	SNP	T	T	C	rs16989753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	65	109	0	0.464286	0	T|0.966;C|0.034	0.034	strong	.	SFI1	78	.	NM_001007467	exon6	c.T492C	p.Y164Y	GACCTATGTGCGT	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105658460	105658460	+	Missense_Mutation	SNP	C	C	G	rs73195662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	55	0	0.407407	0	C|0.945;G|0.055	0.055	strong	.	CDHR3	153	.	NM_152750	exon12	c.C1595G	p.T532S	AAACAACCCCCAT	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57181629	57181629	+	Missense_Mutation	SNP	C	C	T	rs61750793	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	28	33	0	0.622222	0	C|0.760;T|0.240	0.240	strong	.	KIAA1211	178	.	NM_020722	exon8	c.C1961T	p.P654L	CTAAGCCCCGCCA	.	PASS	Atlas-SNP
WDR85	92715	hgsc.bcm.edu	37	9	140472034	140472034	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	92	106	0	0.691729	0	.	.	none	.	WDR85	20	.	NM_138778	exon2	c.C175G	p.P59A	CCTGAGGCTCCTT	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117097931	117097931	+	Silent	SNP	C	C	T	rs45528535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	28	78	0	0.35443	0	C|0.956;T|0.044	0.044	strong	PCSK7,NS,carcinoma,-2,1	PCSK7	59	1	NM_004716	exon5	c.G711A	p.A237A	CACAGCCGCGATC	.	PASS	Atlas-SNP
TRIM5	85363	hgsc.bcm.edu	37	11	5688940	5688940	+	Missense_Mutation	SNP	C	C	T	rs11038628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	45	79	0	0.633803	0	C|0.821;T|0.179	0.179	strong	.	TRIM5	111	.	NM_033093	exon5	c.G746A	p.G249D	TCCACACCCTAGG	.	PASS	Atlas-SNP
ADRB1	153	hgsc.bcm.edu	37	10	115805057	115805057	+	Missense_Mutation	SNP	G	G	T	rs17875445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	17	36	0	0.459459	0	G|0.994;T|0.006	0.006	strong	.	ADRB1	16	.	NM_000684	exon1	c.G1166T	p.G389V	TCCAGGGACTGCT	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226050503	226050503	+	Silent	SNP	G	G	A	rs10915888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	108	170	0	0.53202	0	G|0.956;A|0.044	0.044	strong	.	TMEM63A	75	.	NM_014698	exon11	c.C795T	p.N265N	GGCCACGTTGTAG	.	PASS	Atlas-SNP
EEA1	8411	hgsc.bcm.edu	37	12	93202801	93202801	+	Silent	SNP	C	C	T	rs7970286	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	56	112	0	0.495575	0	C|0.618;T|0.382	0.382	strong	.	EEA1	104	.	NM_003566	exon18	c.G2331A	p.E777E	TTCCTTCTCCATT	.	PASS	Atlas-SNP
ARNT2	9915	hgsc.bcm.edu	37	15	80873642	80873642	+	Silent	SNP	C	C	G	rs79914316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	97	149	0	0.5	0	C|0.947;G|0.053	0.053	strong	.	ARNT2	88	.	NM_014862	exon17	c.C1815G	p.T605T	CCACACCTACCCG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113265448	113265448	+	Silent	SNP	A	A	G	rs10120982	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	59	186	0	0.292079	0	A|0.992;G|0.008	0.008	strong	SVEP1,NS,carcinoma,-1,2	SVEP1	326	2	NM_153366	exon6	c.T1353C	p.C451C	TGTAGAACAGCTG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	81	102	0	1	0	C|0.538;N|0.000	0.538	strong	.	HMCN1	797	.	NM_031935	exon46	c.T7253C	p.I2418T	CTTCCATAACCTG	.	PASS	Atlas-SNP
ADAMTS15	170689	hgsc.bcm.edu	37	11	130318935	130318935	+	Silent	SNP	C	C	A	rs146878786	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	24	82	0	0.40678	0	C|0.997;A|0.003	0.003	strong	.	ADAMTS15	103	.	NM_139055	exon1	c.C67A	p.R23R	CCAGAGCGGGAGG	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506211	11506211	+	Missense_Mutation	SNP	A	A	C	rs76504934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1306	421	425	0	0.322358	0	A|0.446;C|0.554	0.554	strong	PRB1,NS,carcinoma,0,1	PRB1	33	1	NM_199353	exon4	c.T427G	p.S143A	GAGGAGATCGGGC	.	PASS	Atlas-SNP
ALX4	60529	hgsc.bcm.edu	37	11	44286722	44286722	+	Silent	SNP	C	C	T	rs145904583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	109	267	0	0.493213	0	C|0.991;T|0.009	0.009	strong	ALX4,NS,carcinoma,0,1	ALX4	58	1	NM_021926	exon4	c.G918A	p.P306P	CCAGGACGGGTTC	.	PASS	Atlas-SNP
ZNF729	100287226	hgsc.bcm.edu	37	19	22499853	22499853	+	Missense_Mutation	SNP	A	A	G	rs78300029	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	5	15	0	0.416667	0	A|0.971;G|0.029	0.029	strong	.	ZNF729	78	.	NM_001242680	exon4	c.A3634G	p.R1212G	CATACCAGAGAGA	.	PASS	Atlas-SNP
PKP2	5318	hgsc.bcm.edu	37	12	33031023	33031023	+	Missense_Mutation	SNP	G	G	A	rs62001016	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	47	85	0	0.484536	0	G|0.988;A|0.012	0.012	strong	.	PKP2	110	.	NM_004572	exon3	c.C791T	p.A264V	AGCCCTGCCGTCA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919928	12919928	+	Missense_Mutation	SNP	A	A	G	rs72472698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	78	141	0	0.58209	0	A|0.885;G|0.115	0.115	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.A668G	p.K223R	TAAGAAAGCTTTA	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16890243	16890243	+	Missense_Mutation	SNP	C	C	G	rs773930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	48	74	0	0.505263	0	C|0.826;G|0.174	0.174	strong	.	NWD1	303	.	NM_001007525	exon12	c.C2698G	p.Q900E	GAAGAGCAGCATG	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30702602	30702602	+	Missense_Mutation	SNP	T	T	C	rs323345	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	192	178	1	0.994819	0.00561798	T|0.707;C|0.293	0.293	strong	.	TEX15	350	.	NM_031271	exon1	c.A3932G	p.N1311S	ATAATGTTTTGTT	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35434512	35434512	+	Silent	SNP	T	T	C	rs2651109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	108	120	1	0.981818	0.00833333	T|0.345;C|0.655	0.655	strong	.	ZNF30	44	.	NM_001099438	exon5	c.T645C	p.S215S	TATTAGTGGTAGC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149488991	149488991	+	Missense_Mutation	SNP	T	T	C	rs893601	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	40	95	0	0.481928	0	T|0.976;C|0.024	0.024	strong	.	.	.	.	NM_198455	exon35	c.T5332C	p.S1778P	TGCCACTCACCCC	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15604508	15604508	+	Missense_Mutation	SNP	C	C	G	rs144115902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	110	263	0	0.495495	0	C|0.978;G|0.022	0.022	strong	.	ZNF286A	58	.	NM_020652	exon3	c.C80G	p.T27R	AGAGCACAGAAGA	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	95167	95167	+	Silent	SNP	G	G	A	rs202227666	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	8	125	0	0.0540541	0	G|0.980;A|0.019	0.019	strong	TUBB8,colon,carcinoma,-2,2	TUBB8	62	2	NM_177987	exon1	c.C12T	p.I4I	GAGCACGATCTCC	.	scavenged	Atlas-SNP
GUCA2B	2981	hgsc.bcm.edu	37	1	42619139	42619139	+	Silent	SNP	A	A	G	rs1047047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	28	66	0	0.451613	0	A|0.756;G|0.244	0.244	strong	.	GUCA2B	9	.	NM_007102	exon1	c.A18G	p.A6A	GGCTGCATCAGGG	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	10027542	10027542	+	Missense_Mutation	SNP	C	C	T	rs6820230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	124	0	0.515152	0	C|0.682;T|0.318	0.318	strong	SLC2A9,NS,carcinoma,+2,1	SLC2A9	158	1	NM_001001290	exon2	c.G49A	p.A17T	TTTTCGCTGAATC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531426	140531426	+	Missense_Mutation	SNP	G	G	A	rs146552509	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	405	16	297	0	0.0395062	0	G|0.994;A|0.006	0.006	strong	PCDHB6,trunk,malignant_melanoma,0,2	PCDHB6	161	2	NM_018939	exon1	c.G1588A	p.G530S	CGCGTGGGCGCCA	.	scavenged	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261994	39261994	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	3	108	0	0.032967	0	.	.	none	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	NM_001146041	exon1	c.G354A	p.R118R	CCCTAGGTGCTGC	.	scavenged	Atlas-SNP
ADAM33	80332	hgsc.bcm.edu	37	20	3650205	3650205	+	Missense_Mutation	SNP	G	G	A	rs2280090	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	65	144	0	0.481481	0	G|0.871;A|0.129	0.129	strong	.	ADAM33	76	.	NM_025220	exon20	c.C2320T	p.P774S	GCCAGGGCTGTCC	.	PASS	Atlas-SNP
ITIH6	347365	hgsc.bcm.edu	37	X	54815065	54815065	+	Missense_Mutation	SNP	G	G	C	rs140757238	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	50	81	0	0.47619	0	G|0.976;C|0.024	0.024	strong	.	.	.	.	NM_198510	exon5	c.C634G	p.P212A	TGGATGGGGGTGA	.	PASS	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66717910	66717910	+	Silent	SNP	G	G	T	rs34109029	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	35	84	0	0.5	0	G|0.913;T|0.087	0.087	strong	.	HELB	90	.	NM_033647	exon10	c.G2445T	p.T815T	TGGTACGCTTCCT	.	PASS	Atlas-SNP
SNX20	124460	hgsc.bcm.edu	37	16	50709792	50709792	+	Silent	SNP	C	C	T	rs35435054	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	34	66	0	0.425	0	C|0.981;T|0.019	0.019	strong	SNX20_ENST00000300590,NS,carcinoma,-1,2	SNX20	50	2	NM_001144972	exon3	c.G171A	p.T57T	CTCCCGCGTGGTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228547511	228547511	+	Silent	SNP	G	G	A	rs115442906	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	66	109	0	0.545455	0	G|0.950;A|0.050	0.050	strong	.	OBSCN	2142	.	NM_052843	exon81	c.G18918A	p.T6306T	TGTGACGGAGGCC	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782388	54782388	+	Silent	SNP	T	T	C	rs28405793	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	83	218	1	0.393365	0.00458716	T|0.954;C|0.046	0.046	strong	LILRB2,NS,carcinoma,-1,1	LILRB2	94	1	NM_005874	exon7	c.A984G	p.S328S	CTGCACTGAGATG	.	scavenged	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16358584	16358584	+	Silent	SNP	T	T	C	rs690241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	139	1	1	0.00719424	T|0.400;C|0.600	0.600	strong	.	RFTN1	79	.	NM_015150	exon10	c.A1488G	p.S496S	CTGTCCTGAAACA	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18743529	18743529	+	Missense_Mutation	SNP	T	T	C	rs115954314	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	30	50	0	0.422535	0	T|0.992;C|0.008	0.008	strong	.	IGSF22	211	.	NM_173588	exon3	c.A169G	p.S57G	TTGAGCTCCGGGT	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104086631	104086631	+	Silent	SNP	C	C	T	rs703651	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	73	161	0	0.447853	0	C|0.546;T|0.453	0.453	strong	STAB2,rectum,carcinoma,0,2	STAB2	370	2	NM_017564	exon31	c.C3339T	p.N1113N	GGACAACGCAGCC	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1192	558	866	0	0.468121	0	T|0.770;A|0.230	0.230	strong	.	OR2T29	8	.	NM_001004694	exon1	c.A16T	p.R6W	CCATCCTGGTGAT	.	PASS	Atlas-SNP
LRSAM1	90678	hgsc.bcm.edu	37	9	130263362	130263362	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	20	63	0	0.294118	0	.	.	none	.	LRSAM1	40	.	NM_001005373	exon25	c.C1986T	p.S662S	GCCATCCGCTCCC	.	PASS	Atlas-SNP
SLC37A1	54020	hgsc.bcm.edu	37	21	43974226	43974226	+	Silent	SNP	T	T	C	rs2839550	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	36	41	0	0.631579	0	T|0.848;C|0.152	0.152	strong	.	SLC37A1	48	.	NM_018964	exon11	c.T823C	p.L275L	CAAATCTTGAAGA	.	PASS	Atlas-SNP
ZBTB18	10472	hgsc.bcm.edu	37	1	244217662	244217662	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	91	169	0	0.54491	0	.	.	none	.	.	.	.	NM_205768	exon2	c.T586C	p.L196L	ATGCGATTGCCCT	.	PASS	Atlas-SNP
ZP2	7783	hgsc.bcm.edu	37	16	21217061	21217061	+	Silent	SNP	G	G	A	rs16971234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	116	119	1	0.983051	0.00840336	G|0.763;A|0.237	0.237	strong	.	ZP2	92	.	NM_003460	exon6	c.C519T	p.D173D	ACTGTCGTCAGCC	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140671147	140671147	+	Silent	SNP	C	C	T	rs7868455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	122	0	1	0	C|0.939;T|0.061	0.061	strong	.	EHMT1	196	.	NM_001145527	exon12	c.C1869T	p.N623N	CAATAACGCCAGC	.	PASS	Atlas-SNP
RNF181	51255	hgsc.bcm.edu	37	2	85824251	85824251	+	Missense_Mutation	SNP	T	T	C	rs6643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	174	0	0.442708	0	T|0.797;C|0.203	0.203	strong	.	RNF181	10	.	NM_016494	exon4	c.T352C	p.Y118H	TGCCGCTATGAGC	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68631920	68631920	+	Silent	SNP	C	C	T	rs9302249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	32	56	0	0.410256	0	C|0.956;T|0.044	0.044	strong	ITGA11,colon,carcinoma,-1,1	ITGA11	110	1	NM_001004439	exon11	c.G1194A	p.T398T	GGCACTCGTCTCC	.	PASS	Atlas-SNP
DOCK11	139818	hgsc.bcm.edu	37	X	117680019	117680019	+	Silent	SNP	G	G	C	rs61740837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	77	192	0	0.383085	0	G|0.993;C|0.007	0.007	strong	.	DOCK11	185	.	NM_144658	exon6	c.G498C	p.V166V	TGGTGTGATAAAA	.	PASS	Atlas-SNP
TNFRSF10B	8795	hgsc.bcm.edu	37	8	22926313	22926313	+	Missense_Mutation	SNP	G	G	A	rs1129424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	12	0	1	0	G|0.295;A|0.705	0.705	strong	.	TNFRSF10B	34	.	NM_147187	exon1	c.C95T	p.P32L	ACCCGGGGCCCAG	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	47	94	0	0.5	0	G|0.810;C|0.190	0.190	strong	.	TSPYL5	48	.	NM_033512	exon1	c.C359G	p.T120S	AAGACAGTGTCTG	.	PASS	Atlas-SNP
KCNK5	8645	hgsc.bcm.edu	37	6	39158773	39158773	+	Missense_Mutation	SNP	G	G	T	rs9462487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	27	73	0	0.457627	0	G|0.980;T|0.020	0.020	strong	.	KCNK5	57	.	NM_003740	exon5	c.C1393A	p.P465T	AGGAGGGGAACTC	.	PASS	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	32	170	0	0.142222	0	A|0.981;G|0.019	0.019	strong	BOD1,NS,carcinoma,0,1	BOD1	15	1	NM_138369	exon3	c.T543C	p.S181S	GTCCTGAGATGGA	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7410391	7410391	+	Missense_Mutation	SNP	A	A	C	rs76240858	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	32	84	0	0.329897	0	A|0.997;C|0.003	0.003	strong	.	COL28A1	113	.	NM_001037763	exon33	c.T3031G	p.S1011A	GAGTAGATTCACT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281523	152281523	+	Missense_Mutation	SNP	A	A	C	rs80059102	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	859	325	425	2	0.378347	0.00470588	A|0.917;C|0.081;G|0.002	0.081	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.T5839G	p.W1947G	GCTCCCAAGCAGA	.	scavenged	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105671267	105671267	+	Silent	SNP	T	T	C	rs10270308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	85	184	0	0.472222	0	T|0.795;C|0.205	0.205	strong	.	CDHR3	153	.	NM_152750	exon18	c.T2334C	p.D778D	CTTTGATGGAGAA	.	PASS	Atlas-SNP
MAGEC3	139081	hgsc.bcm.edu	37	X	140967195	140967195	+	Missense_Mutation	SNP	T	T	A	rs11095910	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	367	238	332	2	0.648501	0.0060241	T|0.739;A|0.261	0.261	strong	.	MAGEC3	228	.	NM_138702	exon3	c.T493A	p.L165M	AAAAGGTTGTGGG	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115393929	115393929	+	Missense_Mutation	SNP	G	G	A	rs3189030	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	52	135	0	0.42623	0	G|0.727;A|0.273	0.273	strong	NRAP,NS,adenoma,0,1	NRAP	208	1	NM_001261463	exon15	c.C1469T	p.S490L	GTCACCGAGCTGT	.	PASS	Atlas-SNP
PLD3	23646	hgsc.bcm.edu	37	19	40882588	40882588	+	Silent	SNP	C	C	T	rs57187324	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	23	62	0	0.469388	0	C|0.990;T|0.010	0.010	strong	.	PLD3	71	.	NM_012268	exon11	c.C1092T	p.I364I	GCTCATCAGCTGC	.	PASS	Atlas-SNP
LHX8	431707	hgsc.bcm.edu	37	1	75622616	75622616	+	Silent	SNP	C	C	T	rs941032	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	187	136	0	1	0	C|0.598;N|0.000	.	strong	.	LHX8	73	.	NM_001001933	exon9	c.C849T	p.H283H	GAAACACGTCAGT	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4043415	4043415	+	Missense_Mutation	SNP	T	T	C	rs113187435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	116	269	0	0.473469	0	T|0.991;C|0.009	0.009	strong	.	ADCY9	151	.	NM_001116	exon4	c.A1981G	p.S661G	TGGTGCTGTTTTT	.	PASS	Atlas-SNP
OR52A5	390054	hgsc.bcm.edu	37	11	5153261	5153261	+	Silent	SNP	A	A	G	rs2472530	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	46	117	0	0.474227	0	A|0.815;G|0.185	0.185	strong	.	OR52A5	80	.	NM_001005160	exon1	c.T612C	p.F204F	GGCAACAAATAGG	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11622729	11622729	+	Silent	SNP	C	C	T	rs61739488	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	47	114	0	0.443396	0	C|0.950;T|0.050	0.050	strong	.	DNAH9	695	.	NM_001372	exon27	c.C5631T	p.T1877T	CAAGACCGAGACC	.	PASS	Atlas-SNP
PI15	51050	hgsc.bcm.edu	37	8	75737636	75737636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	2	125	1	0.020202	0.008	.	.	none	PI15,colon,carcinoma,0,2	PI15	73	2	NM_015886	exon2	c.C152T	p.A51V	ATTCAGCGGATAT	.	scavenged	Atlas-SNP
C19orf80	55908	hgsc.bcm.edu	37	19	11350340	11350340	+	Silent	SNP	C	C	G	rs892066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	180	114	0	1	0	C|0.688;G|0.312	0.312	strong	.	C19orf80	8	.	NM_018687	exon1	c.C27G	p.L9L	CCTGCTCTGGGCC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921332	12921332	+	Missense_Mutation	SNP	T	T	C	rs78671912		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	504	502	386	24	0.996032	0.0621762	.	.	weak	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon4	c.T1123C	p.C375R	CTGAGCTGCTGCT	.	scavenged	Atlas-SNP
LUZP1	7798	hgsc.bcm.edu	37	1	23415518	23415518	+	Missense_Mutation	SNP	C	C	T	rs12066671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	166	273	0	0.506098	0	C|0.925;T|0.075	0.075	strong	.	LUZP1	83	.	NM_033631	exon5	c.G3101A	p.S1034N	TAGACACTGAGTG	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225528340	225528340	+	Missense_Mutation	SNP	C	C	T	rs12184324	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	85	185	0	0.452128	0	C|0.907;T|0.093	0.093	strong	.	DNAH14	300	.	NM_001373	exon67	c.C10336T	p.L3446F	ATTTCCCTTGATG	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713771	32713771	+	Missense_Mutation	SNP	T	T	C	rs34847266	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	627	129	587	1	0.205742	0.00170358	T|0.667;C|0.333	0.333	strong	.	HLA-DQA2	27	.	NM_020056	exon3	c.T535C	p.F179L	CTCACCTTCCTCC	.	PASS	Atlas-SNP
PRODH2	58510	hgsc.bcm.edu	37	19	36302897	36302897	+	Silent	SNP	G	G	A	rs145376615	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	51	97	0	0.525773	0	A|0.006;G|0.994;T|0.000	0.006	strong	.	PRODH2	68	.	NM_021232	exon5	c.C792T	p.P264P	CCTCTCGGGGCTC	.	PASS	Atlas-SNP
MYL9	10398	hgsc.bcm.edu	37	20	35176541	35176541	+	Silent	SNP	G	G	A	rs11553089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	60	117	0	0.594059	0	G|0.975;A|0.025	0.025	strong	.	MYL9	13	.	NM_006097	exon3	c.G291A	p.T97T	CGGCACGGACCCC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062023	64062023	+	Missense_Mutation	SNP	A	A	C	rs10878073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	73	169	0	0.412429	0	A|0.717;C|0.283	0.283	strong	.	DPY19L2	97	.	NM_173812	exon1	c.T151G	p.S51A	TCCAGGAGCCCCT	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813352	248813352	+	Silent	SNP	G	G	A	rs147773385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	26	246	0	0.156627	0	G|0.986;A|0.014	0.014	strong	OR2T27,colon,carcinoma,0,1	OR2T27	52	1	NM_001001824	exon1	c.C834T	p.Y278Y	GATGGTGTAGAAG	.	scavenged	Atlas-SNP
USP6NL	9712	hgsc.bcm.edu	37	10	11505175	11505175	+	Silent	SNP	A	A	G	rs3740204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	33	36	0	1	0	A|0.502;G|0.498	0.498	strong	.	USP6NL	57	.	NM_001080491	exon14	c.T1803C	p.P601P	CGGGCTAGGAGGG	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29225502	29225502	+	Silent	SNP	T	T	G	rs72786178	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	72	107	0	0.549618	0	T|0.833;G|0.167	0.167	strong	.	FAM179A	106	.	NM_199280	exon5	c.T528G	p.P176P	GATGCCTCTCATC	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38425110	38425110	+	Missense_Mutation	SNP	C	C	A	rs6897179	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	82	166	0	0.49697	0	C|0.880;A|0.120	0.120	strong	.	EGFLAM	302	.	NM_001205301	exon13	c.C1726A	p.H576N	TGCATCCATGGTG	.	PASS	Atlas-SNP
LRTM1	57408	hgsc.bcm.edu	37	3	54958884	54958884	+	Silent	SNP	A	A	G	rs35757787	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	67	122	0	0.540323	0	A|0.971;G|0.029	0.029	strong	.	LRTM1	52	.	NM_020678	exon2	c.T366C	p.P122P	CAGCTGAGGGAGG	.	PASS	Atlas-SNP
FLOT1	10211	hgsc.bcm.edu	37	6	30695920	30695920	+	Silent	SNP	C	C	T	rs1136719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	32	94	0	0.438356	0	T|0.057;G|0.183;C|0.746;A|0.014	0.057	strong	.	FLOT1	28	.	NM_005803	exon13	c.G1257A	p.V419V	GTGATTCACCTGG	.	PASS	Atlas-SNP
ST8SIA3	51046	hgsc.bcm.edu	37	18	55021725	55021725	+	Missense_Mutation	SNP	A	A	C	rs3745060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	83	0	0.45	0	A|0.692;C|0.308	0.308	strong	.	ST8SIA3	73	.	NM_015879	exon2	c.A272C	p.K91T	AGTGGAAATTTAA	.	PASS	Atlas-SNP
CAMK4	814	hgsc.bcm.edu	37	5	110820116	110820116	+	Silent	SNP	T	T	G	rs6886469	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	40	78	0	0.57971	0	T|0.991;G|0.009	0.009	strong	.	CAMK4	77	.	NM_001744	exon11	c.T1374G	p.A458A	CTCTGCTGTGGGT	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49701983	49701983	+	Silent	SNP	G	G	A	rs9858542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	14	46	0	0.341463	0	G|0.749;A|0.251	0.251	strong	BSN,NS,carcinoma,+1,1	BSN	272	1	NM_003458	exon9	c.G11736A	p.T3912T	ACTGACGGAAGGT	.	PASS	Atlas-SNP
TEX11	56159	hgsc.bcm.edu	37	X	69890301	69890301	+	Missense_Mutation	SNP	C	C	T	rs4844247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	319	139	350	0	0.435737	0	C|0.911;T|0.089	0.089	strong	.	TEX11	132	.	NM_001003811	exon17	c.G1351A	p.E451K	CCATTTCATCAGT	.	PASS	Atlas-SNP
UBP1	7342	hgsc.bcm.edu	37	3	33458266	33458266	+	Missense_Mutation	SNP	T	T	C	rs3736563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	371	176	355	0	0.474394	0	T|0.585;C|0.415	0.415	strong	.	UBP1	42	.	NM_001128160	exon3	c.A326G	p.N109S	TTTCCATTGATCT	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373646	5373646	+	Silent	SNP	T	T	C	rs5024041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	59	1	1	0.0169492	T|0.407;C|0.593	0.593	strong	OR51B6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	OR51B6	53	1	NM_001004750	exon1	c.T909C	p.R303R	ACTTCGTTTATTC	.	scavenged	Atlas-SNP
ODAM	54959	hgsc.bcm.edu	37	4	71068489	71068489	+	Missense_Mutation	SNP	T	T	C	rs3196714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	114	201	0	0.487179	0	C|0.258;N|0.001	0.258	strong	.	ODAM	38	.	NM_017855	exon9	c.T665C	p.I222T	AAGAGATACCATA	.	PASS	Atlas-SNP
CA8	767	hgsc.bcm.edu	37	8	61178574	61178574	+	Silent	SNP	T	T	C	rs7464181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	32	65	0	0.380952	0	T|0.488;C|0.512	0.512	strong	.	CA8	31	.	NM_004056	exon3	c.A327G	p.E109E	TTCAAATTCATGC	.	PASS	Atlas-SNP
TSSK3	81629	hgsc.bcm.edu	37	1	32829261	32829261	+	Missense_Mutation	SNP	A	A	G	rs35508255	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	82	120	0	0.557823	0	A|0.981;G|0.019	0.019	strong	.	TSSK3	22	.	NM_052841	exon2	c.A211G	p.I71V	AACATCATCCAGG	.	PASS	Atlas-SNP
ZNF841	284371	hgsc.bcm.edu	37	19	52570783	52570783	+	Silent	SNP	A	A	G	rs16983414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	91	257	0	0.425234	0	A|0.829;G|0.171	0.171	strong	.	ZNF841	183	.	NM_001136499	exon7	c.T352C	p.L118L	CTTCCAACATCAC	.	PASS	Atlas-SNP
ERBB2	2064	hgsc.bcm.edu	37	17	37872035	37872035	+	Missense_Mutation	SNP	G	G	T	rs4252633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	32	42	0	0.484848	0	G|0.979;T|0.021	0.021	strong	.	ERBB2	429	.	NM_004448	exon12	c.G1356T	p.W452C	CAGCTGGCTGGGG	.	PASS	Atlas-SNP
PTGS1	5742	hgsc.bcm.edu	37	9	125143792	125143792	+	Silent	SNP	C	C	A	rs5788	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	174	179	0	0.994286	0	C|0.722;A|0.278	0.278	strong	PTGS1,NS,carcinoma,0,1	PTGS1	84	1	NM_000962	exon6	c.C639A	p.G213G	TTCTGGCAAGATG	.	PASS	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	37	14	23549948	23549948	+	Missense_Mutation	SNP	C	C	T	rs11555803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	48	102	0	0.521739	0	C|0.971;T|0.029	0.029	strong	.	ACIN1	147	.	NM_001164814	exon6	c.G770A	p.R257K	AGGTTTCTGGAAG	.	PASS	Atlas-SNP
SLC10A6	345274	hgsc.bcm.edu	37	4	87769929	87769929	+	Missense_Mutation	SNP	T	T	C	rs13106574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	65	101	0	0.511811	0	T|0.854;C|0.146	0.146	strong	.	SLC10A6	40	.	NM_197965	exon1	c.A340G	p.I114V	TGAAAATGTTAGA	.	PASS	Atlas-SNP
GGT5	2687	hgsc.bcm.edu	37	22	24628928	24628928	+	Silent	SNP	G	G	A	rs762276	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	26	33	0	0.604651	0	G|0.864;A|0.136	0.136	strong	.	GGT5	61	.	NM_001099781	exon4	c.C459T	p.R153R	GCCATGGCGGCGG	.	PASS	Atlas-SNP
CC2D1A	54862	hgsc.bcm.edu	37	19	14029627	14029627	+	Missense_Mutation	SNP	A	A	C	rs11883041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	53	107	0	0.582418	0	A|0.943;C|0.057	0.057	strong	.	CC2D1A	67	.	NM_017721	exon9	c.A1015C	p.T339P	TCCACAACAGGTA	.	PASS	Atlas-SNP
SYCE1L	100130958	hgsc.bcm.edu	37	16	77246093	77246093	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	67	73	0	0.544715	0	.	.	none	.	SYCE1L	10	.	NM_001129979	exon8	c.G490A	p.E164K	CTCTCGGAGAGTG	.	PASS	Atlas-SNP
NOP16	51491	hgsc.bcm.edu	37	5	175811233	175811233	+	Missense_Mutation	SNP	C	C	T	rs1065206	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	102	0	1	0	C|0.924;T|0.076	0.076	strong	.	NOP16	26	.	NM_001256539	exon5	c.G448A	p.D150N	ACCAGTCACTCCA	.	PASS	Atlas-SNP
ALDH1B1	219	hgsc.bcm.edu	37	9	38395928	38395928	+	Silent	SNP	C	C	T	rs2073477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	31	57	0	0.534483	0	C|0.796;T|0.204	0.204	strong	ALDH1B1,NS,carcinoma,0,1	ALDH1B1	50	1	NM_000692	exon2	c.C183T	p.T61T	TACCACCGGGGAG	.	PASS	Atlas-SNP
UGT3A2	167127	hgsc.bcm.edu	37	5	36049324	36049324	+	Silent	SNP	G	G	A	rs148290056	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	46	101	0	0.410714	0	G|0.996;A|0.004	0.004	strong	.	UGT3A2	117	.	NM_174914	exon4	c.C510T	p.F170F	AGAGCCGAATGAA	.	PASS	Atlas-SNP
GPR87	53836	hgsc.bcm.edu	37	3	151017855	151017855	+	Missense_Mutation	SNP	T	T	G	rs141290943	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	44	76	0	0.60274	0	T|0.998;G|0.002	0.002	strong	.	GPR87	52	.	NM_023915	exon2	c.A34C	p.N12H	GCTTACTTGGTAA	.	PASS	Atlas-SNP
CHDH	55349	hgsc.bcm.edu	37	3	53857676	53857676	+	Silent	SNP	C	C	T	rs17053532	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	11	13	0	0.785714	0	C|0.905;T|0.095	0.095	strong	.	CHDH	34	.	NM_018397	exon3	c.G360A	p.L120L	CCAGTACAGCACG	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	89	190	0	0.517442	0	G|0.850;T|0.150	0.150	strong	.	ADCY2	337	.	NM_020546	exon3	c.G439T	p.V147L	TTCGTGGTGTACA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895950	1895950	+	Missense_Mutation	SNP	C	C	G	rs138283486	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	339	21	533	0	0.0619469	0	C|0.693;G|0.307	0.307	strong	.	SIRPA	83	.	NM_001040022	exon3	c.C285G	p.D95E	TTCAGACCTCACA	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232943513	232943513	+	Missense_Mutation	SNP	A	A	T	rs61735509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	55	89	0	0.518868	0	A|0.989;T|0.011	0.011	strong	.	.	.	.	NM_019090	exon1	c.A2744T	p.H915L	CTGTACACTCATA	.	PASS	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	37	2	71043607	71043607	+	Silent	SNP	G	G	C	rs114209954	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	82	186	0	0.479532	0	G|0.985;C|0.015	0.015	strong	.	CLEC4F	95	.	NM_173535	exon4	c.C906G	p.T302T	GGCCTGGGTCTGG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276490	152276490	+	Silent	SNP	C	C	T	rs199933055	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	631	9	401	0	0.0142631	0	C|0.999;G|0.001	.	weak	FLG,NS,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.G10872A	p.E3624E	ATGTCTCTCTCCT	.	scavenged	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69246129	69246129	+	Silent	SNP	A	A	G	rs78327349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	73	118	0	0.536765	0	A|0.976;G|0.024	0.024	strong	.	FRMD4B	90	.	NM_015123	exon13	c.T1014C	p.A338A	AGAGTTAGCATAC	.	PASS	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	37	19	5831840	5831840	+	Missense_Mutation	SNP	C	C	T	rs17855739	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	376	166	375	0	0.441489	0	C|0.878;T|0.122	0.122	strong	FUT6,NS,carcinoma,+2,1	FUT6	30	1	NM_000150	exon3	c.G739A	p.E247K	AGTTCTCGAAGGC	.	PASS	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	122	0	0.467213	0	C|0.513;G|0.487	0.487	strong	.	IQGAP3	146	.	NM_178229	exon12	c.G1228C	p.V410L	GGTACACTGGAGG	.	PASS	Atlas-SNP
TNFRSF18	8784	hgsc.bcm.edu	37	1	1141824	1141824	+	Missense_Mutation	SNP	G	G	C	rs11466676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	9	33	0	0.409091	0	G|0.955;C|0.045	0.045	strong	.	TNFRSF18	13	.	NM_148902	exon1	c.C128G	p.T43R	GTTCCCGTCCCAA	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240611	39240611	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	35	113	0	0.198864	0	.	.	none	KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-7	49	2	NM_033061	exon1	c.G153A	p.R51R	CTGCAGGCCCCAG	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113386779	113386779	+	Missense_Mutation	SNP	C	C	G	rs2285933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	71	148	0	0.405714	0	C|0.724;G|0.276	0.276	strong	OAS3,brain,glioma,0,1	OAS3	63	1	NM_006187	exon6	c.C1143G	p.S381R	AGGGAGCAAACCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507780	195507780	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	52	336	0	0.284153	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	NM_018406	exon2	c.C10671T	p.D3557D	GGAAGCGTCGGTG	.	scavenged	Atlas-SNP
MFSD4	148808	hgsc.bcm.edu	37	1	205561372	205561372	+	Silent	SNP	C	C	T	rs7529077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	176	166	1	1	0.0060241	C|0.812;T|0.188	0.188	strong	.	MFSD4	46	.	NM_181644	exon7	c.C1254T	p.F418F	CACCTTCCCCAGC	.	PASS	Atlas-SNP
TMIGD2	126259	hgsc.bcm.edu	37	19	4292597	4292597	+	Silent	SNP	C	C	T	rs888932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	41	40	0	1	0	C|0.569;T|0.431	0.431	strong	.	TMIGD2	38	.	NM_144615	exon5	c.G848A	p.X283X	ATCTCTCACTCCT	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30702785	30702785	+	Missense_Mutation	SNP	T	T	C	rs61736163	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	121	0	1	0	T|0.886;C|0.114	0.114	strong	.	TEX15	350	.	NM_031271	exon1	c.A3749G	p.N1250S	CAATCGTTGCCTG	.	PASS	Atlas-SNP
EIF4EBP2	1979	hgsc.bcm.edu	37	10	72179746	72179746	+	Silent	SNP	C	C	T	rs1043098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	122	0	0.508065	0	C|0.528;T|0.472	0.472	strong	.	EIF4EBP2	7	.	NM_004096	exon2	c.C222T	p.H74H	CTGCCACCTGCCC	.	PASS	Atlas-SNP
CDC5L	988	hgsc.bcm.edu	37	6	44371714	44371714	+	Silent	SNP	C	C	T	rs6934058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	50	0	1	0	C|0.795;T|0.205	0.205	strong	.	CDC5L	86	.	NM_001253	exon6	c.C708T	p.D236D	TCTTGACGCAGAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417732	105417732	+	Silent	SNP	G	G	A	rs190986194	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	105	363	0	0.406977	0	G|0.914;A|0.086	0.086	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4056T	p.D1352D	AGACAGGTCCACG	.	PASS	Atlas-SNP
TRIM39	56658	hgsc.bcm.edu	37	6	30309508	30309508	+	Silent	SNP	T	T	C	rs2074474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	101	0	0.466667	0	T|0.701;C|0.299	0.299	strong	TRIM39_ENST00000376656,NS,malignant_melanoma,+2,1	TRIM39	56	1	NM_021253	exon9	c.T1029C	p.P343P	GGACCCTGAGACA	.	PASS	Atlas-SNP
ITGAD	3681	hgsc.bcm.edu	37	16	31422071	31422071	+	Missense_Mutation	SNP	C	C	G	rs142278416	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	89	209	0	0.468421	0	C|0.991;G|0.009	0.009	strong	.	ITGAD	154	.	NM_005353	exon12	c.C1228G	p.L410V	ACCGAGCTAGCCC	.	PASS	Atlas-SNP
NUDCD1	84955	hgsc.bcm.edu	37	8	110301998	110301998	+	Missense_Mutation	SNP	T	T	C	rs2980618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	98	283	0	0.382812	0	T|0.657;C|0.343	0.343	strong	.	NUDCD1	58	.	NM_032869	exon5	c.A805G	p.I269V	CTGATATGTCTTC	.	PASS	Atlas-SNP
SLC9A4	389015	hgsc.bcm.edu	37	2	103095531	103095531	+	Silent	SNP	T	T	C	rs61731286	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	55	87	0	0.462185	0	T|0.874;C|0.126	0.126	strong	.	SLC9A4	115	.	NM_001011552	exon2	c.T490C	p.L164L	GCAGTATTGGGGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416344	105416344	+	Missense_Mutation	SNP	T	T	G	rs368838079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	16	290	0	0.0531561	0	.	.	weak	.	AHNAK2	719	.	NM_138420	exon7	c.A5444C	p.D1815A	GTCACATCCTTGT	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141036337	141036337	+	Silent	SNP	A	A	G	rs7703648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	122	1	1	0.00819672	A|0.497;G|0.503	0.503	strong	ARAP3,NS,carcinoma,0,1	ARAP3	139	1	NM_022481	exon26	c.T3603C	p.A1201A	CAGGGAAGCTGAG	.	PASS	Atlas-SNP
MCEE	84693	hgsc.bcm.edu	37	2	71351403	71351403	+	Missense_Mutation	SNP	C	C	A	rs6748672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	74	148	0	0.490066	0	C|0.817;A|0.183	0.183	strong	MCEE,NS,carcinoma,-1,1	MCEE	19	1	NM_032601	exon2	c.G311T	p.R104L	CTGTCACGTCCCA	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	37	12	94972290	94972290	+	Silent	SNP	C	C	T	rs2270893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	48	86	0	0.510638	0	C|0.474;T|0.526	0.526	strong	TMCC3,NS,carcinoma,0,1	TMCC3	63	1	NM_020698	exon3	c.G1011A	p.E337E	CTGGTCCTCCAGT	.	PASS	Atlas-SNP
ZC3H12C	85463	hgsc.bcm.edu	37	11	110007834	110007834	+	Silent	SNP	T	T	C	rs78240010	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	24	91	0	0.444444	0	T|0.992;C|0.008	0.008	strong	.	ZC3H12C	83	.	NM_033390	exon2	c.T468C	p.P156P	ACCACCTGATGTG	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671795	25671795	+	Missense_Mutation	SNP	C	C	T	rs113416318	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	5	97	0	0.0442478	0	C|0.988;T|0.012	0.012	strong	PABPC3,rectum,carcinoma,0,1	PABPC3	129	1	NM_030979	exon1	c.C1459T	p.R487C	GGTCCACGTCCTG	.	scavenged	Atlas-SNP
PTAFR	5724	hgsc.bcm.edu	37	1	28476520	28476520	+	Missense_Mutation	SNP	T	T	C	rs5939	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	68	121	0	0.450331	0	T|0.975;C|0.025	0.025	strong	.	PTAFR	30	.	NM_001164723	exon3	c.A1013G	p.N338S	AGGGAATTGCCAG	.	PASS	Atlas-SNP
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	106	151	0	0.535354	0	G|0.422;N|0.000	0.422	strong	.	ATG16L1	83	.	NM_030803	exon9	c.A898G	p.T300A	GTGGATACTCATC	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	68968166	68968166	+	Silent	SNP	C	C	A	rs1434774	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	26	80	0	0.313253	0	C|0.420;A|0.580	0.580	strong	PREX2_ENST00000354677,NS,malignant_melanoma,-1,2	PREX2	614	2	NM_025170	exon10	c.C1195A	p.R399R	AAAGACCGAAAGA	.	PASS	Atlas-SNP
SLC37A4	2542	hgsc.bcm.edu	37	11	118895686	118895686	+	Silent	SNP	C	C	T	rs8192696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	44	102	0	0.419048	0	C|0.768;T|0.232	0.232	strong	.	SLC37A4	19	.	NM_001164278	exon12	c.G1290A	p.T430T	GGCAGCCGTGCTG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	40	114	0	0.39604	0	T|0.628;G|0.372	0.372	strong	.	ZNF835	106	.	NM_001005850	exon2	c.A263C	p.E88A	GGGCTCTCCCCAG	.	PASS	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282651	59282651	+	Missense_Mutation	SNP	C	C	T	rs76276934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	88	177	0	0.505747	0	C|0.979;T|0.021	0.021	strong	.	OR4D9	47	.	NM_001004711	exon1	c.C266T	p.T89I	CAGAGACAAAAAC	.	PASS	Atlas-SNP
SPATC1L	84221	hgsc.bcm.edu	37	21	47588365	47588365	+	Missense_Mutation	SNP	G	G	A	rs73908565	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	57	116	0	0.448819	0	G|0.978;A|0.022	0.022	strong	.	.	.	.	NM_001142854	exon3	c.C401T	p.S134F	AGCGGGGACAGCT	.	PASS	Atlas-SNP
CHCHD3	54927	hgsc.bcm.edu	37	7	132470419	132470419	+	Silent	SNP	G	G	A	rs147050556	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	186	329	0	0.574074	0	G|0.998;A|0.002	0.002	strong	.	CHCHD3	21	.	NM_017812	exon8	c.C663T	p.S221S	AAGCATGCTCTGC	.	PASS	Atlas-SNP
NOL10	79954	hgsc.bcm.edu	37	2	10729257	10729257	+	Missense_Mutation	SNP	T	T	C	rs34359340	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	116	239	0	0.469636	0	T|0.964;C|0.036	0.036	strong	.	NOL10	22	.	NM_024894	exon19	c.A1756G	p.T586A	GGACTGTCTGCTG	.	PASS	Atlas-SNP
NGEF	25791	hgsc.bcm.edu	37	2	233757679	233757679	+	Silent	SNP	G	G	A	rs748002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	79	142	0	0.523179	0	G|0.695;A|0.305	0.305	strong	NGEF_ENST00000264051,caecum,carcinoma,-1,4	NGEF	198	4	NM_019850	exon7	c.C1071T	p.A357A	GTGGTCGGCCGCA	.	PASS	Atlas-SNP
RNF130	55819	hgsc.bcm.edu	37	5	179393867	179393867	+	Silent	SNP	T	T	C	rs10060093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	82	148	0	0.450549	0	T|0.972;C|0.028	0.028	strong	.	RNF130	49	.	NM_018434	exon7	c.A1089G	p.S363S	AAGAGGTGAGATC	.	PASS	Atlas-SNP
RIMKLB	57494	hgsc.bcm.edu	37	12	8926015	8926015	+	Silent	SNP	C	C	T	rs2302488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	116	263	0	0.434457	0	C|0.911;T|0.089	0.089	strong	.	RIMKLB	47	.	NM_020734	exon7	c.C796T	p.L266L	GATCTGCTGATGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060541	9060541	+	Missense_Mutation	SNP	C	C	T	rs11882256	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	116	284	0	0.418773	0	C|0.615;T|0.385	0.385	strong	.	MUC16	4315	.	NM_024690	exon3	c.G26905A	p.V8969M	TGACCACTGGAGA	.	PASS	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755561	146755561	+	Missense_Mutation	SNP	C	C	G	rs146753539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	23	63	0	0.338235	0	C|0.993;G|0.007	0.007	strong	GRM1,NS,carcinoma,-1,1	GRM1	419	1	NM_000838	exon9	c.C3214G	p.P1072A	CCACCTCCGCAGC	.	PASS	Atlas-SNP
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747445	7747445	+	Silent	SNP	G	G	A	rs1053363	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	41	67	0	0.630769	0	T|0.000;G|0.798;C|0.000;A|0.202	0.202	strong	.	TRAPPC5	11	.	NM_001042461	exon2	c.G306A	p.A102A	GGAGGCGGACAAG	.	PASS	Atlas-SNP
TSKS	60385	hgsc.bcm.edu	37	19	50251701	50251701	+	Missense_Mutation	SNP	C	C	T	rs199829146	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	71	167	0	0.430303	0	.	.	weak	TSKS,NS,carcinoma,+1,2	TSKS	97	2	NM_021733	exon3	c.G425A	p.R142H	TTGGCGCGGACCA	.	PASS	Atlas-SNP
PSG9	5678	hgsc.bcm.edu	37	19	43773572	43773572	+	Silent	SNP	G	G	A	rs8101210	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	26	62	0	0.382353	0	G|0.863;A|0.137	0.137	strong	PSG9,NS,carcinoma,-2,1	PSG9	77	1	NM_002784	exon1	c.C12T	p.L4L	GGCTGGGAGGGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511338	195511338	+	Silent	SNP	G	G	A	rs201931644	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	61	519	0	0.564815	0	G|0.995;A|0.005	0.005	strong	.	MUC4	1505	.	NM_018406	exon2	c.C7113T	p.V2371V	GCTGGTGACAGGA	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52712975	52712975	+	Silent	SNP	G	G	A	rs56040851		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	195	372	0	0.474453	0	.	.	weak	.	KRT83	64	.	NM_002282	exon2	c.C558T	p.N186N	CACGTGGTTGAGC	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	37	20	18395988	18395988	+	Missense_Mutation	SNP	C	C	T	rs6035037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	53	64	0	0.576087	0	C|0.764;T|0.236	0.236	strong	DZANK1,NS,carcinoma,0,2	DZANK1	65	2	NM_001099407	exon11	c.G1060A	p.G354S	ACCAGCCGCAGAA	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173526520	173526520	+	Missense_Mutation	SNP	C	C	T	rs116588526	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	118	238	0	0.529148	0	C|0.989;T|0.011	0.011	strong	.	.	.	.	NM_178527	exon10	c.G1174A	p.V392I	TATAAACATCAGG	.	PASS	Atlas-SNP
GPATCH2	55105	hgsc.bcm.edu	37	1	217793718	217793718	+	Silent	SNP	A	A	G	rs34839777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	51	0	0.431373	0	A|0.990;G|0.010	0.010	strong	.	GPATCH2	53	.	NM_018040	exon2	c.T180C	p.P60P	TTTCAGAGGGCAA	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15793282	15793282	+	Silent	SNP	A	A	G	rs35352350	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	395	56	326	0	0.141772	0	A|0.991;G|0.009	0.009	strong	.	CYP4F12	89	.	NM_023944	exon6	c.A609G	p.L203L	CAGTCTACAGAAA	.	PASS	Atlas-SNP
IFNA16	3449	hgsc.bcm.edu	37	9	21216910	21216910	+	Missense_Mutation	SNP	A	A	G	rs28368162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	123	328	0	0.415541	0	A|0.974;G|0.026	0.026	strong	.	IFNA16	27	.	NM_002173	exon1	c.T395C	p.I132T	AGGGCAATCTCTT	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002381	36002381	+	Missense_Mutation	SNP	C	C	T	rs12981076	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	80	90	0	0.963855	0	C|0.689;T|0.311	0.311	strong	.	DMKN	116	.	NM_001126058	exon5	c.G850A	p.G284S	TGCTGCCGCCACT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179498303	179498303	+	Silent	SNP	T	T	C	rs16866425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	106	214	0	0.439834	0	A|0.000;C|0.061;T|0.938	0.061	strong	.	TTN	18412	.	NM_001267550	exon232	c.A42783G	p.K14261K	GAACCATTTCACT	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26536299	26536299	+	Silent	SNP	C	C	G	rs11886746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	54	95	0	0.453782	0	C|0.631;G|0.369	0.369	strong	.	GPR113	134	.	NM_001145168	exon9	c.G1419C	p.P473P	GTGGACCGGCCCC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910586	29910586	+	Silent	SNP	G	G	A	rs12721672	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	23	94	0	0.207207	0	A|0.105;G|0.895	0.105	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G126A	p.G42G	CCGCGGGGAGCCC	.	PASS	Atlas-SNP
CUX2	23316	hgsc.bcm.edu	37	12	111785586	111785586	+	Silent	SNP	T	T	C	rs3803167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	55	0	0.486486	0	T|0.524;C|0.476	0.476	strong	.	CUX2	145	.	NM_015267	exon22	c.T3918C	p.D1306D	GGAGGATGCTGAG	.	PASS	Atlas-SNP
SNX27	81609	hgsc.bcm.edu	37	1	151638486	151638486	+	Silent	SNP	T	T	C	rs150091333	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	50	95	0	0.454545	0	T|0.994;C|0.006	0.006	strong	.	SNX27	44	.	NM_030918	exon6	c.T984C	p.F328F	CTCCTTTGGTAAG	.	PASS	Atlas-SNP
GNA14	9630	hgsc.bcm.edu	37	9	80144099	80144099	+	Silent	SNP	G	G	A	rs12346870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	213	291	0	0.657407	0	G|0.976;A|0.024	0.024	strong	.	GNA14	50	.	NM_004297	exon2	c.C195T	p.D65D	GTCTTCGTCGCTG	.	PASS	Atlas-SNP
STRN4	29888	hgsc.bcm.edu	37	19	47226450	47226450	+	Silent	SNP	A	A	G	rs28684509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	61	184	0	0.388535	0	A|0.904;G|0.096	0.096	strong	.	STRN4	33	.	NM_001039877	exon13	c.T1707C	p.C569C	AGCAGAACAGGAG	.	PASS	Atlas-SNP
AKR7A2	8574	hgsc.bcm.edu	37	1	19634964	19634964	+	Missense_Mutation	SNP	C	C	G	rs859208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	99	172	0	0.515625	0	C|0.915;G|0.085	0.085	strong	.	AKR7A2	19	.	NM_003689	exon2	c.G471C	p.Q157H	CAGCCGCTGGCAG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18735480	18735480	+	Missense_Mutation	SNP	G	G	A	rs111397851	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	107	165	0	0.551546	0	G|0.961;A|0.039	0.039	strong	.	IGSF22	211	.	NM_173588	exon14	c.C2014T	p.R672C	CTTCACGCACACA	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6271125	6271125	+	Silent	SNP	A	A	G	rs1052598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	99	110	0	0.611111	0	A|0.878;G|0.122	0.122	strong	RNF207,NS,carcinoma,+1,1	RNF207	45	1	NM_207396	exon12	c.A1056G	p.P352P	GGAGCCACTGCTG	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117243260	117243260	+	Silent	SNP	T	T	C	rs7764347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	17	35	0	0.485714	0	T|0.750;C|0.250	0.250	strong	.	RFX6	141	.	NM_173560	exon13	c.T1383C	p.T461T	TGCCACTGTGGAG	.	PASS	Atlas-SNP
QPCT	25797	hgsc.bcm.edu	37	2	37579937	37579937	+	Silent	SNP	C	C	T	rs2230299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	78	100	0	0.586466	0	C|0.765;T|0.235	0.235	strong	QPCT,NS,carcinoma,0,1	QPCT	34	1	NM_012413	exon2	c.C126T	p.Y42Y	GAATTACCACCAG	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2373687	2373687	+	Silent	SNP	C	C	T	rs74002800	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	46	111	0	0.365079	0	C|0.963;T|0.037	0.037	strong	.	ABCA3	176	.	NM_001089	exon7	c.G450A	p.V150V	ATATTTCACCTGT	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58540875	58540875	+	Silent	SNP	G	G	A	rs17821543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	66	0	0.448718	0	G|0.951;A|0.049	0.049	strong	.	NDRG4	29	.	NM_001130487	exon10	c.G732A	p.V244V	GAACGTGGTGAAC	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	C	rs41288743		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	14	76	0	0.166667	0	.	.	weak	TUBB8,NS,carcinoma,0,1	TUBB8	62	1	NM_177987	exon4	c.T618G	p.A206A	ATACAGAGCTTCG	.	scavenged	Atlas-SNP
CLSTN1	22883	hgsc.bcm.edu	37	1	9804693	9804693	+	Missense_Mutation	SNP	C	C	T	rs7550295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	22	44	0	0.44898	0	C|0.864;T|0.136	0.136	strong	.	CLSTN1	88	.	NM_001009566	exon8	c.G994A	p.A332T	TGCCCGCGGCCGC	.	PASS	Atlas-SNP
OAS1	4938	hgsc.bcm.edu	37	12	113348870	113348870	+	Missense_Mutation	SNP	G	G	A	rs1131454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	89	0	0.450549	0	A|0.381;C|0.108;G|0.441;T|0.070	0.381	strong	.	OAS1	128	.	NM_001032409	exon3	c.G484A	p.G162S	ACTGGCGGCTATA	.	PASS	Atlas-SNP
OTUD1	220213	hgsc.bcm.edu	37	10	23729362	23729362	+	Missense_Mutation	SNP	A	A	T	rs139969083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	83	0	0.460674	0	A|0.989;T|0.011	0.011	strong	.	OTUD1	9	.	NM_001145373	exon1	c.A976T	p.S326C	GCTGTCAGCAAGA	.	PASS	Atlas-SNP
INSL6	11172	hgsc.bcm.edu	37	9	5185365	5185365	+	Missense_Mutation	SNP	A	A	G	rs2149554	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	61	84	1	0.521368	0.0119048	A|0.897;G|0.103	0.103	strong	INSL6,NS,carcinoma,+2,1	INSL6	35	1	NM_007179	exon1	c.T238C	p.F80L	TTTCGAACTGGTA	.	scavenged	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222721288	222721288	+	Silent	SNP	C	C	T	rs4846382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	77	159	0	0.5	0	C|0.444;T|0.556	0.556	strong	.	HHIPL2	122	.	NM_024746	exon1	c.G99A	p.L33L	CTGGCCCAACAAG	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	37	19	10404588	10404588	+	Silent	SNP	T	T	C	rs116688659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	12	45	0	0.333333	0	T|0.995;C|0.005	0.005	strong	.	ICAM5	53	.	NM_003259	exon7	c.T1680C	p.S560S	GGGCTCTGCGGCC	.	PASS	Atlas-SNP
PUS7L	83448	hgsc.bcm.edu	37	12	44148259	44148259	+	Missense_Mutation	SNP	T	T	C	rs1057190	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	283	284	0	0.992982	0	T|0.749;C|0.251	0.251	strong	.	PUS7L	73	.	NM_001098614	exon2	c.A790G	p.K264E	TCATTTTAGAAAA	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	15	189	2	0.0887574	0.010582	.	.	none	KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	NM_033059	exon1	c.T208A	p.C70S	AGATGCAGCATCT	.	scavenged	Atlas-SNP
LAD1	3898	hgsc.bcm.edu	37	1	201355669	201355669	+	Missense_Mutation	SNP	T	T	C	rs68021059	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	187	0	1	0	T|0.917;C|0.083	0.083	strong	.	LAD1	42	.	NM_005558	exon3	c.A820G	p.T274A	CTGCAGTTGGGCT	.	PASS	Atlas-SNP
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988062	50988062	+	Silent	SNP	G	G	T	rs140519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	52	0	0.545455	0	G|0.594;T|0.406	0.406	strong	KLHDC7B,extremity,malignant_melanoma,+2,1	KLHDC7B	39	1	NM_138433	exon1	c.G1467T	p.V489V	CATCGTGGCACTG	.	PASS	Atlas-SNP
EXOC3L2	90332	hgsc.bcm.edu	37	19	45719426	45719426	+	Silent	SNP	G	G	A	rs34958174	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	54	88	0	0.477876	0	G|0.946;A|0.054	0.054	strong	.	EXOC3L2	30	.	NM_138568	exon9	c.C846T	p.A282A	CACCACGGCATCC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225355716	225355716	+	Missense_Mutation	SNP	T	T	C	rs78614986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	131	271	0	0.469534	0	T|0.993;C|0.007	0.007	strong	.	DNAH14	300	.	NM_001373	exon35	c.T5455C	p.Y1819H	CAGTTTTATAATC	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141754625	141754625	+	Silent	SNP	C	C	T	rs115294234	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	95	169	0	0.5	0	C|0.985;T|0.015	0.015	strong	.	MGAM	767	.	NM_004668	exon27	c.C3231T	p.T1077T	CAGCACCCCTGAG	.	PASS	Atlas-SNP
SLC37A3	84255	hgsc.bcm.edu	37	7	140051116	140051116	+	Missense_Mutation	SNP	G	G	A	rs76089276	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	83	171	0	0.44385	0	G|0.969;A|0.031	0.031	strong	.	SLC37A3	80	.	NM_207113	exon9	c.C839T	p.A280V	CTTATCGCCTTGA	.	PASS	Atlas-SNP
RNF186	54546	hgsc.bcm.edu	37	1	20141528	20141528	+	Missense_Mutation	SNP	C	C	T	rs1541185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	150	213	1	0.543478	0.00469484	C|0.735;T|0.265	0.265	strong	.	RNF186	14	.	NM_019062	exon1	c.G67A	p.A23T	CCACAGCGGTGGT	.	PASS	Atlas-SNP
CLDN22	53842	hgsc.bcm.edu	37	4	184240777	184240777	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	153	243	2	0.51	0.00823045	.	.	none	CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	NM_001111319	exon1	c.T595C	p.Y199H	CTGCGTAGTGGCC	.	scavenged	Atlas-SNP
NAA16	79612	hgsc.bcm.edu	37	13	41929296	41929296	+	Missense_Mutation	SNP	A	A	G	rs17062054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	13	33	0	0.361111	0	A|0.919;G|0.081	0.081	strong	.	NAA16	74	.	NM_001110798	exon10	c.A1031G	p.E344G	TCCAGGAACTTGT	.	PASS	Atlas-SNP
ADAM12	8038	hgsc.bcm.edu	37	10	127737930	127737930	+	Silent	SNP	G	G	A	rs2292692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	60	141	0	0.441176	0	G|0.869;A|0.131	0.131	strong	.	ADAM12	388	.	NM_021641	exon16	c.C1818T	p.P606P	CTGCAGGGGGATG	.	PASS	Atlas-SNP
GIMAP7	168537	hgsc.bcm.edu	37	7	150217248	150217248	+	Silent	SNP	A	A	G	rs3735081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	89	0	1	0	A|0.252;G|0.748	0.748	strong	GIMAP7,NS,carcinoma,+2,1	GIMAP7	47	1	NM_153236	exon2	c.A186G	p.V62V	TGTTGTAGACACT	.	PASS	Atlas-SNP
PELP1	27043	hgsc.bcm.edu	37	17	4586220	4586220	+	Silent	SNP	G	G	A	rs35109567	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	84	185	0	0.477273	0	G|0.974;A|0.026	0.026	strong	.	PELP1	102	.	NM_014389	exon4	c.C448T	p.L150L	CGGCCAGCTCCAT	.	PASS	Atlas-SNP
AHSG	197	hgsc.bcm.edu	37	3	186338634	186338634	+	Missense_Mutation	SNP	G	G	A	rs77385737	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	86	124	1	0.508876	0.00806452	G|0.996;A|0.004	0.004	strong	AHSG,NS,carcinoma,+1,1	AHSG	40	1	NM_001622	exon7	c.G1019A	p.R340H	AAACACGCACAGT	.	scavenged	Atlas-SNP
CBLN1	869	hgsc.bcm.edu	37	16	49314837	49314837	+	Silent	SNP	T	T	G	rs61735589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	71	130	0	0.438272	0	T|0.937;G|0.063	0.063	strong	.	CBLN1	26	.	NM_004352	exon2	c.A381C	p.I127I	GACCTGTATGGTT	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2555002	2555002	+	Silent	SNP	C	C	T	rs12607882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	43	81	0	0.488636	0	C|0.894;T|0.106	0.106	strong	.	METTL4	40	.	NM_022840	exon4	c.G495A	p.L165L	CTGGATCAACTGT	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	929606	929606	+	Silent	SNP	C	C	T	rs61740409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	160	110	0	0.987654	0	C|0.940;T|0.060	0.060	strong	.	LMF1	42	.	NM_022773	exon6	c.G861A	p.A287A	GATGCACGCCCGC	.	PASS	Atlas-SNP
C10orf12	26148	hgsc.bcm.edu	37	10	98742605	98742605	+	Silent	SNP	C	C	T	rs3814163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	34	46	1	0.607143	0.0217391	C|0.862;T|0.138	0.138	strong	C10orf12,NS,carcinoma,0,1	C10orf12	94	1	NM_015652	exon1	c.C1458T	p.L486L	CTCACTCGAAGAG	.	scavenged	Atlas-SNP
LMAN1L	79748	hgsc.bcm.edu	37	15	75113083	75113083	+	Silent	SNP	A	A	G	rs1531163	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	32	28	0	1	0	A|0.825;G|0.175	0.175	strong	.	LMAN1L	43	.	NM_021819	exon8	c.A882G	p.K294K	TCCAAAATCAGAC	.	PASS	Atlas-SNP
ZNF729	100287226	hgsc.bcm.edu	37	19	22496625	22496625	+	Missense_Mutation	SNP	A	A	G	rs75458675	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	40	56	0	1	0	A|0.960;G|0.040	0.040	strong	.	ZNF729	78	.	NM_001242680	exon4	c.A406G	p.K136E	ATGCACAAAGAAG	.	PASS	Atlas-SNP
TACR1	6869	hgsc.bcm.edu	37	2	75425728	75425728	+	Silent	SNP	A	A	G	rs6715729	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	98	91	0	1	0	A|0.425;G|0.575	0.575	strong	.	TACR1	62	.	NM_001058	exon1	c.T333C	p.F111F	GATGGGAAAGAAG	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	649164	649164	+	Missense_Mutation	SNP	G	G	A	rs34519093	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	22	46	0	0.628571	0	G|0.978;A|0.022	0.022	strong	.	GEMIN4	116	.	NM_015721	exon2	c.C2119T	p.R707C	TGAAGCGGTCCAA	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1538174	1538174	+	Silent	SNP	C	C	T	rs143126716	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	166	131	0	1	0	C|0.988;T|0.012	0.012	strong	INTS1,NS,carcinoma,-1,1	INTS1	145	1	NM_001080453	exon10	c.G1299A	p.A433A	CTTGTGCGCGCTC	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15838972	15838972	+	Missense_Mutation	SNP	T	T	A	rs61733719	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	140	356	0	0.436137	0	T|0.581;A|0.419	0.419	strong	OR10H2,NS,carcinoma,-1,1	OR10H2	59	1	NM_013939	exon1	c.T119A	p.L40Q	CGCTGCTGGGCAA	.	PASS	Atlas-SNP
SLC6A18	348932	hgsc.bcm.edu	37	5	1240757	1240757	+	Nonsense_Mutation	SNP	C	C	G	rs7447815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	103	0	1	0	C|0.649;G|0.351	0.351	strong	.	SLC6A18	84	.	NM_182632	exon7	c.C957G	p.Y319X	TGACTACGAGCAC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20864049	20864049	+	Silent	SNP	A	A	G	rs2228026	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	66	140	0	0.519685	0	A|0.963;G|0.037	0.037	strong	.	TEP1	224	.	NM_007110	exon11	c.T1719C	p.I573I	GGCATCAATGGCA	.	PASS	Atlas-SNP
AWAT1	158833	hgsc.bcm.edu	37	X	69455671	69455671	+	Missense_Mutation	SNP	G	G	A	rs61995694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	49	127	0	0.411765	0	G|0.967;A|0.033	0.033	strong	.	AWAT1	74	.	NM_001013579	exon2	c.G182A	p.R61Q	CAGAGCGAGGTAA	.	PASS	Atlas-SNP
SCAF11	9169	hgsc.bcm.edu	37	12	46339033	46339033	+	Silent	SNP	A	A	G	rs11183245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	42	97	0	0.466667	0	A|0.972;G|0.028	0.028	strong	.	SCAF11	145	.	NM_004719	exon6	c.T462C	p.H154H	CTTACTATGTATC	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64450479	64450479	+	Missense_Mutation	SNP	A	A	G	rs78191145	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	80	149	0	0.57971	0	A|0.996;G|0.004	0.004	strong	.	SYNE2	577	.	NM_182914	exon18	c.A2026G	p.K676E	ATGATAAAAAAAC	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31349795	31349795	+	Silent	SNP	G	G	A	rs142879690	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	70	119	0	0.496454	0	G|0.998;A|0.002	0.002	strong	.	SDC3	45	.	NM_014654	exon3	c.C474T	p.T158T	GGAGACGGTGGTG	.	PASS	Atlas-SNP
PHF21B	112885	hgsc.bcm.edu	37	22	45312244	45312244	+	Silent	SNP	G	G	A	rs6519902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	41	0	0.482143	0	G|0.850;A|0.150	0.150	strong	PHF21B,colon,carcinoma,0,1	PHF21B	61	1	NM_138415	exon4	c.C480T	p.A160A	GGCGGCGGCATTG	.	PASS	Atlas-SNP
CUEDC1	404093	hgsc.bcm.edu	37	17	55950064	55950064	+	Silent	SNP	C	C	T	rs35704289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	42	100	0	0.396226	0	C|0.717;T|0.283	0.283	strong	.	CUEDC1	37	.	NM_001271875	exon5	c.G744A	p.E248E	TTGCAGCTCCTTC	.	PASS	Atlas-SNP
ELL	8178	hgsc.bcm.edu	37	19	18561420	18561420	+	Silent	SNP	C	C	T	rs34078075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	134	189	0	0.503759	0	C|0.976;T|0.024	0.024	strong	.	ELL	52	.	NM_006532	exon8	c.G1332A	p.S444S	GCTGCGCGAGGGG	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38843426	38843426	+	Silent	SNP	C	C	T	rs6458080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	41	96	0	0.471264	0	C|0.539;T|0.461	0.461	strong	DNAH8_ENST00000359357,NS,carcinoma,+1,2	DNAH8	1239	2	NM_001206927	exon53	c.C7680T	p.V2560V	CTGTGTCGAACAT	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38146029	38146029	+	Silent	SNP	C	C	T	rs147619484	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	120	221	0	0.474308	0	C|0.900;T|0.100	0.100	strong	.	RPGR	175	.	NM_001034853	exon15	c.G2223A	p.E741E	TCCCTCCTCTTCT	.	PASS	Atlas-SNP
P2RY14	9934	hgsc.bcm.edu	37	3	150931385	150931385	+	Silent	SNP	A	A	G	rs12631155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	64	91	0	0.547009	0	A|0.934;G|0.066	0.066	strong	.	P2RY14	50	.	NM_014879	exon3	c.T720C	p.F240F	AAACACAAACACG	.	PASS	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120744399	120744399	+	Missense_Mutation	SNP	C	C	T	rs956749	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	63	110	0	0.552632	0	C|0.895;T|0.105	0.105	strong	.	TAF2	204	.	NM_003184	exon26	c.G3365A	p.S1122N	TGCATACTCATCT	.	PASS	Atlas-SNP
LFNG	3955	hgsc.bcm.edu	37	7	2566484	2566484	+	Silent	SNP	C	C	T	rs61743870	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	50	111	0	0.434783	0	C|0.965;T|0.035	0.035	strong	.	LFNG	57	.	NM_001040167	exon7	c.C1002T	p.Y334Y	GAGCTACGGTATG	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	37	20	47858695	47858695	+	Missense_Mutation	SNP	G	G	A	rs143843778	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	56	139	0	0.421053	0	G|0.996;A|0.004	0.004	strong	.	DDX27	74	.	NM_017895	exon18	c.G2161A	p.A721T	CGCAGAGCCAAGC	.	PASS	Atlas-SNP
RERE	473	hgsc.bcm.edu	37	1	8421092	8421092	+	Silent	SNP	C	C	T	rs2784735	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	11	15	0	0.611111	0	C|0.486;T|0.514	0.514	strong	RERE,NS,carcinoma,0,1	RERE	129	1	NM_012102	exon19	c.G2475A	p.P825P	CTGCAGCGGGGGA	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376434	52376434	+	Missense_Mutation	SNP	T	T	C	rs34295271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	30	73	0	0.352941	0	T|0.960;C|0.040	0.040	strong	.	ZNF577	63	.	NM_032679	exon7	c.A809G	p.Y270C	CACCCATAGAGTT	.	PASS	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23824783	23824783	+	Silent	SNP	T	T	G	rs1800351	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	97	0	0.470588	0	T|0.510;G|0.490	0.490	strong	.	SGCG	64	.	NM_000231	exon4	c.T312G	p.L104L	TCTGCTTCTACAA	.	PASS	Atlas-SNP
OR8D2	283160	hgsc.bcm.edu	37	11	124190036	124190036	+	Missense_Mutation	SNP	G	G	A	rs61735123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	28	61	0	0.424242	0	G|0.972;A|0.028	0.028	strong	.	OR8D2	65	.	NM_001002918	exon1	c.C58T	p.R20C	CTGGGCGTTGTGT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179400895	179400895	+	Missense_Mutation	SNP	C	C	T	rs2278196	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	107	220	0	0.516908	0	C|0.930;T|0.070	0.070	strong	.	TTN	18412	.	NM_001267550	exon357	c.G100579A	p.V33527I	ATTTGACGATAGG	.	PASS	Atlas-SNP
EPN3	55040	hgsc.bcm.edu	37	17	48619249	48619249	+	Missense_Mutation	SNP	C	C	A	rs4794159	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	54	0	1	0	C|0.565;A|0.435	0.435	strong	EPN3,NS,carcinoma,0,1	EPN3	32	1	NM_017957	exon10	c.C1630A	p.P544T	GGCGAGCCGGGCA	.	PASS	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	70	0	1	0	G|0.595;A|0.405	0.405	strong	.	RNF111	179	.	NM_017610	exon7	c.G1701A	p.V567V	GCCAGTGGACCTG	.	PASS	Atlas-SNP
TRIM49C	642612	hgsc.bcm.edu	37	11	89774448	89774448	+	Silent	SNP	G	G	A	rs77759231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	130	113	0	0.59633	0	G|0.693;A|0.307	0.307	strong	.	TRIM49C	48	.	NM_001195234	exon8	c.G1089A	p.K363K	TCGGAAGGAGAAG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31118304	31118304	+	Silent	SNP	C	C	T	rs139910767	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	45	76	0	0.483871	0	C|0.999;T|0.001	0.001	strong	.	CCHCR1	68	.	NM_001105564	exon7	c.G1140A	p.A380A	CAGCTCCGCGGTG	.	PASS	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46914526	46914526	+	Silent	SNP	C	C	T	rs61741501	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	66	0	0.517857	0	C|0.947;T|0.053	0.053	strong	.	LRP4	160	.	NM_002334	exon13	c.G1695A	p.E565E	TTACCCCTCCATG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679296	100679296	+	Silent	SNP	C	C	T	rs73168392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	44	157	0	0.247191	0	C|0.867;T|0.133	0.133	strong	.	MUC17	804	.	NM_001040105	exon3	c.C4599T	p.S1533S	CAACAGCCTTTCA	.	PASS	Atlas-SNP
CATSPER3	347732	hgsc.bcm.edu	37	5	134347241	134347241	+	Silent	SNP	T	T	C	rs7719874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	77	0	0.46988	0	T|0.929;C|0.071	0.071	strong	.	CATSPER3	38	.	NM_178019	exon8	c.T1125C	p.H375H	CGTGCATGTGCTG	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778690	84778690	+	Silent	SNP	C	C	T	rs1812062	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	103	188	0	0.492823	0	C|0.773;T|0.227	0.227	strong	.	USP10	51	.	NM_001272075	exon5	c.C615T	p.P205P	CATGCCCCCGTCA	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25049676	25049676	+	Silent	SNP	G	G	A	rs73463182	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	89	169	0	0.502825	0	G|0.865;A|0.135	0.135	strong	.	PARP4	142	.	NM_006437	exon15	c.C1848T	p.A616A	CCCAGAGGCATCC	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs71354064		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	52	340	0	0.147309	0	C|0.500;A|0.500	0.500	weak	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.G947T	p.R316L	TGAACACGCTGAT	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1522330	1522330	+	Silent	SNP	C	C	T	rs11553057	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	98	154	0	0.518519	0	C|0.982;T|0.018	0.018	strong	.	ASMTL	56	.	NM_004192	exon13	c.G1698A	p.A566A	GCGCTGCGCCACC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628239	33628239	+	Silent	SNP	G	G	A	rs9527026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	56	84	0	0.448	0	G|0.844;A|0.156	0.156	strong	.	KL	106	.	NM_004795	exon2	c.G1155A	p.K385K	CATGAAGTTCCGC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216424275	216424275	+	Missense_Mutation	SNP	C	C	G	rs696723	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	95	182	0	0.458937	0	C|0.942;G|0.058	0.058	strong	.	USH2A	1168	.	NM_007123	exon12	c.G2137C	p.G713R	ACTGGCCTGAATT	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73558886	73558886	+	Missense_Mutation	SNP	G	G	A	rs4747194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	44	65	0	0.556962	0	G|0.658;A|0.342	0.342	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon49	c.G7073A	p.R2358Q	CCAACCGGACAGT	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16184366	16184366	+	Silent	SNP	G	G	T	rs28364004	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	31	66	0	0.430556	0	G|0.983;T|0.017	0.017	strong	.	ABCC1	156	.	NM_004996	exon19	c.G2565T	p.L855L	GGAGCTGCTGGCT	.	PASS	Atlas-SNP
ZBTB7B	51043	hgsc.bcm.edu	37	1	154988957	154988957	+	Silent	SNP	A	A	G	rs2242195	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	139	0	1	0	A|0.422;G|0.578	0.578	strong	ZBTB7B,NS,carcinoma,+1,1	ZBTB7B	69	1	NM_001252406	exon5	c.A1518G	p.P506P	CTACCCACCACCC	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	93	0	0.450549	0	G|0.922;A|0.078	0.078	strong	.	.	.	.	NM_175882	exon1	c.G368A	p.R123Q	TGAGCCGGGTCAG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52391735	52391735	+	Silent	SNP	A	A	C	rs11714402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	70	147	1	0.514706	0.00680272	A|0.837;C|0.163	0.163	strong	DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	2	NM_015512	exon23	c.A3964C	p.R1322R	ACCAAGAGGAGCG	.	scavenged	Atlas-SNP
DCST1	149095	hgsc.bcm.edu	37	1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	rs11264300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	179	200	0	1	0	A|0.559;C|0.441	0.441	strong	DCST1,rectum,carcinoma,0,1	DCST1	69	1	NM_152494	exon14	c.A1534C	p.M512L	GACTCCATGCTAG	.	PASS	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186196	39186196	+	Silent	SNP	A	A	G	rs150267202	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	53	116	0	0.495327	0	A|0.898;G|0.102	0.102	strong	.	KRTAP1-4	4	.	NM_001257305	exon1	c.T135C	p.I45I	ATAGCCAATGCCA	.	PASS	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	37	19	12766624	12766624	+	Missense_Mutation	SNP	C	C	A	rs377104016		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	21	32	0	0.567568	0	.	.	weak	MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	NM_000528	exon14	c.G1714T	p.A572S	CCAGGGCGGGCAG	.	PASS	Atlas-SNP
CDK2	1017	hgsc.bcm.edu	37	12	56363357	56363357	+	Silent	SNP	G	G	A	rs2069406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	48	106	0	0.387097	0	G|0.958;A|0.042	0.042	strong	.	CDK2	27	.	NM_001798	exon5	c.G585A	p.E195E	TGCTGAGATGGTA	.	PASS	Atlas-SNP
ACVR2B	93	hgsc.bcm.edu	37	3	38523754	38523754	+	Silent	SNP	C	C	T	rs149695736	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	141	218	1	0.509025	0.00458716	C|0.999;T|0.001	0.001	strong	ACVR2B_ENST00000352511,caecum,carcinoma,0,2	ACVR2B	88	2	NM_001106	exon9	c.C1140T	p.A380A	AGATGCCTTCCTG	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39155881	39155881	+	Silent	SNP	C	C	T	rs3813048	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	65	338	0	0.300926	0	C|0.778;T|0.222	0.222	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.G225A	p.P75P	CAGGCCCGGAGTT	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	107937768	107937768	+	Missense_Mutation	SNP	G	G	A	rs1558781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	87	0	1	0	G|0.845;A|0.155	0.155	strong	BTBD11,NS,carcinoma,-1,2	BTBD11	122	2	NM_001018072	exon3	c.G1342A	p.G448S	CACCACGGCAATG	.	PASS	Atlas-SNP
TMPRSS7	344805	hgsc.bcm.edu	37	3	111760812	111760812	+	Missense_Mutation	SNP	G	G	C	rs11914332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	73	121	1	0.514085	0.00826446	G|0.957;C|0.043	0.043	strong	TMPRSS7_ENST00000419127,colon,carcinoma,+1,2	TMPRSS7	126	2	NM_001042575	exon2	c.G8C	p.R3P	TGTTTCGCATCAC	.	scavenged	Atlas-SNP
PROS1	5627	hgsc.bcm.edu	37	3	93624961	93624961	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	3	248	0	0.0136364	0	.	.	none	PROS1,NS,carcinoma,0,1	PROS1	126	1	NM_000313	exon5	c.C373T	p.P125S	TGCATGGCAGAGG	.	scavenged	Atlas-SNP
CEP85L	387119	hgsc.bcm.edu	37	6	118791804	118791804	+	Missense_Mutation	SNP	T	T	C	rs7743702	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	69	127	0	0.526718	0	T|0.975;C|0.025	0.025	strong	.	CEP85L	26	.	NM_001178035	exon12	c.A1927G	p.M643V	CTTGCATAGACTA	.	PASS	Atlas-SNP
C3orf22	152065	hgsc.bcm.edu	37	3	126272160	126272160	+	Missense_Mutation	SNP	T	T	C	rs146981008	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	114	0	0.453333	0	T|0.999;C|0.001	0.001	strong	.	C3orf22	17	.	NM_152533	exon2	c.A74G	p.K25R	AACTTCTTGGCAA	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106317	55106317	+	Silent	SNP	A	A	G	rs10416917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	302	300	0	0.9967	0	A|0.762;G|0.238	0.238	strong	.	LILRA1	105	.	NM_006863	exon4	c.A258G	p.P86P	CATCCCATCCATC	.	PASS	Atlas-SNP
CETP	1071	hgsc.bcm.edu	37	16	57015084	57015084	+	Silent	SNP	C	C	G	rs7192120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	68	0	0.542857	0	C|0.979;G|0.021	0.021	strong	CETP,colon,carcinoma,+2,1	CETP	50	1	NM_000078	exon12	c.C1161G	p.T387T	GACTACCGTCCAG	.	PASS	Atlas-SNP
GYS2	2998	hgsc.bcm.edu	37	12	21692210	21692210	+	Silent	SNP	T	T	C	rs142883971	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	46	88	0	0.505495	0	T|0.995;C|0.005	0.005	strong	GYS2,NS,carcinoma,-2,1	GYS2	110	1	NM_021957	exon15	c.A1872G	p.E624E	TGTTAGTTCCACA	.	PASS	Atlas-SNP
HEXDC	284004	hgsc.bcm.edu	37	17	80377690	80377690	+	Silent	SNP	T	T	G	rs1141463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	124	252	0	0.450909	0	T|0.535;G|0.465	0.465	strong	.	HEXDC	43	.	NM_173620	exon2	c.T15G	p.T5T	TTCCACTCCATTT	.	PASS	Atlas-SNP
PRR5	55615	hgsc.bcm.edu	37	22	45075738	45075738	+	Missense_Mutation	SNP	T	T	C	rs763213	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	63	158	0	0.453237	0	T|0.308;C|0.692	0.692	strong	.	PRR5	75	.	NM_001198721	exon2	c.T59C	p.M20T	AAAAGATGCCGGC	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27220066	27220066	+	Silent	SNP	G	G	A	rs2273719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	82	168	0	0.509317	0	G|0.791;A|0.209	0.209	strong	.	TEK	250	.	NM_000459	exon21	c.G3123A	p.G1041G	CTGCGGGATGACT	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79959197	79959197	+	Silent	SNP	G	G	A	rs73449933	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	57	69	0	0.703704	0	G|0.986;A|0.014	0.014	strong	.	VPS13A	735	.	NM_001018038	exon51	c.G7155A	p.E2385E	TAACGAGGTAAGT	.	PASS	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39581417	39581417	+	Missense_Mutation	SNP	A	A	G	rs76378145	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	55	0	1	0	A|0.972;G|0.028	0.028	strong	.	ADAM18	169	.	NM_014237	exon19	c.A2168G	p.E723G	ATGCAGAGTATAA	.	PASS	Atlas-SNP
CAT	847	hgsc.bcm.edu	37	11	34482908	34482908	+	Silent	SNP	C	C	T	rs769217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	68	134	0	0.552846	0	C|0.745;T|0.255	0.255	strong	.	CAT	42	.	NM_001752	exon9	c.C1167T	p.D389D	GCGTGACGGCCCG	.	PASS	Atlas-SNP
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	76878097	76878097	+	Silent	SNP	G	G	A	rs17098940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	42	0	0.522388	0	G|0.955;A|0.045	0.045	strong	.	ST6GALNAC3	71	.	NM_001160011	exon3	c.G618A	p.K206K	TGGGAAGGACAGG	.	PASS	Atlas-SNP
OR2T6	254879	hgsc.bcm.edu	37	1	248551203	248551203	+	Silent	SNP	T	T	C	rs6700947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	55	124	0	0.470085	0	T|0.722;C|0.278	0.278	strong	.	OR2T6	101	.	NM_001005471	exon1	c.T294C	p.T98T	CTGCACTGCTCAG	.	PASS	Atlas-SNP
ENTPD2	954	hgsc.bcm.edu	37	9	139945363	139945363	+	Silent	SNP	G	G	A	rs2292925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	44	64	0	0.637681	0	G|0.806;A|0.194	0.194	strong	.	ENTPD2	30	.	NM_203468	exon5	c.C765T	p.S255S	GAGGGCGCTGGCC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79024779	79024779	+	Missense_Mutation	SNP	A	A	G	rs16877109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	110	0	1	0	A|0.702;G|0.298	0.298	strong	.	CMYA5	643	.	NM_153610	exon2	c.A191G	p.Y64C	AGGAGTATATCAT	.	PASS	Atlas-SNP
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	55	111	0	0.528846	0	C|0.765;T|0.235	0.235	strong	.	TRIM26	74	.	NM_001242783	exon4	c.G474A	p.R158R	TCTGTCCCTCCTT	.	PASS	Atlas-SNP
TIMMDC1	51300	hgsc.bcm.edu	37	3	119222456	119222456	+	Silent	SNP	G	G	C	rs1131265	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	43	92	0	0.434343	0	G|0.795;C|0.205	0.205	strong	TIMMDC1,NS,carcinoma,0,1	TIMMDC1	29	1	NM_016589	exon3	c.G438C	p.V146V	GTTTGTGACTATA	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	21	0	1	0	T|0.360;C|0.640	0.640	strong	AZU1,NS,carcinoma,0,1	AZU1	31	1	NM_001700	exon4	c.T507C	p.F169F	CAGGTTTGTCAAC	.	PASS	Atlas-SNP
MROH6	642475	hgsc.bcm.edu	37	8	144652780	144652780	+	Silent	SNP	T	T	A	rs11990485	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	14	14	0	0.518519	0	T|0.989;A|0.011	0.011	strong	.	.	.	.	NM_001100878	exon5	c.A768T	p.G256G	CGTGGCTCCCACG	.	PASS	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	37	22	44586522	44586522	+	Silent	SNP	C	C	T	rs2272942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	51	71	0	0.62963	0	C|0.747;T|0.253	0.253	strong	.	PARVG	41	.	NM_001137606	exon7	c.C480T	p.V160V	CAACGTCCAGGTG	.	PASS	Atlas-SNP
SLC4A11	83959	hgsc.bcm.edu	37	20	3214581	3214581	+	Silent	SNP	C	C	T	rs3803956	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	66	59	0	1	0	C|0.820;T|0.180	0.180	strong	.	SLC4A11	188	.	NM_001174090	exon6	c.G720A	p.S240S	GAGCCACGACTGC	.	PASS	Atlas-SNP
KIF6	221458	hgsc.bcm.edu	37	6	39688551	39688551	+	Missense_Mutation	SNP	T	T	C	rs114269617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	31	68	0	0.525424	0	T|0.984;C|0.016	0.016	strong	.	KIF6	233	.	NM_145027	exon2	c.A103G	p.S35G	CCAAGCTAGGTAT	.	PASS	Atlas-SNP
CLDN15	24146	hgsc.bcm.edu	37	7	100875772	100875772	+	Silent	SNP	T	T	G	rs1047319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	41	51	0	0.97619	0	T|0.787;G|0.213	0.213	strong	CLDN15,NS,lymphoid_neoplasm,0,1	CLDN15	20	1	NM_014343	exon5	c.A606C	p.P202P	GGACACTGGAGCC	.	PASS	Atlas-SNP
OR1E2	8388	hgsc.bcm.edu	37	17	3336723	3336723	+	Missense_Mutation	SNP	A	A	G	rs73296096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	98	214	0	0.439462	0	A|0.975;G|0.025	0.025	strong	.	OR1E2	25	.	NM_003554	exon1	c.T413C	p.L138P	TGCAGGAGGAAGC	.	PASS	Atlas-SNP
FGFRL1	53834	hgsc.bcm.edu	37	4	1019011	1019011	+	Missense_Mutation	SNP	C	C	T	rs4647932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	74	115	0	0.524823	0	C|0.955;T|0.045	0.045	strong	FGFRL1,NS,carcinoma,0,1	FGFRL1	77	1	NM_001004356	exon7	c.C1391T	p.P464L	CAGGCCCAGTTGC	.	PASS	Atlas-SNP
TARP	0	hgsc.bcm.edu	37	7	38305142	38305142	+	Silent	SNP	G	G	C	rs113809137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	83	180	0	0.456044	0	G|0.805;C|0.195	0.195	strong	.	.	.	.	NM_001003799	exon2	c.C126G	p.G42G	TTTCTTGCCAATG	.	PASS	Atlas-SNP
C3orf33	285315	hgsc.bcm.edu	37	3	155493497	155493497	+	Silent	SNP	T	T	C	rs377018605	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	55	111	0	0.55	0	.	.	weak	.	C3orf33	18	.	NM_173657	exon4	c.A186G	p.S62S	TCTCAATGAAGCT	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124134743	124134743	+	Silent	SNP	G	G	A	rs2466637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	83	0	1	0	G|0.522;A|0.478	0.478	strong	.	.	.	.	NM_001005198	exon1	c.G21A	p.G7G	ACAAGGGATCACT	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238253332	238253332	+	Silent	SNP	G	G	A	rs10084221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	34	54	0	0.441558	0	G|0.935;A|0.065	0.065	strong	.	COL6A3	608	.	NM_004369	exon36	c.C7329T	p.A2443A	CACCCGGGCCCCC	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92568196	92568196	+	Silent	SNP	C	C	T	rs374591402		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	83	195	0	0.553333	0	.	.	weak	.	FAT3	1822	.	NM_001008781	exon14	c.C10032T	p.D3344D	CCAAGACGTCTAC	.	PASS	Atlas-SNP
APEH	327	hgsc.bcm.edu	37	3	49714225	49714225	+	Silent	SNP	T	T	C	rs1131095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	166	314	0	0.551495	0	T|0.737;C|0.263	0.263	strong	APEH,NS,carcinoma,0,1	APEH	45	1	NM_001640	exon9	c.T852C	p.Y284Y	GTATTATGTGGAC	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229783328	229783328	+	Silent	SNP	G	G	C	rs115914317	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	76	163	0	0.517007	0	G|0.997;C|0.003	0.003	strong	.	URB2	152	.	NM_014777	exon7	c.G3978C	p.L1326L	TGTCCTGGCTGCA	.	PASS	Atlas-SNP
LRRC37B	114659	hgsc.bcm.edu	37	17	30372739	30372739	+	Missense_Mutation	SNP	C	C	T	rs1638299	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	17	33	0	0.288136	0	C|0.910;T|0.090	0.090	strong	LRRC37B,NS,carcinoma,0,1	LRRC37B	67	1	NM_052888	exon8	c.C2144T	p.A715V	ATATGGCCTGCTG	.	scavenged	Atlas-SNP
TM2D3	80213	hgsc.bcm.edu	37	15	102192540	102192540	+	Silent	SNP	T	T	G	rs675436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	21	44	0	0.362069	0	T|0.666;G|0.334	0.334	strong	.	TM2D3	18	.	NM_025141	exon1	c.A25C	p.R9R	GGCCCCTCAGCGG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242035544	242035544	+	Missense_Mutation	SNP	G	G	C	rs2240539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	125	249	0	0.538793	0	G|0.889;C|0.111	0.111	strong	.	MTERFD2	33	.	NM_182501	exon4	c.C1015G	p.L339V	CATCCAGACTTGC	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109371659	109371659	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	922	10	844	3	0.010846	0.0035545	.	.	none	RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	NM_006267	exon17	c.G2410A	p.A804T	CGATGGGCAGAAG	.	scavenged	Atlas-SNP
CYP4A11	1579	hgsc.bcm.edu	37	1	47398496	47398496	+	Missense_Mutation	SNP	A	A	G	rs45564940	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	101	238	0	0.412245	0	A|0.500;G|0.500	0.500	weak	.	CYP4A11	77	.	NM_000778	exon11	c.T1301C	p.F434S	AAACGGAAAGGGT	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	130008285	130008285	+	Missense_Mutation	SNP	T	T	C	rs17164867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	31	70	0	0.442857	0	C|0.201;T|0.799	0.201	strong	.	CPA5	61	.	NM_001127442	exon11	c.T1073C	p.M358T	GGCCTATGACAGT	.	PASS	Atlas-SNP
SMR3A	26952	hgsc.bcm.edu	37	4	71232701	71232701	+	Missense_Mutation	SNP	C	C	T	rs6853742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	67	94	0	0.563025	0	C|0.296;N|0.000	.	strong	SMR3A,NS,carcinoma,0,1	SMR3A	35	1	NM_012390	exon3	c.C395T	p.P132L	CTACTCCTGCACC	.	PASS	Atlas-SNP
OAS1	4938	hgsc.bcm.edu	37	12	113357237	113357237	+	Missense_Mutation	SNP	G	G	C	rs1051042	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	69	0	1	0	G|0.261;C|0.739	0.739	strong	.	OAS1	128	.	NM_016816	exon6	c.G1082C	p.R361T	CCAGGAGGTATCA	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22363448	22363448	+	Silent	SNP	A	A	T	rs200452805	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	10	34	2	0.172414	0.0588235	.	.	weak	ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	NM_001001411	exon3	c.T1071A	p.I357I	ATGAATAATCTTA	.	scavenged	Atlas-SNP
ARHGAP40	343578	hgsc.bcm.edu	37	20	37257590	37257590	+	Silent	SNP	C	C	G	rs6070809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	99	209	0	0.447964	0	C|0.699;G|0.301	0.301	strong	.	ARHGAP40	50	.	NM_001164431	exon4	c.C576G	p.G192G	GAATGGCGACTCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418275	105418275	+	Silent	SNP	T	T	C	rs2819441	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	309	166	284	1	0.537217	0.00352113	C|0.267;T|0.733	0.267	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A3513G	p.P1171P	GAACGATGGCATC	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103506690	103506690	+	Missense_Mutation	SNP	G	G	A	rs4987063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	35	93	0	0.364583	0	G|0.993;A|0.007	0.007	strong	.	.	.	.	NM_001204425	exon12	c.G1795A	p.V599I	CTCTATGTTTTGC	.	PASS	Atlas-SNP
UVSSA	57654	hgsc.bcm.edu	37	4	1374769	1374769	+	Silent	SNP	G	G	A	rs115722661	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	97	213	0	0.480198	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_020894	exon12	c.G1854A	p.E618E	GCAGGAGCGCCCG	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549264	158549264	+	Silent	SNP	G	G	A	rs863360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	127	267	0	0.503968	0	G|0.489;A|0.511	0.511	strong	OR10X1,NS,carcinoma,0,1	OR10X1	96	1	NM_001004477	exon1	c.C426T	p.I142I	GTTACAGATGGCC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8137052	8137052	+	Silent	SNP	G	G	A	rs10420783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	72	0	1	0	G|0.949;A|0.051	0.051	strong	.	FBN3	300	.	NM_032447	exon62	c.C7968T	p.P2656P	GGGTCCGGGGCTG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6588553	6588553	+	Silent	SNP	C	C	T	rs56313830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	49	57	0	0.576471	0	C|0.870;T|0.130	0.130	strong	.	DNHD1	198	.	NM_144666	exon36	c.C11814T	p.G3938G	ATTGGGCGCTTTG	.	PASS	Atlas-SNP
HCLS1	3059	hgsc.bcm.edu	37	3	121361787	121361787	+	Silent	SNP	G	G	A	rs2070178	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	85	0	0.486486	0	G|0.772;A|0.228	0.228	strong	.	HCLS1	78	.	NM_005335	exon6	c.C441T	p.H147H	AGATGTGTGCTTC	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52866060	52866060	+	Missense_Mutation	SNP	C	C	T	rs11608915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	147	331	1	0.44012	0.00302115	C|0.677;T|0.323	0.323	strong	.	KRT6C	55	.	NM_173086	exon2	c.G545A	p.R182Q	AGGAACCGCACCT	.	PASS	Atlas-SNP
NMU	10874	hgsc.bcm.edu	37	4	56475330	56475330	+	Missense_Mutation	SNP	T	T	C	rs35892915	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	43	71	0	0.494253	0	T|0.978;C|0.022	0.022	strong	.	NMU	17	.	NM_006681	exon4	c.A236G	p.E79G	AGCTCCTCCAGTG	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30831088	30831088	+	Missense_Mutation	SNP	G	G	A	rs35897481	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	84	0	0.515789	0	G|0.881;A|0.119	0.119	strong	.	FAM188B	62	.	NM_032222	exon5	c.G971A	p.R324K	CGGACAGGATGCC	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26936766	26936766	+	Silent	SNP	G	G	A	rs58274935	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	10	28	0	0.434783	0	G|0.952;A|0.048	0.048	strong	.	TPST2	23	.	NM_001008566	exon3	c.C831T	p.V277V	CAGGGAGACACCA	.	PASS	Atlas-SNP
TSPAN9	10867	hgsc.bcm.edu	37	12	3387697	3387697	+	Silent	SNP	T	T	C	rs16930370	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	221	192	0	1	0	T|0.797;C|0.203	0.203	strong	.	TSPAN9	20	.	NM_006675	exon4	c.T174C	p.I58I	GGTCATTGCCATA	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22575423	22575423	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	6	275	0	0.0217391	0	.	.	none	ZNF98_ENST00000357774,NS,carcinoma,+1,2	ZNF98	230	2	NM_001098626	exon4	c.G614C	p.S205T	TCTCCACTATGAA	.	scavenged	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887149	9887149	+	Missense_Mutation	SNP	G	G	C	rs11662946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	84	134	3	0.545455	0.0223881	G|0.937;C|0.063	0.063	strong	TXNDC2_ENST00000306084,colon,carcinoma,-1,2	TXNDC2	168	2	NM_001098529	exon2	c.G673C	p.A225P	AATATTGCCAAGA	.	scavenged	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	52	63	0	0.514852	0	G|0.756;A|0.244	0.244	strong	.	SNED1	76	.	NM_001080437	exon15	c.G2073A	p.R691R	ACGCCGGTGCCAG	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060658	16060658	+	Missense_Mutation	SNP	A	A	G	rs11880184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	107	0	1	0	A|0.722;G|0.278	0.278	strong	.	OR10H4	48	.	NM_001004465	exon1	c.A841G	p.T281A	ACCTATACTGTCT	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30071330	30071330	+	Missense_Mutation	SNP	C	C	T	rs1116221	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	32	47	0	0.592593	0	C|0.710;T|0.290	0.290	strong	.	TRIM31	40	.	NM_007028	exon9	c.G1261A	p.E421K	GAACCTCACAAAA	.	PASS	Atlas-SNP
ASB18	401036	hgsc.bcm.edu	37	2	237103697	237103697	+	Missense_Mutation	SNP	G	G	T	rs10177957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	131	124	0	1	0	G|0.894;T|0.106	0.106	strong	.	ASB18	34	.	NM_212556	exon6	c.C1219A	p.H407N	GCTTGTGCATCTG	.	PASS	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	76	133	0	0.535211	0	C|0.766;T|0.234	0.234	strong	.	C20orf111	28	.	NM_016470	exon4	c.G642A	p.V214V	GGAATACACTTCC	.	PASS	Atlas-SNP
ATP1A4	480	hgsc.bcm.edu	37	1	160136350	160136350	+	Silent	SNP	G	G	A	rs7529215	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	108	204	0	0.545455	0	G|0.522;A|0.478	0.478	strong	.	ATP1A4	167	.	NM_144699	exon8	c.G1080A	p.A360A	CATGGCGCGGAAG	.	PASS	Atlas-SNP
NCOA6	23054	hgsc.bcm.edu	37	20	33338099	33338099	+	Silent	SNP	G	G	A	rs61736335	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	101	155	0	0.510101	0	G|0.996;A|0.004	0.004	strong	.	NCOA6	219	.	NM_014071	exon9	c.C1899T	p.G633G	CATCTGGCCCTGG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6550309	6550309	+	Missense_Mutation	SNP	G	G	A	rs2344829	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	67	118	0	0.507576	0	G|0.292;A|0.708	0.708	strong	.	DNHD1	198	.	NM_144666	exon12	c.G2305A	p.G769R	AAAGGCGGGTTGC	.	PASS	Atlas-SNP
LIPG	9388	hgsc.bcm.edu	37	18	47088741	47088741	+	Silent	SNP	C	C	T	rs874566	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	113	0	0.494624	0	C|0.953;T|0.047	0.047	strong	.	LIPG	47	.	NM_006033	exon1	c.C63T	p.S21S	GGGGAGCCCCGTA	.	PASS	Atlas-SNP
MFSD3	113655	hgsc.bcm.edu	37	8	145736101	145736101	+	Silent	SNP	G	G	A	rs34730139	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	17	41	0	0.447368	0	G|0.966;A|0.034	0.034	strong	.	MFSD3	17	.	NM_138431	exon3	c.G951A	p.L317L	AATCTTGAGAGGT	.	PASS	Atlas-SNP
RMDN2	151393	hgsc.bcm.edu	37	2	38178406	38178406	+	Silent	SNP	A	A	G	rs4670799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	12	37	0	0.387097	0	A|0.638;G|0.362	0.362	strong	.	.	.	.	NM_144713	exon2	c.A48G	p.R16R	CCAACGATGTTCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228468244	228468244	+	Silent	SNP	G	G	A	rs12061320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	54	118	0	0.580645	0	G|0.865;A|0.135	0.135	strong	.	OBSCN	2142	.	NM_001271223	exon35	c.G9231A	p.V3077V	GGTGGTGTTCCTG	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	50280469	50280469	+	Silent	SNP	C	C	T	rs74714098	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	104	198	0	0.509804	0	C|0.983;T|0.017	0.017	strong	.	NRXN1	1118	.	NM_001135659	exon22	c.G4188A	p.T1396T	CAGGGTCGTGGTA	.	PASS	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169562904	169562904	+	Silent	SNP	C	C	T	rs6128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	45	86	0	0.436893	0	C|0.687;T|0.313	0.313	strong	SELP,NS,carcinoma,-1,2	SELP	132	2	NM_003005	exon14	c.G2346A	p.T782T	ACCTATCGTAGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513318	195513318	+	Silent	SNP	G	G	A	rs199718749	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	475	164	510	0	0.345263	0	G|0.993;A|0.007	0.007	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5133T	p.T1711T	AAGAGGGGTGGCC	.	PASS	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19547503	19547503	+	Missense_Mutation	SNP	C	C	T	rs3751821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	88	0	1	0	C|0.801;T|0.199	0.199	strong	CCP110,NS,carcinoma,0,1	CCP110	57	1	NM_001199022	exon4	c.C512T	p.P171L	ATTCTCCGAAGCA	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860602	16860602	+	Silent	SNP	T	T	C	rs61731252	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	55	52	0	0.982143	0	T|0.927;C|0.073	0.073	strong	.	NWD1	303	.	NM_001007525	exon6	c.T1149C	p.R383R	TGCCCGTGGCCTG	.	PASS	Atlas-SNP
IGSF5	150084	hgsc.bcm.edu	37	21	41143018	41143018	+	Missense_Mutation	SNP	T	T	A	rs74817033	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	35	64	0	0.5	0	T|0.959;A|0.041	0.041	strong	.	IGSF5	62	.	NM_001080444	exon4	c.T594A	p.S198R	TCAAAGTGCAGTG	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	37	9	20820346	20820346	+	Silent	SNP	A	A	T	rs147147351	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	55	127	0	0.447154	0	A|1.000;T|0.000	0.000	strong	KIAA1797,rectum,carcinoma,+1,1	.	.	1	NM_017794	exon15	c.A1584T	p.R528R	TCTACGAATAATA	.	PASS	Atlas-SNP
ZBTB38	253461	hgsc.bcm.edu	37	3	141162185	141162185	+	Missense_Mutation	SNP	T	T	G	rs16851435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	50	95	0	0.403226	0	G|0.170;N|0.000	0.170	strong	.	ZBTB38	92	.	NM_001080412	exon8	c.T955G	p.S319A	CATTTTTCCAGGG	.	PASS	Atlas-SNP
RGS13	6003	hgsc.bcm.edu	37	1	192613522	192613522	+	Missense_Mutation	SNP	C	C	T	rs146420296		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	96	235	0	0.448598	0	C|1.000;T|0.000	0.000	weak	.	RGS13	31	.	NM_002927	exon4	c.C58T	p.P20S	AGGCCCCCTTCAA	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	94	176	0	0.439252	0	C|0.845;T|0.155	0.155	strong	.	CILP2	84	.	NM_153221	exon8	c.C3261T	p.G1087G	TGACGGCTTCTCC	.	PASS	Atlas-SNP
TAS2R41	259287	hgsc.bcm.edu	37	7	143175345	143175345	+	Missense_Mutation	SNP	C	C	T	rs10278721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	59	115	0	0.513043	0	C|0.770;T|0.230	0.230	strong	.	TAS2R41	43	.	NM_176883	exon1	c.C380T	p.P127L	GGTTCCCAGGGTG	.	PASS	Atlas-SNP
FIG4	9896	hgsc.bcm.edu	37	6	110064928	110064928	+	Missense_Mutation	SNP	A	A	T	rs2295837	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	76	114	0	0.531469	0	A|0.937;T|0.063	0.063	strong	.	FIG4	77	.	NM_014845	exon10	c.A1090T	p.M364L	GACCAGATGTTCC	.	PASS	Atlas-SNP
IQCK	124152	hgsc.bcm.edu	37	16	19800213	19800213	+	Missense_Mutation	SNP	T	T	C	rs7191155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	56	99	0	0.504505	0	T|0.841;C|0.159	0.159	strong	.	IQCK	35	.	NM_153208	exon8	c.T659C	p.L220P	CAGCCCTCTACAT	.	PASS	Atlas-SNP
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628414	60628414	+	Silent	SNP	G	G	T	rs111274143	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	54	89	0	0.477876	0	G|0.894;T|0.106	0.106	strong	.	ZSWIM6	51	.	NM_020928	exon1	c.G315T	p.V105V	GCCGGTGCAGCGC	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	37	36	0	0.685185	0	T|0.745;C|0.255	0.255	strong	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	NM_002609	exon19	c.A2601G	p.L867L	CCACTTTAAAGGC	.	PASS	Atlas-SNP
MBOAT7	79143	hgsc.bcm.edu	37	19	54682538	54682538	+	Silent	SNP	C	C	T	rs116423748	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	61	100	0	0.504132	0	C|0.991;T|0.009	0.009	strong	.	MBOAT7	37	.	NM_001146082	exon7	c.G975A	p.Q325Q	CCACCACTGCACC	.	PASS	Atlas-SNP
NFAM1	150372	hgsc.bcm.edu	37	22	42805444	42805444	+	Missense_Mutation	SNP	G	G	C	rs17003048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	42	72	0	0.525	0	G|0.962;C|0.038	0.038	strong	.	NFAM1	12	.	NM_145912	exon3	c.C561G	p.N187K	TACCTTGTTCCAG	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862532	5862532	+	Missense_Mutation	SNP	A	A	C	rs10742809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	58	121	0	0.456693	0	A|0.670;C|0.330	0.330	strong	.	OR52E6	70	.	NM_001005167	exon1	c.T596G	p.M199R	CCAAACATAATGT	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38851669	38851669	+	Silent	SNP	C	C	T	rs4714192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	20	52	0	0.434783	0	C|0.782;T|0.218	0.218	strong	DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	NM_001206927	exon56	c.C8154T	p.Y2718Y	AAGCTACGTGGAT	.	PASS	Atlas-SNP
TLR5	7100	hgsc.bcm.edu	37	1	223284528	223284528	+	Missense_Mutation	SNP	A	A	G	rs5744174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	70	162	0	0.416667	0	A|0.691;G|0.309	0.309	strong	.	TLR5	86	.	NM_003268	exon6	c.T1846C	p.F616L	CAGAGAACGAGTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	81	149	0	0.50625	0	T|0.764;A|0.236	0.236	strong	.	RP1L1	453	.	NM_178857	exon4	c.A5666T	p.D1889V	TCTACATCTTCTG	.	PASS	Atlas-SNP
GABRP	2568	hgsc.bcm.edu	37	5	170215670	170215670	+	Silent	SNP	G	G	A	rs7725726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	169	162	0	1	0	G|0.788;A|0.212	0.212	strong	.	GABRP	65	.	NM_014211	exon2	c.G51A	p.E17E	CACTGAGAGGTGA	.	PASS	Atlas-SNP
PPP1R1C	151242	hgsc.bcm.edu	37	2	182981968	182981968	+	Silent	SNP	A	A	G	rs1882212	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	321	307	2	1	0.00651466	A|0.704;G|0.296	0.296	strong	.	PPP1R1C	14	.	NM_001261424	exon5	c.A297G	p.A99A	ATCAGCATTCCCT	.	PASS	Atlas-SNP
TCEAL5	340543	hgsc.bcm.edu	37	X	102529190	102529190	+	Missense_Mutation	SNP	C	C	G	rs6621640	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	205	335	0	0.587393	0	C|0.861;G|0.139	0.139	strong	.	TCEAL5	28	.	NM_001012979	exon3	c.G302C	p.R101P	GCGGCCCGCGGCT	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	23	80	0	0.365079	0	C|0.792;N|0.000	.	strong	.	OR10S1	78	.	NM_001004474	exon1	c.G187A	p.G63S	CAGAGCCCACAGT	.	PASS	Atlas-SNP
CDT1	81620	hgsc.bcm.edu	37	16	88872229	88872229	+	Missense_Mutation	SNP	A	A	G	rs480727	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	81	0	1	0	A|0.452;G|0.548	0.548	strong	.	CDT1	30	.	NM_030928	exon5	c.A784G	p.T262A	GATGGCACCAGGA	.	PASS	Atlas-SNP
HIPK1	204851	hgsc.bcm.edu	37	1	114505000	114505000	+	Silent	SNP	G	G	A	rs17852555	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	67	120	0	0.468531	0	G|0.743;A|0.257	0.257	strong	.	HIPK1	195	.	NM_198268	exon9	c.G2043A	p.P681P	TGTACCGATTGTA	.	PASS	Atlas-SNP
FRZB	2487	hgsc.bcm.edu	37	2	183702691	183702691	+	Silent	SNP	G	G	A	rs1561367	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	44	0	0.48	0	G|0.997;A|0.003	0.003	strong	.	FRZB	42	.	NM_001463	exon5	c.C846T	p.L282L	TTTACCGAGTCGA	.	PASS	Atlas-SNP
ATOH1	474	hgsc.bcm.edu	37	4	94750227	94750227	+	Silent	SNP	G	G	A	rs138388359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	52	133	0	0.452174	0	A|0.001;G|0.999;T|0.000	0.001	strong	.	ATOH1	40	.	NM_005172	exon1	c.G150A	p.P50P	CTACCCGCCTGAG	.	PASS	Atlas-SNP
UTP3	57050	hgsc.bcm.edu	37	4	71555656	71555656	+	Missense_Mutation	SNP	T	T	G	rs111975570	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	71	0	0.486842	0	T|0.994;G|0.006	0.006	strong	.	UTP3	40	.	NM_020368	exon1	c.T1262G	p.L421R	GGGGACTTACTCC	.	PASS	Atlas-SNP
SRCIN1	80725	hgsc.bcm.edu	37	17	36708277	36708277	+	Missense_Mutation	SNP	C	C	T	rs7222929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	90	1	0.5	0.0111111	C|0.930;T|0.070	0.070	strong	SRCIN1,rectum,carcinoma,0,1	SRCIN1	66	1	NM_025248	exon14	c.G2572A	p.V858M	AGTCCACGCTCTT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677556	100677556	+	Silent	SNP	A	A	C	rs4373459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	62	153	3	0.253061	0.0196078	A|0.947;C|0.053	0.053	strong	MUC17,colon,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A2859C	p.T953T	CAGCACACCTGTG	.	scavenged	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	37	3	171320907	171320907	+	Silent	SNP	C	C	T	rs6766336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	36	0	0.428571	0	C|0.942;T|0.058	0.058	strong	.	PLD1	134	.	NM_002662	exon27	c.G3186A	p.G1062G	TTTGGTCCCAACA	.	PASS	Atlas-SNP
PRSS36	146547	hgsc.bcm.edu	37	16	31151622	31151622	+	Missense_Mutation	SNP	C	C	T	rs61729752	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	50	93	0	0.520833	0	C|0.982;T|0.018	0.018	strong	.	PRSS36	50	.	NM_173502	exon14	c.G2282A	p.R761K	TCACACCTGTTCT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103387667	103387667	+	Missense_Mutation	SNP	G	G	A	rs79455872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	132	271	0	0.461538	0	G|0.970;A|0.030	0.030	strong	.	.	.	.	NM_001146197	exon4	c.C15380T	p.S5127L	TCACTTGAAAGTT	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1552457	1552457	+	Silent	SNP	G	G	A	rs16995332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	688	344	672	0	0.5	0	G|0.896;A|0.104	0.104	strong	.	SIRPB1	83	.	NM_006065	exon3	c.C660T	p.D220D	GTGAACGTCCCCA	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957693	111957693	+	Missense_Mutation	SNP	A	A	G	rs2485319	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	134	292	0	0.465278	0	A|0.440;G|0.560	0.560	strong	.	OVGP1	177	.	NM_002557	exon11	c.T1430C	p.M477T	ATGGTCATTGCCC	.	PASS	Atlas-SNP
CTC1	80169	hgsc.bcm.edu	37	17	8141779	8141779	+	Silent	SNP	T	T	C	rs73244859	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	102	208	0	0.507463	0	T|0.984;C|0.016	0.016	strong	.	CTC1	75	.	NM_025099	exon3	c.A366G	p.A122A	CAAGTCTGCCGAT	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32014190	32014190	+	Silent	SNP	G	G	A	rs116701346	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	47	82	0	0.594937	0	G|0.996;A|0.004	0.004	strong	.	TNXB	553	.	NM_019105	exon31	c.C10362T	p.T3454T	AGCCACGGTCAGT	.	PASS	Atlas-SNP
ZNF429	353088	hgsc.bcm.edu	37	19	21719401	21719401	+	Silent	SNP	T	T	C	rs35782355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	26	58	0	0.38806	0	T|0.444;C|0.556	0.556	strong	.	ZNF429	338	.	NM_001001415	exon4	c.T546C	p.F182F	ATCATTTTGCATG	.	PASS	Atlas-SNP
PLEKHN1	84069	hgsc.bcm.edu	37	1	902128	902128	+	Missense_Mutation	SNP	C	C	T	rs28499371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	6	8	0	0.4	0	C|0.935;T|0.065	0.065	strong	.	PLEKHN1	49	.	NM_001160184	exon2	c.C128T	p.A43V	CCGAGGCTGCTCG	.	PASS	Atlas-SNP
RPH3AL	9501	hgsc.bcm.edu	37	17	171098	171098	+	Silent	SNP	T	T	G	rs73971738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	26	76	0	0.412698	0	T|0.845;G|0.155	0.155	strong	.	RPH3AL	18	.	NM_001190413	exon3	c.A186C	p.A62A	CCGCTCTGCCCTC	.	PASS	Atlas-SNP
NETO1	81832	hgsc.bcm.edu	37	18	70417378	70417378	+	Missense_Mutation	SNP	G	G	C	rs17086286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	93	181	0	0.438679	0	G|0.978;C|0.022	0.022	strong	.	NETO1	178	.	NM_001201465	exon9	c.C1460G	p.A487G	GCATCTGCAGCAT	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982009	240982009	+	Missense_Mutation	SNP	G	G	A	rs202192655		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	2	35	0	0.166667	0	.	.	weak	PRR21,NS,malignant_melanoma,0,2	PRR21	53	2	NM_001080835	exon1	c.C391T	p.P131S	CCGTGGGTGAAGA	.	scavenged	Atlas-SNP
SPOCK2	9806	hgsc.bcm.edu	37	10	73826775	73826775	+	Silent	SNP	G	G	A	rs7079142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	58	0	0.459459	0	G|0.990;A|0.010	0.010	strong	.	SPOCK2	32	.	NM_001244950	exon8	c.C813T	p.A271A	GATGGCGGCCAGC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31380198	31380198	+	Missense_Mutation	SNP	C	C	T	rs61738275	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	93	0	1	0	C|0.748;T|0.252	0.252	strong	.	MICA	21	.	NM_001177519	exon5	c.C989T	p.P330L	TATGTCCGTTGTT	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587067	15587067	+	Silent	SNP	T	T	A	rs35927052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	59	116	0	0.541284	0	T|0.981;A|0.019	0.019	strong	.	PGLYRP2	116	.	NM_052890	exon2	c.A414T	p.I138I	CAAATTTATGACC	.	PASS	Atlas-SNP
OR2A25	392138	hgsc.bcm.edu	37	7	143771937	143771937	+	Missense_Mutation	SNP	G	G	C	rs2961135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	133	259	1	0.498127	0.003861	G|0.409;C|0.590	0.590	strong	.	OR2A25	66	.	NM_001004488	exon1	c.G625C	p.A209P	GTGGGAGCCTTCT	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41525914	41525914	+	Silent	SNP	C	C	T	rs750625	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	107	203	0	0.488584	0	C|0.778;A|0.001	.	strong	.	ANK1	497	.	NM_001142446	exon40	c.G5388A	p.V1796V	TACAGACACCAGG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38377404	38377404	+	Missense_Mutation	SNP	C	C	T	rs201328117		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	12	30	0	0.179104	0	.	.	weak	.	WDR87	191	.	NM_031951	exon6	c.G6790A	p.E2264K	CCTCCTCCCTTAC	.	PASS	Atlas-SNP
MYRIP	25924	hgsc.bcm.edu	37	3	40251392	40251392	+	Silent	SNP	T	T	C	rs1799418	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	175	140	0	0.983146	0	C|0.439;N|0.001	0.439	strong	.	MYRIP	98	.	NM_015460	exon11	c.T1713C	p.D571D	TCGGGATCCCCAG	.	PASS	Atlas-SNP
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	146	0	1	0	C|0.738;T|0.261	0.261	strong	.	MAPRE1	17	.	NM_012325	exon5	c.C570T	p.D190D	CGGAGACGACGAG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891748	44891748	+	Missense_Mutation	SNP	T	T	C	rs60800862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	60	134	0	0.451128	0	T|0.983;C|0.017	0.017	strong	.	ZNF285	86	.	NM_152354	exon4	c.A659G	p.E220G	CGTTTTTCAACCG	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68628049	68628049	+	Missense_Mutation	SNP	T	T	G	rs2306024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	127	0	1	0	T|0.895;G|0.105	0.105	strong	.	ITGA11	110	.	NM_001004439	exon12	c.A1411C	p.M471L	CCCGCATAGCCTG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	62	95	0	0.568807	0	T|0.164;G|0.282	0.164	strong	.	MYOM1	192	.	NM_003803	exon6	c.G999A	p.G333G	GTGCATCCCATAT	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	37	MT	6253	6253	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	11	0	1	0	.	.	none	.	.	.	.	ENST00000361624	exon1	c.T350C	p.M117T	CTGCTATAGTGGA	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443853	100443853	+	Silent	SNP	A	A	G	rs17029090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	69	0	0.469388	0	A|0.895;G|0.105	0.105	strong	.	C4orf17	42	.	NM_032149	exon3	c.A324G	p.P108P	GCCTCCACGGCCT	.	PASS	Atlas-SNP
SLC27A3	11000	hgsc.bcm.edu	37	1	153748219	153748219	+	Silent	SNP	C	C	T	rs36064263	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	8	27	0	0.470588	0	C|0.897;T|0.103	0.103	strong	.	SLC27A3	42	.	NM_024330	exon1	c.C387T	p.T129T	GCACACCTTTCTC	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70845400	70845400	+	Missense_Mutation	SNP	A	A	G	rs59354595	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	103	218	0	0.451754	0	A|0.963;G|0.037	0.037	strong	.	BDP1	204	.	NM_018429	exon34	c.A6962G	p.K2321R	TGGTCAAATCAGT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272858	1272858	+	Silent	SNP	C	C	T	rs4963059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	50	113	0	0.555556	0	C|0.663;T|0.337	0.337	strong	.	MUC5B	473	.	NM_002458	exon31	c.C14748T	p.F4916F	AACCTTCAGCGTG	.	PASS	Atlas-SNP
CLEC3A	10143	hgsc.bcm.edu	37	16	78064733	78064733	+	Missense_Mutation	SNP	C	C	A	rs2072663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	60	115	0	0.495868	0	C|0.867;A|0.133	0.133	strong	.	CLEC3A	39	.	NM_005752	exon3	c.C616A	p.Q206K	ATCCCTCAATAGG	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518233	161518233	+	Silent	SNP	C	C	A	rs139622799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	585	181	488	2	0.309402	0.00409836	C|0.985;A|0.015	0.015	strong	FCGR3A,lower_third,carcinoma,-2,1	FCGR3A	38	1	NM_000569	exon3	c.G405T	p.P135P	CTGCACCGGGTCA	.	scavenged	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	37	4	187004544	187004544	+	Silent	SNP	C	C	T	rs35111588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	45	116	0	0.412844	0	C|0.949;T|0.051	0.051	strong	.	TLR3	83	.	NM_003265	exon4	c.C1704T	p.N568N	CCTTAACTTGGAG	.	PASS	Atlas-SNP
ORAOV1	220064	hgsc.bcm.edu	37	11	69490001	69490001	+	Missense_Mutation	SNP	C	C	T	rs56107468	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	101	227	0	0.463303	0	C|0.978;T|0.022	0.022	strong	.	ORAOV1	11	.	NM_153451	exon1	c.G7A	p.G3S	GACTGCCAGCCAT	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786681	75786681	+	Missense_Mutation	SNP	G	G	A	rs75784751	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	11	33	0	0.211538	0	G|0.083;A|0.917	0.917	weak	.	ZNF717	160	.	NM_001128223	exon5	c.C2093T	p.P698L	TTCCCCGGTGTGA	.	PASS	Atlas-SNP
C8orf82	414919	hgsc.bcm.edu	37	8	145754187	145754187	+	Silent	SNP	C	C	G	rs115228909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	44	0	0.490909	0	C|0.864;G|0.136	0.136	strong	.	C8orf82	7	.	NM_001001795	exon1	c.G114C	p.P38P	GGTCCGCGGCTCC	.	PASS	Atlas-SNP
USP17L2	377630	hgsc.bcm.edu	37	8	11995276	11995276	+	Missense_Mutation	SNP	C	C	T	rs372605534		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	351	148	322	2	0.421652	0.00621118	.	.	weak	USP17L2,NS,carcinoma,0,1	USP17L2	47	1	NM_201402	exon1	c.G994A	p.D332N	GTCCGTCGTGACA	.	scavenged	Atlas-SNP
RACGAP1	29127	hgsc.bcm.edu	37	12	50384469	50384469	+	Silent	SNP	A	A	G	rs56699050	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	70	136	0	0.530303	0	A|0.918;G|0.082	0.082	strong	.	RACGAP1	36	.	NM_013277	exon18	c.T1821C	p.P607P	ATACCTAGGAGTG	.	PASS	Atlas-SNP
SLC27A6	28965	hgsc.bcm.edu	37	5	128362830	128362830	+	Silent	SNP	A	A	G	rs2304578	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	87	127	0	0.540373	0	A|0.935;G|0.065	0.065	strong	.	SLC27A6	112	.	NM_001017372	exon7	c.A1260G	p.E420E	AGGAGAACCTGGA	.	PASS	Atlas-SNP
ZNF80	7634	hgsc.bcm.edu	37	3	113955726	113955726	+	Nonsense_Mutation	SNP	G	G	A	rs79892855	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	88	0	0.449438	0	G|0.987;A|0.013	0.013	strong	.	ZNF80	75	.	NM_007136	exon1	c.C196T	p.R66X	GATGTCGAACAAG	.	PASS	Atlas-SNP
LDB3	11155	hgsc.bcm.edu	37	10	88446985	88446985	+	Silent	SNP	T	T	C	rs76615432	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	69	149	0	0.5	0	T|0.954;C|0.046	0.046	strong	.	LDB3	164	.	NM_001171610	exon6	c.T849C	p.D283D	CATGGATGCCATC	.	PASS	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52822464	52822464	+	Missense_Mutation	SNP	T	T	C	rs2232402	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	73	153	0	0.489933	0	T|0.969;C|0.031	0.031	strong	KRT75,NS,carcinoma,+2,3	KRT75	75	3	NM_004693	exon6	c.A1099G	p.I367V	CAGAGATCTCTTG	.	PASS	Atlas-SNP
TMEM47	83604	hgsc.bcm.edu	37	X	34674970	34674970	+	Silent	SNP	C	C	G	rs5928617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	85	124	0	0.512048	0	C|0.689;G|0.311	0.311	strong	.	TMEM47	45	.	NM_031442	exon1	c.G177C	p.R59R	GGGTTTCCGGCAG	.	PASS	Atlas-SNP
MARCO	8685	hgsc.bcm.edu	37	2	119739063	119739063	+	Missense_Mutation	SNP	T	T	C	rs6761637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	23	68	0	0.418182	0	T|0.873;C|0.127	0.127	strong	MARCO,brain,glioma,0,1	MARCO	120	1	NM_006770	exon9	c.T845C	p.F282S	GTGACTTCGGGAG	.	PASS	Atlas-SNP
PCDHGB6	56100	hgsc.bcm.edu	37	5	140789933	140789933	+	Missense_Mutation	SNP	G	G	A	rs3749767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	157	268	1	0.455072	0.00373134	G|0.702;A|0.298	0.298	strong	.	PCDHGB6	120	.	NM_032100	exon1	c.G2164A	p.A722T	AGCCCTGCTACTT	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167000256	167000256	+	Missense_Mutation	SNP	G	G	C	rs12638625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	75	136	0	0.438596	0	G|0.622;C|0.378	0.378	strong	.	ZBBX	299	.	NM_001199201	exon20	c.C2024G	p.A675G	AAATTTGCTGTTG	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6182828	6182828	+	Missense_Mutation	SNP	A	A	T	rs1800387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	28	77	0	0.318182	0	A|0.839;T|0.161	0.161	strong	.	VWF	338	.	NM_000552	exon8	c.T954A	p.N318K	CATTTCATTGATG	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44102193	44102193	+	Silent	SNP	G	G	A	rs187103862	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	44	94	0	0.431373	0	G|1.000;A|0.000	0.000	strong	LOXHD1_ENST00000398722,NS,carcinoma,0,2	LOXHD1	367	2	NM_144612	exon32	c.C4956T	p.I1652I	CTCCCCGATGAGA	.	PASS	Atlas-SNP
NSMCE1	197370	hgsc.bcm.edu	37	16	27238110	27238110	+	Silent	SNP	C	C	T	rs1127228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	35	80	0	0.443038	0	C|0.668;T|0.332	0.332	strong	.	NSMCE1	28	.	NM_145080	exon6	c.G531A	p.E177E	GTATTGCTCCATC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547090	132547090	+	Silent	SNP	A	A	G	rs7974276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	75	120	1	0.669643	0.00833333	A|0.794;G|0.206	0.206	strong	EP400,colon,carcinoma,0,3	EP400	370	3	NM_015409	exon47	c.A8178G	p.Q2726Q	GCAGCAACAACAG	.	scavenged	Atlas-SNP
TEX19	400629	hgsc.bcm.edu	37	17	80320303	80320303	+	Missense_Mutation	SNP	G	G	T	rs147220016	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	26	51	0	0.351351	0	G|0.997;T|0.003	0.003	strong	.	TEX19	17	.	NM_207459	exon2	c.G277T	p.G93W	GTGCAGGGGGGCT	.	PASS	Atlas-SNP
HTR6	3362	hgsc.bcm.edu	37	1	19992372	19992372	+	Silent	SNP	G	G	T	rs8192529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	8	15	0	0.347826	0	G|0.970;T|0.030	0.030	strong	.	HTR6	38	.	NM_000871	exon1	c.G126T	p.A42A	GGCGGCGGCCAAC	.	PASS	Atlas-SNP
CNGB3	54714	hgsc.bcm.edu	37	8	87680282	87680282	+	Missense_Mutation	SNP	C	C	T	rs16916632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	86	163	0	0.464865	0	C|0.951;T|0.049	0.049	strong	.	CNGB3	176	.	NM_019098	exon5	c.G608A	p.R203Q	TTAATTCGCTTTA	.	PASS	Atlas-SNP
FOXN1	8456	hgsc.bcm.edu	37	17	26864302	26864302	+	Missense_Mutation	SNP	G	G	C	rs532648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	176	190	0	0.99435	0	G|0.618;C|0.382	0.382	strong	.	FOXN1	51	.	NM_003593	exon8	c.G1795C	p.A599P	TTGGCAGCCCCGG	.	PASS	Atlas-SNP
MRPS27	23107	hgsc.bcm.edu	37	5	71524163	71524163	+	Silent	SNP	A	A	T	rs10942927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	30	65	0	0.46875	0	A|0.768;T|0.232	0.232	strong	.	MRPS27	23	.	NM_015084	exon8	c.T624A	p.L208L	AAGCAAAAGGGAT	.	PASS	Atlas-SNP
DLK1	8788	hgsc.bcm.edu	37	14	101201206	101201206	+	Silent	SNP	C	C	T	rs139584149	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	16	30	0	0.615385	0	C|0.991;T|0.009	0.009	strong	.	DLK1	57	.	NM_003836	exon5	c.C1125T	p.S375S	CTTCAGCAAGGAG	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825280	825280	+	Missense_Mutation	SNP	C	C	T	rs1809008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	208	108	0	1	0	C|0.724;T|0.276	0.276	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.G1022A	p.R341Q	CTTACCCGTGCCG	.	PASS	Atlas-SNP
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	37	56	0	0.569231	0	C|0.967;T|0.033	0.033	strong	.	WBP4	40	.	NM_007187	exon4	c.C216T	p.A72A	AGCTGCCCTGAAA	.	PASS	Atlas-SNP
SSRP1	6749	hgsc.bcm.edu	37	11	57101000	57101000	+	Silent	SNP	G	G	C	rs7932705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	144	0	0.567568	0	G|0.986;C|0.014	0.014	strong	.	SSRP1	75	.	NM_003146	exon4	c.C255G	p.L85L	ATCAGAGAGTTTC	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	119	102	0	0.991667	0	G|0.728;A|0.272	0.272	strong	.	PALLD	179	.	NM_001166108	exon2	c.G186A	p.K62K	GGAAAAGGAGATC	.	PASS	Atlas-SNP
CDH26	60437	hgsc.bcm.edu	37	20	58558015	58558015	+	Missense_Mutation	SNP	T	T	C	rs6015609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	107	194	0	0.488584	0	T|0.938;C|0.062	0.062	strong	CDH26_ENST00000244047,colon,carcinoma,0,2	CDH26	229	2	NM_177980	exon5	c.T431C	p.I144T	GAAAAATTGTGGA	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12225946	12225946	+	Silent	SNP	T	T	G	rs3763823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	130	104	0	0.992366	0	T|0.332;G|0.668	0.668	strong	MICAL2,colon,carcinoma,0,2	MICAL2	114	2	NM_014632	exon4	c.T414G	p.R138R	CCTTCGTGGCCTG	.	PASS	Atlas-SNP
PLAC4	191585	hgsc.bcm.edu	37	21	42551183	42551183	+	Missense_Mutation	SNP	G	G	A	rs202000983	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	158	263	1	0.531987	0.00380228	.	.	weak	.	.	.	.	NM_182832	exon1	c.C373T	p.P125S	AGTGAGGGAGTCC	.	PASS	Atlas-SNP
ERCC4	2072	hgsc.bcm.edu	37	16	14031695	14031695	+	Silent	SNP	A	A	G	rs2020958	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	41	70	0	0.506173	0	A|0.982;G|0.018	0.018	strong	.	ERCC4	100	.	NM_005236	exon9	c.A1884G	p.E628E	AAAGGAAGCTTTT	.	PASS	Atlas-SNP
LYPD4	147719	hgsc.bcm.edu	37	19	42342319	42342319	+	Silent	SNP	A	A	G	rs2290695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	30	32	0	1	0	A|0.389;G|0.611	0.611	strong	.	LYPD4	30	.	NM_173506	exon4	c.T228C	p.V76V	GCCCACAACTCCC	.	PASS	Atlas-SNP
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246979	47246979	+	Silent	SNP	A	A	G	rs16946912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	8	26	0	0.307692	0	A|0.888;G|0.112	0.112	strong	.	B4GALNT2	67	.	NM_153446	exon11	c.A1590G	p.E530E	CTCAGAACTGGCT	.	PASS	Atlas-SNP
TRMT2B	79979	hgsc.bcm.edu	37	X	100278558	100278558	+	Silent	SNP	T	T	C	rs61745518	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	175	165	0	0.972222	0	T|0.979;C|0.021	0.021	strong	.	TRMT2B	33	.	NM_001167972	exon7	c.A657G	p.V219V	ATGAAATACAAGG	.	PASS	Atlas-SNP
IRGM	345611	hgsc.bcm.edu	37	5	150227998	150227998	+	Silent	SNP	C	C	T	rs10065172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	80	199	0	0.446927	0	C|0.714;T|0.286	0.286	strong	.	IRGM	8	.	NM_001145805	exon2	c.C313T	p.L105L	AACTACCTGATGG	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	125	249	0	0.469925	0	A|0.655;C|0.345	0.345	strong	.	OR2D3	51	.	NM_001004684	exon1	c.A396C	p.A132A	GCTGGCAGTGATG	.	PASS	Atlas-SNP
SPHK1	8877	hgsc.bcm.edu	37	17	74383475	74383475	+	Silent	SNP	T	T	C	rs3744037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	62	109	0	0.607843	0	T|0.796;C|0.204	0.204	strong	.	SPHK1	24	.	NM_182965	exon6	c.T1221C	p.Y407Y	GGTATATGTGCCC	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444012	20444012	+	Missense_Mutation	SNP	A	A	T	rs3861512	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	196	187	0	0.989899	0	A|0.772;T|0.228	0.228	strong	OR4K15,colon,carcinoma,0,2	OR4K15	82	2	NM_001005486	exon1	c.A335T	p.E112V	TGGTTGAGCGCAA	.	PASS	Atlas-SNP
PNPLA3	80339	hgsc.bcm.edu	37	22	44324727	44324727	+	Missense_Mutation	SNP	C	C	G	rs738409	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	76	181	0	0.447059	0	C|0.774;G|0.226	0.226	strong	PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	NM_025225	exon3	c.C444G	p.I148M	CTTCATCCCCTTC	.	PASS	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129772309	129772309	+	Silent	SNP	G	G	A	rs12275633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	146	299	0	0.523297	0	G|0.921;A|0.079	0.079	strong	.	PRDM10	120	.	NM_020228	exon22	c.C3382T	p.L1128L	GGTCCAGGGAGTC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46760086	46760086	+	Missense_Mutation	SNP	C	C	T	rs35364389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	38	50	0	0.513514	0	C|0.794;T|0.206	0.206	strong	.	CELSR1	242	.	NM_014246	exon34	c.G8842A	p.G2948S	GCCGGCCCTTCAG	.	PASS	Atlas-SNP
AKR7A3	22977	hgsc.bcm.edu	37	1	19611227	19611227	+	Silent	SNP	G	G	A	rs1065658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	96	199	0	0.419214	0	G|0.842;A|0.158	0.158	strong	.	AKR7A3	30	.	NM_012067	exon5	c.C657T	p.P219P	GCCCACGGGCTGT	.	PASS	Atlas-SNP
ANKFN1	162282	hgsc.bcm.edu	37	17	54431364	54431364	+	Silent	SNP	T	T	C	rs9902114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	60	119	0	0.526316	0	T|0.926;C|0.074	0.074	strong	.	ANKFN1	115	.	NM_153228	exon5	c.T567C	p.I189I	GCCCATTGCAAGG	.	PASS	Atlas-SNP
CD300E	342510	hgsc.bcm.edu	37	17	72608834	72608834	+	Silent	SNP	G	G	A	rs579238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	29	45	0	0.47541	0	G|0.713;A|0.287	0.287	strong	.	CD300E	70	.	NM_181449	exon4	c.C576T	p.V192V	CCAGAAGACAGCA	.	PASS	Atlas-SNP
CAPN5	726	hgsc.bcm.edu	37	11	76796022	76796022	+	Silent	SNP	C	C	A	rs34236021	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	24	85	0	0.328767	0	C|0.973;A|0.027	0.027	strong	.	CAPN5	67	.	NM_004055	exon2	c.C90A	p.P30P	GGACCCCCTCTTC	.	PASS	Atlas-SNP
SSR2	6746	hgsc.bcm.edu	37	1	155988108	155988108	+	Silent	SNP	A	A	G	rs34428308	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	37	61	0	0.560606	0	A|0.990;G|0.010	0.010	strong	.	SSR2	20	.	NM_003145	exon3	c.T207C	p.F69F	AATGCCAAAGTCT	.	PASS	Atlas-SNP
TRIM29	23650	hgsc.bcm.edu	37	11	119996490	119996490	+	Silent	SNP	G	G	A	rs61753082	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	78	151	0	0.661017	0	G|0.979;A|0.021	0.021	strong	.	TRIM29	78	.	NM_012101	exon4	c.C1242T	p.D414D	CAGGTCGTCCTTG	.	PASS	Atlas-SNP
PDIA5	10954	hgsc.bcm.edu	37	3	122864436	122864436	+	Silent	SNP	G	G	A	rs8739	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	97	0	1	0	A|0.501;C|0.057;G|0.305;T|0.138	0.501	strong	PDIA5,caecum,carcinoma,+1,2	PDIA5	66	2	NM_006810	exon12	c.G978A	p.A326A	AGAAGCGGATGTA	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15791212	15791212	+	Silent	SNP	A	A	C	rs61731188	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	48	211	0	0.186047	0	A|0.969;C|0.031	0.031	strong	.	CYP4F12	89	.	NM_023944	exon5	c.A408C	p.I136I	AGGGATACTGCTG	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101719138	101719138	+	Missense_Mutation	SNP	C	C	T	rs79940439	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	22	96	0	0.244444	0	.	.	weak	.	PABPC1	76	.	NM_002568	exon10	c.G1424A	p.R475Q	ATGACTCGTGGAA	.	PASS	Atlas-SNP
RETSAT	54884	hgsc.bcm.edu	37	2	85570849	85570849	+	Missense_Mutation	SNP	C	C	T	rs4832168	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	418	38	542	0	0.0909091	0	C|0.990;T|0.010	0.010	strong	.	RETSAT	56	.	NM_017750	exon10	c.G1606A	p.G536R	CAGCCCCGTAGCA	.	PASS	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53671754	53671754	+	Missense_Mutation	SNP	C	C	T	rs2111119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	37	94	0	0.33945	0	C|0.869;T|0.131	0.131	strong	RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	NM_015272	exon21	c.G3073A	p.G1025S	CACTGCCTTCTTG	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48145742	48145742	+	Missense_Mutation	SNP	T	T	A	rs34135219	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	118	224	0	0.502128	0	T|0.963;A|0.037	0.037	strong	.	ABCC12	190	.	NM_033226	exon14	c.A2069T	p.E690V	CTCTCCTCCATTA	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406892	50406892	+	Silent	SNP	C	C	T	rs61737143	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	55	171	0	0.348101	0	C|0.982;T|0.018	0.018	strong	.	SALL4	168	.	NM_020436	exon2	c.G2130A	p.T710T	AAGAGGCGTGGGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149515824	149515824	+	Missense_Mutation	SNP	C	C	T	rs745044	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	60	0	1	0	C|0.940;T|0.060	0.060	strong	.	.	.	.	NM_198455	exon83	c.C11725T	p.R3909C	CGCACCCGCCTCT	.	PASS	Atlas-SNP
KCNMB2	10242	hgsc.bcm.edu	37	3	178546026	178546026	+	Silent	SNP	T	T	C	rs9831934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	161	148	0	1	0	T|0.360;C|0.640	0.640	strong	.	KCNMB2	35	.	NM_005832	exon5	c.T288C	p.N96N	ATTTAATTGCTCC	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112642568	112642568	+	Missense_Mutation	SNP	C	C	G	rs9865242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	206	244	0	0.995169	0	C|0.406;G|0.594	0.594	strong	.	CD200R1	91	.	NM_138806	exon8	c.G1003C	p.E335Q	ATGCCTCAGATGC	.	PASS	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801298	140801298	+	Silent	SNP	C	C	A	rs73792198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	25	44	0	0.454545	0	C|0.885;A|0.115	0.115	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.C504A	p.L168L	CTCCCTCCAGAGC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134682802	134682802	+	Missense_Mutation	SNP	C	C	T	rs7084629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	33	77	0	0.464789	0	C|0.878;T|0.122	0.122	strong	.	TTC40	100	.	NM_001200049	exon33	c.G4586A	p.C1529Y	CTGACGCACACCT	.	PASS	Atlas-SNP
CXXC11	285093	hgsc.bcm.edu	37	2	242814604	242814604	+	Silent	SNP	G	G	C	rs78628254	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	56	0	0.547945	0	G|0.967;C|0.033	0.033	strong	.	.	.	.	NM_173821	exon2	c.G897C	p.P299P	CAGCCCGGTTGGC	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	166	208	0	0.994012	0	G|0.754;C|0.246	0.246	strong	.	CILP2	84	.	NM_153221	exon7	c.G1038C	p.L346L	GGAGCTGCGGGGA	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640274	3640274	+	Missense_Mutation	SNP	G	G	A	rs714181	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	148	158	1	0.993289	0.00632911	G|0.785;N|0.000	.	strong	.	SLX4	173	.	NM_032444	exon12	c.C3365T	p.P1122L	ATAGACGGAGATT	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24498674	24498674	+	Silent	SNP	C	C	T	rs77507357	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	104	172	0	0.517413	0	C|0.989;T|0.011	0.011	strong	.	ITSN2	224	.	NM_147152	exon18	c.G1989A	p.Q663Q	ATAAAGCTGTTCA	.	PASS	Atlas-SNP
UBE2U	148581	hgsc.bcm.edu	37	1	64686577	64686577	+	Missense_Mutation	SNP	C	C	T	rs139887828	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	78	187	0	0.490566	0	C|0.991;T|0.009	0.009	strong	.	UBE2U	16	.	NM_152489	exon6	c.C493T	p.R165C	GACCCACGTAAAT	.	PASS	Atlas-SNP
TNS4	84951	hgsc.bcm.edu	37	17	38645125	38645125	+	Missense_Mutation	SNP	A	A	G	rs3764424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	75	185	0	0.477707	0	A|0.708;G|0.292	0.292	strong	TNS4,NS,carcinoma,0,2	TNS4	72	2	NM_032865	exon3	c.T536C	p.L179P	CTGCGAAGGGAGC	.	PASS	Atlas-SNP
YEATS4	8089	hgsc.bcm.edu	37	12	69783937	69783937	+	Silent	SNP	T	T	C	rs315121	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	36	113	0	0.363636	0	T|0.931;G|0.001	.	strong	.	YEATS4	15	.	NM_006530	exon7	c.T525C	p.L175L	AGAGCTTGAAGTG	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107706208	107706208	+	Silent	SNP	C	C	T	rs73725316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	51	118	0	0.472222	0	C|0.992;T|0.008	0.008	strong	.	LAMB4	253	.	NM_007356	exon21	c.G2835A	p.T945T	CATACCCGTATAA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2152850	2152850	+	Silent	SNP	A	A	G	rs9926309	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	24	80	0	0.352941	0	A|0.976;G|0.024	0.024	strong	.	PKD1	184	.	NM_000296	exon24	c.T8913C	p.A2971A	GTGGTCAGCACCC	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151672285	151672285	+	Missense_Mutation	SNP	A	A	G	rs13212161	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	47	78	0	0.435185	0	A|0.908;G|0.092	0.092	strong	.	AKAP12	170	.	NM_005100	exon4	c.A2759G	p.E920G	TGACAGAACCTCT	.	PASS	Atlas-SNP
CETN1	1068	hgsc.bcm.edu	37	18	580623	580623	+	Missense_Mutation	SNP	T	T	C	rs61734344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	38	54	0	1	0	T|0.833;C|0.167	0.167	strong	.	CETN1	48	.	NM_004066	exon1	c.T215C	p.M72T	AGAAAATGATCTC	.	PASS	Atlas-SNP
ZBTB38	253461	hgsc.bcm.edu	37	3	141163655	141163655	+	Missense_Mutation	SNP	G	G	A	rs3732867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	53	97	0	0.53	0	G|0.980;A|0.020	0.020	strong	ZBTB38,NS,carcinoma,-1,1	ZBTB38	92	1	NM_001080412	exon8	c.G2425A	p.A809T	AATATTGCTGAAG	.	PASS	Atlas-SNP
IFNA16	3449	hgsc.bcm.edu	37	9	21216934	21216934	+	Missense_Mutation	SNP	G	G	A	rs28368161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	150	332	0	0.436047	0	G|0.966;A|0.034	0.034	strong	.	IFNA16	27	.	NM_002173	exon1	c.C371T	p.T124I	TCCTGTGTCACAC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50019740	50019740	+	Missense_Mutation	SNP	T	T	C	rs114590878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	69	112	0	0.560976	0	T|0.992;C|0.008	0.008	strong	.	WDFY4	205	.	NM_020945	exon30	c.T5201C	p.M1734T	AGCTGATGGACGG	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860084	16860084	+	Missense_Mutation	SNP	C	C	T	rs11668502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	89	0	1	0	C|0.936;T|0.064	0.064	strong	.	NWD1	303	.	NM_001007525	exon6	c.C631T	p.L211F	GACCGGCTCGCGG	.	PASS	Atlas-SNP
CEP250	11190	hgsc.bcm.edu	37	20	34089679	34089679	+	Silent	SNP	C	C	T	rs224379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	21	31	0	0.6	0	C|0.996;T|0.004	0.004	strong	.	CEP250	141	.	NM_007186	exon29	c.C3906T	p.S1302S	GAAATCCAAGTGG	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38798648	38798648	+	Missense_Mutation	SNP	C	C	A	rs76798247	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	179	1	1	0.00558659	.	.	weak	.	TLR1	70	.	NM_003263	exon4	c.G1805T	p.S602I	AAGTAGCTGCAGA	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48628470	48628470	+	Missense_Mutation	SNP	T	T	A	rs9913430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	96	94	0	0.950495	0	T|0.605;A|0.395	0.395	strong	SPATA20,colon,carcinoma,0,1	SPATA20	59	1	NM_022827	exon12	c.T1495A	p.S499T	CTCAATTCAGGGC	.	PASS	Atlas-SNP
DNAJC15	29103	hgsc.bcm.edu	37	13	43597865	43597865	+	Missense_Mutation	SNP	A	A	G	rs12015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	43	81	0	0.425743	0	A|0.735;G|0.265	0.265	strong	DNAJC15_ENST00000379221,NS,carcinoma,0,2	DNAJC15	16	2	NM_013238	exon1	c.A103G	p.R35G	CAGCAGAGACTGG	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	60	130	0	0.441176	0	C|0.443;T|0.557	0.557	strong	POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	NM_006231	exon26	c.G3156A	p.T1052T	GATGGACGTAGAC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224578	248224578	+	Missense_Mutation	SNP	T	T	C	rs60743763	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	23	532	1	0.0688623	0.0018797	T|0.933;C|0.067	0.067	strong	OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	NM_001004687	exon1	c.T595C	p.F199L	ACAGTGTTTTTGA	.	scavenged	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7064271	7064271	+	Silent	SNP	T	T	C	rs116753166	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	82	127	0	0.493976	0	T|0.983;C|0.017	0.017	strong	.	NLRP14	187	.	NM_176822	exon4	c.T1014C	p.Y338Y	GGAGTATATTTAC	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965956	49965956	+	Missense_Mutation	SNP	G	G	A	rs10406757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	171	275	0	0.529412	0	A|0.034;C|0.000;G|0.965	0.034	strong	.	ALDH16A1	54	.	NM_153329	exon8	c.G1042A	p.A348T	GGGGCTGCCGCAT	.	PASS	Atlas-SNP
FGF6	2251	hgsc.bcm.edu	37	12	4554549	4554549	+	Missense_Mutation	SNP	G	G	A	rs17183529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	44	59	0	0.494382	0	G|0.996;A|0.004	0.004	strong	FGF6,colon,carcinoma,-1,2	FGF6	40	2	NM_020996	exon1	c.C188T	p.A63V	AGCCCGGCGCGAG	.	PASS	Atlas-SNP
IL1A	3552	hgsc.bcm.edu	37	2	113539224	113539224	+	Silent	SNP	G	G	A	rs20540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	112	243	1	0.46281	0.00411523	G|0.980;A|0.020	0.020	strong	.	IL1A	19	.	NM_000575	exon4	c.C276T	p.I92I	ATCAGTGATGGAT	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373966	27373966	+	Silent	SNP	C	C	T	rs2234899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	30	79	0	0.309278	0	C|0.966;T|0.034	0.034	strong	IL4R,lymph_node,lymphoid_neoplasm,+2,1	IL4R	70	1	NM_000418	exon11	c.C1293T	p.C431C	GTCATGCCTTCTT	.	PASS	Atlas-SNP
C10orf111	221060	hgsc.bcm.edu	37	10	15138615	15138615	+	Missense_Mutation	SNP	C	C	T	rs7896053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	206	185	0	1	0	C|0.740;T|0.260	0.260	strong	.	C10orf111	11	.	NM_153244	exon2	c.G209A	p.R70K	GGTAGCCTGAGTC	.	PASS	Atlas-SNP
SUPT7L	9913	hgsc.bcm.edu	37	2	27883958	27883958	+	Silent	SNP	C	C	T	rs6756254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	440	194	358	0	0.440909	0	C|0.940;T|0.060	0.060	strong	.	SUPT7L	36	.	NM_014860	exon3	c.G312A	p.S104S	AGGGCACGAGGGA	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47295906	47295906	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	16	36	0	0.470588	0	.	.	none	.	PREX1	441	.	NM_020820	exon13	c.G1581A	p.P527P	GATCACCGGGGTG	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254318	39254318	+	Missense_Mutation	SNP	C	C	T	rs138296121	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	122	252	0	0.440433	0	C|0.900;T|0.100	0.100	strong	.	KRTAP4-8	57	.	NM_031960	exon1	c.G19A	p.G7S	CGGAGCCACAACA	.	PASS	Atlas-SNP
TRIM36	55521	hgsc.bcm.edu	37	5	114480364	114480364	+	Silent	SNP	C	C	T	rs7716270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	69	152	0	0.479167	0	C|0.732;T|0.268	0.268	strong	.	TRIM36	126	.	NM_018700	exon4	c.G702A	p.L234L	CTTACACAGATGG	.	PASS	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36453208	36453208	+	Missense_Mutation	SNP	T	T	C	rs149988943	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	151	99	4	1	0.040404	T|0.781;C|0.219	0.219	strong	MRPL45,NS,carcinoma,0,1	MRPL45	27	1	NM_032351	exon1	c.T59C	p.F20S	GGTGGTTTCGGCA	.	scavenged	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91770308	91770308	+	Silent	SNP	C	C	T	rs112741231	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	31	54	0	0.534483	0	C|0.983;T|0.017	0.017	strong	CCDC88C_ENST00000389857,NS,carcinoma,0,2	CCDC88C	192	2	NM_001080414	exon20	c.G3372A	p.T1124T	ACTCAGCGTGGAG	.	PASS	Atlas-SNP
KRT34	3885	hgsc.bcm.edu	37	17	39535388	39535388	+	Missense_Mutation	SNP	T	T	C	rs2071599	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	203	208	1	0.980676	0.00480769	T|0.874;C|0.126	0.126	strong	.	KRT34	71	.	NM_021013	exon6	c.A1043G	p.H348R	CTGTAGTGGGCCT	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17146590	17146590	+	Silent	SNP	A	A	G	rs12571671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	73	124	0	0.514085	0	A|0.935;G|0.065	0.065	strong	CUBN,NS,carcinoma,0,1	CUBN	515	1	NM_001081	exon12	c.T1245C	p.G415G	AAAATAACCAGAG	.	PASS	Atlas-SNP
GNRHR	2798	hgsc.bcm.edu	37	4	68619601	68619601	+	Silent	SNP	G	G	A	rs4986942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	64	129	0	0.390244	0	G|0.914;A|0.086	0.086	strong	.	GNRHR	31	.	NM_000406	exon1	c.C453T	p.S151S	GCTGTTGCTTTTC	.	PASS	Atlas-SNP
ATP12A	479	hgsc.bcm.edu	37	13	25266932	25266932	+	Silent	SNP	C	C	A	rs963984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	53	103	0	0.424	0	C|0.845;A|0.155	0.155	strong	.	ATP12A	172	.	NM_001185085	exon10	c.C1293A	p.V431V	CCAAGTCTTTGAC	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76922208	76922208	+	Silent	SNP	G	G	A	rs111033209	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	24	83	0	0.387097	0	G|0.966;A|0.034	0.034	strong	.	MYO7A	164	.	NM_000260	exon45	c.G6063A	p.K2021K	GCCCAAGTATCTC	.	PASS	Atlas-SNP
UPP2	151531	hgsc.bcm.edu	37	2	158958605	158958605	+	Missense_Mutation	SNP	G	G	T	rs6710480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	49	102	0	0.480392	0	G|0.846;T|0.154	0.154	strong	.	UPP2	60	.	NM_001135098	exon3	c.G201T	p.R67S	CAATAGGTCCATG	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	816973	816973	+	Missense_Mutation	SNP	A	A	G	rs35317722	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	58	0	0.493506	0	A|0.970;G|0.030	0.030	strong	.	MSLN	109	.	NM_013404	exon14	c.A1486G	p.N496D	AACATGAACGGGT	.	PASS	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131822055	131822055	+	Silent	SNP	T	T	C	rs9282762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	16	50	0	0.4	0	T|0.623;C|0.377	0.377	strong	.	IRF1	26	.	NM_002198	exon7	c.A555G	p.P185P	AGCACATGGCGAC	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	37	19	42873089	42873089	+	Silent	SNP	G	G	A	rs10425783	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	48	78	0	0.539326	0	G|0.969;A|0.031	0.031	strong	.	MEGF8	358	.	NM_001271938	exon37	c.G6576A	p.T2192T	CGAGACGCAGAAT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23914286	23914286	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	62	79	0	0.512397	0	.	.	none	.	SACS	871	.	NM_014363	exon10	c.A3729G	p.E1243E	GTAGTCTTCATCA	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11272227	11272227	+	Missense_Mutation	SNP	C	C	T	rs61744103	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	46	73	0	0.597403	0	C|0.991;T|0.009	0.009	strong	.	CLEC16A	101	.	NM_015226	exon23	c.C2842T	p.L948F	CCTCACCTTCCTG	.	PASS	Atlas-SNP
CCL18	6362	hgsc.bcm.edu	37	17	34391721	34391721	+	Missense_Mutation	SNP	G	G	A	rs73290772	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	74	115	0	0.493333	0	G|0.994;A|0.006	0.006	strong	.	CCL18	9	.	NM_002988	exon1	c.G19A	p.A7T	GCAGCTGCCCTCC	.	PASS	Atlas-SNP
FRMPD2	143162	hgsc.bcm.edu	37	10	49440168	49440168	+	Silent	SNP	C	C	T	rs11816450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	42	94	0	0.43299	0	C|0.961;T|0.039	0.039	strong	.	FRMPD2	157	.	NM_001018071	exon10	c.G1158A	p.A386A	CATATACGCCAAG	.	PASS	Atlas-SNP
DNAJB1	3337	hgsc.bcm.edu	37	19	14629150	14629150	+	Silent	SNP	G	G	A	rs3962158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	17	32	0	0.5	0	G|0.685;A|0.315	0.315	strong	.	DNAJB1	38	.	NM_006145	exon1	c.C12T	p.D4D	GTAGTAGTCTTTA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677279	100677279	+	Missense_Mutation	SNP	G	G	C	rs76184171	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	50	132	1	0.247525	0.00757576	G|0.992;C|0.008	0.008	strong	MUC17,colon,carcinoma,+1,9	MUC17	804	9	NM_001040105	exon3	c.G2582C	p.S861T	CTTATAGTGAAGG	.	scavenged	Atlas-SNP
PHF21B	112885	hgsc.bcm.edu	37	22	45283897	45283897	+	Silent	SNP	C	C	T	rs6006901	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	50	72	0	0.526316	0	C|0.826;T|0.174	0.174	strong	.	PHF21B	61	.	NM_138415	exon10	c.G1143A	p.P381P	GAGGGGCGGCTCC	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50726570	50726570	+	Silent	SNP	G	G	A	rs4801822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	79	124	0	0.544828	0	G|0.507;A|0.494	0.494	strong	MYH14_ENST00000262269,NS,carcinoma,0,2	MYH14	261	2	NM_001077186	exon5	c.G657A	p.A219A	CGTGGCGTCGTCT	.	PASS	Atlas-SNP
LMAN1L	79748	hgsc.bcm.edu	37	15	75111530	75111530	+	Missense_Mutation	SNP	G	G	A	rs62621375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	224	236	0	0.995556	0	G|0.924;A|0.076	0.076	strong	.	LMAN1L	43	.	NM_021819	exon6	c.G635A	p.G212D	ATCCAGGTGAGTT	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71838597	71838597	+	Silent	SNP	C	C	A	rs2303606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	51	55	0	1	0	C|0.529;A|0.471	0.471	strong	.	DYSF	536	.	NM_001130982	exon39	c.C4104A	p.I1368I	TTAGATCCTGGCA	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169648723	169648723	+	Missense_Mutation	SNP	G	G	C	rs36088849	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	60	84	0	0.545455	0	G|0.977;C|0.023	0.023	strong	.	THBS2	230	.	NM_003247	exon4	c.C398G	p.T133S	TGCCGGGTGCCGT	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	37	9	95768396	95768396	+	Silent	SNP	C	C	T	rs199786328	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	56	68	0	0.658824	0	C|1.000;T|0.000	0.000	strong	.	FGD3	116	.	NM_001083536	exon6	c.C771T	p.A257A	CCGAGCCGTAGGG	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10624502	10624502	+	Silent	SNP	G	G	A	rs56225585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	58	0	1	0	G|0.914;A|0.086	0.086	strong	.	JAG1	213	.	NM_000214	exon20	c.C2382T	p.S794S	GGTGCCGCTGTTG	.	PASS	Atlas-SNP
TRAF3	7187	hgsc.bcm.edu	37	14	103336654	103336654	+	Missense_Mutation	SNP	A	A	G	rs147686384		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	4	112	1	0.036036	0.00892857	A|1.000;G|0.000	0.000	weak	TRAF3,NS,carcinoma,0,1	TRAF3	60	1	NM_145726	exon3	c.A116G	p.Y39C	GAGGTTACAAGGA	.	scavenged	Atlas-SNP
NEFM	4741	hgsc.bcm.edu	37	8	24771318	24771318	+	Silent	SNP	G	G	A	rs61735462	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	68	0	0.419753	0	G|0.992;A|0.008	0.008	strong	.	NEFM	115	.	NM_005382	exon1	c.G12A	p.T4T	CTACACGTTGGAC	.	PASS	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32852172	32852172	+	Missense_Mutation	SNP	G	G	A	rs33962176	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	18	38	0	0.409091	0	G|0.902;A|0.098	0.098	strong	PRRG4,NS,carcinoma,0,1	PRRG4	15	1	NM_024081	exon2	c.G97A	p.E33K	GCGGGAGAAGAAG	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102262227	102262227	+	Silent	SNP	C	C	G	rs143541316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	18	42	0	0.45	0	C|0.990;G|0.010	0.010	strong	.	SEC31B	84	.	NM_015490	exon11	c.G1194C	p.L398L	AGTAACCAGCTTC	.	PASS	Atlas-SNP
GAS2L3	283431	hgsc.bcm.edu	37	12	101018161	101018161	+	Silent	SNP	C	C	T	rs1045603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	20	45	0	0.425532	0	C|0.901;T|0.099	0.099	strong	.	GAS2L3	76	.	NM_174942	exon10	c.C1578T	p.S526S	CAGTTCCAAAACC	.	PASS	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	36	71	0	0.391304	0	T|0.917;C|0.083	0.083	strong	RAB3IL1,NS,carcinoma,0,1	RAB3IL1	39	1	NM_001271686	exon2	c.A287G	p.Q96R	TGGCCTTGGGCCT	.	PASS	Atlas-SNP
LGR4	55366	hgsc.bcm.edu	37	11	27402475	27402475	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	2	197	0	0.0112994	0	.	.	none	LGR4,NS,NS,0,1	LGR4	87	1	NM_018490	exon8	c.G797A	p.G266E	AATGCTCCATCAG	.	scavenged	Atlas-SNP
PDLIM4	8572	hgsc.bcm.edu	37	5	131607721	131607721	+	Missense_Mutation	SNP	C	C	T	rs10479001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	41	71	0	0.5125	0	C|0.913;T|0.087	0.087	strong	PDLIM4,NS,carcinoma,0,1	PDLIM4	22	1	NM_001131027	exon6	c.C674T	p.A225V	CAGGGGCACCATC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512676	4512676	+	Silent	SNP	T	T	G	rs59593546	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	12	206	0	0.0810811	0	T|0.939;G|0.061	0.061	strong	.	PLIN4	191	.	NM_001080400	exon3	c.A1254C	p.T418T	GTCCTTTGTACCT	.	PASS	Atlas-SNP
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702846	40702846	+	Missense_Mutation	SNP	C	C	T	rs273319		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	80	364	0	0.249221	0	.	.	weak	FAM75A3_ENST00000356699,NS,carcinoma,-1,6	.	.	6	NM_001083124	exon4	c.C503T	p.T168I	CCTCCACCCCATC	.	scavenged	Atlas-SNP
PIK3C3	5289	hgsc.bcm.edu	37	18	39576682	39576682	+	Silent	SNP	G	G	A	rs140083392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	65	186	1	0.398773	0.00537634	G|0.999;A|0.001	0.001	strong	PIK3C3,NS,carcinoma,+1,1	PIK3C3	138	1	NM_002647	exon9	c.G972A	p.T324T	TCTTACGAATCAA	.	scavenged	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	37	19	59074653	59074653	+	Missense_Mutation	SNP	T	T	C	rs4756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	49	59	0	0.960784	0	T|0.658;C|0.342	0.342	strong	.	MZF1	37	.	NM_198055	exon6	c.A991G	p.I331V	TGGTGATCAGAGC	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33486992	33486992	+	Missense_Mutation	SNP	A	A	C	rs75351369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	143	311	0	0.493103	0	A|0.973;C|0.027	0.027	strong	.	RHPN2	107	.	NM_033103	exon11	c.T1360G	p.Y454D	GGGCGTACGTGAG	.	PASS	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33475426	33475426	+	Silent	SNP	C	C	T	rs16970656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	77	0	0.476744	0	C|0.975;T|0.025	0.025	strong	.	UNC45B	133	.	NM_001267052	exon2	c.C144T	p.N48N	TCGGAACCGGGCA	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193209178	193209178	+	Missense_Mutation	SNP	T	T	C	rs6788448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	76	0	0.485294	0	T|0.559;C|0.441	0.441	strong	.	ATP13A4	154	.	NM_032279	exon6	c.A543G	p.I181M	CCCACATATTAAC	.	PASS	Atlas-SNP
FES	2242	hgsc.bcm.edu	37	15	91434277	91434277	+	Silent	SNP	C	C	T	rs2229074	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	98	75	0	0.98	0	C|0.935;T|0.065	0.065	strong	.	FES	102	.	NM_002005	exon11	c.C1386T	p.H462H	GTACCACGGGGCC	.	PASS	Atlas-SNP
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	56	49	0	0.583333	0	C|0.893;A|0.107	0.107	strong	PTGER3_ENST00000460330,NS,carcinoma,0,5	PTGER3	246	5	NM_001126044	exon1	c.G618T	p.T206T	GCACCACGTCCCG	.	PASS	Atlas-SNP
CPXM2	119587	hgsc.bcm.edu	37	10	125651150	125651150	+	Missense_Mutation	SNP	G	G	A	rs112027854	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	7	12	0	0.388889	0	G|0.500;A|0.500	0.500	weak	CPXM2,rectum,carcinoma,0,1	CPXM2	120	1	NM_198148	exon1	c.C26T	p.P9L	AGCGCTGGGGTAG	.	PASS	Atlas-SNP
MMS22L	253714	hgsc.bcm.edu	37	6	97613299	97613299	+	Missense_Mutation	SNP	G	G	A	rs10484830	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	42	81	0	0.47191	0	G|0.898;A|0.102	0.102	strong	.	MMS22L	102	.	NM_198468	exon21	c.C3044T	p.P1015L	GCATTCGGATTTT	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52865924	52865924	+	Silent	SNP	G	G	A	rs77218649	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	398	189	340	0	0.474874	0	G|0.976;A|0.024	0.024	strong	.	KRT6C	55	.	NM_173086	exon2	c.C681T	p.S227S	GACGATGCTGTCC	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7565596	7565596	+	Missense_Mutation	SNP	C	C	T	rs139509870	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	22	58	0	0.44	0	C|1.000;T|0.000	0.000	strong	.	DSP	306	.	NM_004415	exon7	c.C782T	p.A261V	AGAAAGCGTCCTT	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16276292	16276292	+	Missense_Mutation	SNP	T	T	C	rs59593133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	65	131	0	0.503876	0	T|0.975;C|0.025	0.025	strong	.	ABCC6	110	.	NM_001171	exon17	c.A2224G	p.I742V	TGTGGATTCCCTC	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	G	A	rs202060459		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	3	241	0	0.0111524	0	.	.	weak	PABPC1,NS,carcinoma,0,2	PABPC1	76	2	NM_002568	exon7	c.C956T	p.T319I	GTGATTGTACCAA	.	scavenged	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	37	17	66928470	66928470	+	Silent	SNP	C	C	T	rs28385895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	80	0	0.470588	0	C|0.959;T|0.041	0.041	strong	.	ABCA8	213	.	NM_007168	exon6	c.G756A	p.K252K	CAAGGCCTTCATC	.	PASS	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	6986589	6986589	+	Missense_Mutation	SNP	A	A	C	rs111451391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	89	162	1	0.511494	0.00617284	A|0.995;C|0.004;T|0.000	0.004	strong	KDM4C,NS,carcinoma,-2,1	KDM4C	186	1	NM_001146696	exon11	c.A1666C	p.S556R	GTGGAGAGCCATG	.	scavenged	Atlas-SNP
MICALL2	79778	hgsc.bcm.edu	37	7	1481983	1481983	+	Missense_Mutation	SNP	G	G	A	rs4075307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	86	0	1	0	G|0.965;A|0.035	0.035	strong	.	MICALL2	63	.	NM_182924	exon7	c.C1556T	p.P519L	CTCAGCGGGGCTG	.	PASS	Atlas-SNP
E4F1	1877	hgsc.bcm.edu	37	16	2273676	2273676	+	Missense_Mutation	SNP	C	C	A	rs200831818	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	12	8	0	0.6	0	.	.	weak	.	E4F1	53	.	NM_004424	exon1	c.C62A	p.A21D	CCGAAGCCGGGCG	.	PASS	Atlas-SNP
ANKLE1	126549	hgsc.bcm.edu	37	19	17394124	17394124	+	Missense_Mutation	SNP	T	T	G	rs2363956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	26	91	0	0.412698	0	T|0.509;G|0.491	0.491	strong	.	ANKLE1	27	.	NM_152363	exon5	c.T551G	p.L184W	TTGGCTTGGAGGC	.	PASS	Atlas-SNP
OR8J1	219477	hgsc.bcm.edu	37	11	56128226	56128226	+	Silent	SNP	T	T	C	rs11823483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	73	146	0	0.453416	0	T|0.955;C|0.045	0.045	strong	.	OR8J1	87	.	NM_001005205	exon1	c.T504C	p.Y168Y	GTCTTATTGCTCT	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15611495	15611495	+	Missense_Mutation	SNP	T	T	C	rs3760299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	58	97	0	0.557692	0	T|0.541;C|0.459	0.459	strong	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon5	c.T268C	p.Y90H	GAGAGCTACAACT	.	PASS	Atlas-SNP
OR6C68	403284	hgsc.bcm.edu	37	12	55887054	55887054	+	Missense_Mutation	SNP	C	C	G	rs56760228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	23	61	0	0.370968	0	C|0.953;G|0.047	0.047	strong	.	OR6C68	36	.	NM_001005519	exon1	c.C893G	p.A298G	AACAAGCCTTTCA	.	PASS	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137128830	137128830	+	Silent	SNP	T	T	C	rs1918837	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	42	96	0	0.461538	0	T|0.641;C|0.359	0.359	strong	.	DGKI	335	.	NM_004717	exon29	c.A2778G	p.E926E	ATGATCTTCTGAA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79068649	79068649	+	Silent	SNP	G	G	A	rs59275951	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	50	83	0	0.49505	0	G|0.940;A|0.060	0.060	strong	.	ADAMTS7	142	.	NM_014272	exon11	c.C1587T	p.P529P	GCCCACGGGTACG	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124281322	124281322	+	Silent	SNP	T	T	C	rs76791219	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	166	159	0	1	0	T|0.812;C|0.188	0.188	strong	.	DNAH10	888	.	NM_207437	exon12	c.T1752C	p.H584H	TAAGCATACCATC	.	PASS	Atlas-SNP
MAVS	57506	hgsc.bcm.edu	37	20	3846397	3846397	+	Missense_Mutation	SNP	C	C	T	rs7269320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	52	103	0	0.536082	0	C|0.786;T|0.214	0.214	strong	.	MAVS	34	.	NM_020746	exon7	c.C1226T	p.S409F	GCAGCTCTGAGAA	.	PASS	Atlas-SNP
CAMK1	8536	hgsc.bcm.edu	37	3	9804658	9804658	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	70	127	0	0.578512	0	.	.	none	.	CAMK1	32	.	NM_003656	exon5	c.C369T	p.F123F	CACCTGGAAGATG	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs7245423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	36	0	1	0	G|0.635;A|0.365	0.365	strong	.	PSG8	101	.	NM_001130168	exon1	c.C29T	p.T10I	CGCTGTGTGCAGG	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28611061	28611061	+	Missense_Mutation	SNP	A	A	T	rs276937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	89	90	0	0.988889	0	A|0.626;T|0.374	0.374	strong	.	DSC3	225	.	NM_024423	exon3	c.T232A	p.S78T	ACACTGACCCATC	.	PASS	Atlas-SNP
RBAK	57786	hgsc.bcm.edu	37	7	5103773	5103773	+	Missense_Mutation	SNP	G	G	A	rs35352738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	26	57	0	0.481481	0	G|0.959;A|0.041	0.041	strong	.	RBAK	82	.	NM_001204456	exon6	c.G686A	p.G229E	ACATAGGGGAGAA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2159341	2159341	+	Missense_Mutation	SNP	C	C	T	rs137978188	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	7	21	0	0.35	0	C|0.958;T|0.042	0.042	strong	.	PKD1	184	.	NM_000296	exon15	c.G5827A	p.V1943I	CTCCGACGCGGGG	.	PASS	Atlas-SNP
KIAA1107	23285	hgsc.bcm.edu	37	1	92646431	92646431	+	Missense_Mutation	SNP	A	A	G	rs7523466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	44	80	0	0.511628	0	A|0.994;G|0.006	0.006	strong	.	KIAA1107	60	.	NM_015237	exon8	c.A1877G	p.D626G	CAGATGATTGCGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415899	105415899	+	Silent	SNP	A	A	G	rs11850869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	294	276	0	0.993243	0	A|0.965;G|0.035	0.035	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T5889C	p.A1963A	CAGCTTAGCCTTC	.	PASS	Atlas-SNP
ARRDC2	27106	hgsc.bcm.edu	37	19	18121154	18121154	+	Silent	SNP	G	G	A	rs17852059	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	25	49	0	0.510204	0	G|0.939;A|0.061	0.061	strong	.	ARRDC2	60	.	NM_015683	exon6	c.G999A	p.P333P	CTTGCCGGAGCGG	.	PASS	Atlas-SNP
GSE1	23199	hgsc.bcm.edu	37	16	85695298	85695298	+	Silent	SNP	C	C	T	rs61737039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	125	0	0.484127	0	C|0.988;T|0.012	0.012	strong	.	.	.	.	NM_014615	exon9	c.C2187T	p.F729F	TGAGTTCCTGCAG	.	PASS	Atlas-SNP
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743086	22743086	+	Missense_Mutation	SNP	C	C	T	rs201721928	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	348	72	208	0	0.206897	0	.	.	weak	.	GOLGA6L1	20	.	NM_001001413	exon8	c.C1471T	p.R491W	AAGATACGGAAGC	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289986	98289986	+	Silent	SNP	C	C	T	rs28669903	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	19	26	0	0.527778	0	C|0.406;T|0.594	0.594	strong	TSPYL5,NS,carcinoma,-2,1	TSPYL5	48	1	NM_033512	exon1	c.G87A	p.P29P	GTCGTCCGGAGCA	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27803810	27803810	+	Silent	SNP	C	C	T	rs13408423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	42	62	0	0.617647	0	C|0.986;T|0.014	0.014	strong	.	C2orf16	357	.	NM_032266	exon1	c.C4371T	p.P1457P	CAAGCCCACAGAT	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32087828	32087828	+	Missense_Mutation	SNP	C	C	T	rs36097367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	89	95	0	0.597315	0	C|0.961;T|0.039	0.039	strong	PDZD2,NS,carcinoma,-1,1	PDZD2	306	1	NM_178140	exon19	c.C4274T	p.T1425M	CTGTGACGGACAT	.	PASS	Atlas-SNP
WNT16	51384	hgsc.bcm.edu	37	7	120969769	120969769	+	Missense_Mutation	SNP	G	G	A	rs2908004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	25	54	1	0.520833	0.0185185	G|0.462;A|0.538	0.538	strong	WNT16_ENST00000361301,brain,glioma,0,2	WNT16	97	2	NM_057168	exon2	c.G244A	p.G82R	GAGTGCGGGAGCC	.	scavenged	Atlas-SNP
KIAA0319	9856	hgsc.bcm.edu	37	6	24596433	24596433	+	Missense_Mutation	SNP	A	A	C	rs73727343	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	25	55	0	0.462963	0	A|0.970;C|0.030	0.030	strong	.	KIAA0319	117	.	NM_001168377	exon3	c.T469G	p.S157A	CATCTGAGTACTC	.	PASS	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62291912	62291912	+	Missense_Mutation	SNP	C	C	T	rs115362908	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	45	80	0	0.592105	0	C|0.996;T|0.004	0.004	strong	.	AHNAK	532	.	NM_001620	exon5	c.G9977A	p.S3326N	TCCAAACTGGGAG	.	PASS	Atlas-SNP
MX2	4600	hgsc.bcm.edu	37	21	42749081	42749081	+	Missense_Mutation	SNP	T	T	C	rs56680307	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	21	46	0	0.4375	0	T|0.941;C|0.059	0.059	strong	.	MX2	84	.	NM_002463	exon2	c.T248C	p.M83T	GGGCAATGGTAAG	.	PASS	Atlas-SNP
NOL10	79954	hgsc.bcm.edu	37	2	10797952	10797952	+	Silent	SNP	G	G	A	rs61737663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	92	199	0	0.479167	0	G|0.988;A|0.012	0.012	strong	.	NOL10	22	.	NM_024894	exon11	c.C822T	p.P274P	CTTAATGGGCAGC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155158104	155158104	+	Missense_Mutation	SNP	G	G	A	rs17031279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	90	162	0	0.505618	0	G|0.979;A|0.021	0.021	strong	.	DCHS2	594	.	NM_017639	exon25	c.C6335T	p.T2112M	ACAAGCGTGCTTC	.	PASS	Atlas-SNP
USP2	9099	hgsc.bcm.edu	37	11	119243612	119243612	+	Silent	SNP	T	T	C	rs4938649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	29	55	0	0.630435	0	T|0.959;C|0.041	0.041	strong	.	USP2	71	.	NM_004205	exon2	c.A579G	p.E193E	CAGGTATTCAGGG	.	PASS	Atlas-SNP
CNST	163882	hgsc.bcm.edu	37	1	246755204	246755204	+	Missense_Mutation	SNP	C	C	T	rs116182112	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	22	54	0	0.488889	0	C|0.998;T|0.002	0.002	strong	.	CNST	73	.	NM_152609	exon2	c.C340T	p.P114S	AGAAGTCCAAGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513598	195513598	+	Missense_Mutation	SNP	G	G	A	rs57748294	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	455	286	537	0	0.628571	0	A|0.075;G|0.923;T|0.002	0.075	strong	.	MUC4	1505	.	NM_018406	exon2	c.C4853T	p.P1618L	GTGACAGGAAGAG	.	PASS	Atlas-SNP
AACS	65985	hgsc.bcm.edu	37	12	125626685	125626685	+	Silent	SNP	C	C	T	rs3751180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	119	0	0.483051	0	C|0.931;T|0.069	0.069	strong	AACS,NS,carcinoma,0,1	AACS	59	1	NM_023928	exon18	c.C1929T	p.I643I	GATCATCGCTGGA	.	PASS	Atlas-SNP
PISD	23761	hgsc.bcm.edu	37	22	32015766	32015766	+	Silent	SNP	G	G	A	rs41282571	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	110	186	0	0.474138	0	A|0.028;C|0.000;G|0.972	0.028	strong	.	PISD	53	.	NM_014338	exon9	c.C960T	p.F320F	CGTCACGAAGCTG	.	PASS	Atlas-SNP
MRPL23	6150	hgsc.bcm.edu	37	11	1972229	1972229	+	Missense_Mutation	SNP	G	G	A	rs377324983		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	64	0	0.528571	0	.	.	weak	.	MRPL23	14	.	NM_021134	exon2	c.G118A	p.V40M	GACACCGTGCAGT	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41756965	41756965	+	Missense_Mutation	SNP	C	C	T	rs61744388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	75	0	1	0	C|0.772;T|0.228	0.228	strong	.	ULK4	150	.	NM_017886	exon24	c.G2551A	p.V851I	GCACTACAGGCAT	.	PASS	Atlas-SNP
ANGPT4	51378	hgsc.bcm.edu	37	20	860426	860426	+	Silent	SNP	G	G	A	rs61737018	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	16	43	0	0.372093	0	G|0.879;A|0.121	0.121	strong	.	ANGPT4	77	.	NM_015985	exon6	c.C1017T	p.T339T	ATTCACGGTGCCA	.	PASS	Atlas-SNP
FCER2	2208	hgsc.bcm.edu	37	19	7754101	7754101	+	Missense_Mutation	SNP	G	G	A	rs34694289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	138	156	0	0.587234	0	G|0.990;A|0.010	0.010	strong	.	FCER2	19	.	NM_002002	exon11	c.C944T	p.P315L	GCAGAGGGGGTGG	.	PASS	Atlas-SNP
FAM118A	55007	hgsc.bcm.edu	37	22	45723842	45723842	+	Silent	SNP	G	G	A	rs17851057	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	81	150	0	0.543624	0	G|0.539;A|0.461	0.461	strong	.	FAM118A	32	.	NM_017911	exon4	c.G420A	p.R140R	GGACAGGGGCGCC	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117089801	117089801	+	Missense_Mutation	SNP	T	T	C	rs61729982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	29	44	0	0.707317	0	T|0.996;C|0.004	0.004	strong	.	PCSK7	59	.	NM_004716	exon11	c.A1403G	p.N468S	CAGGCGTTGAGGA	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	37	16	71317567	71317567	+	Missense_Mutation	SNP	A	A	G	rs16970857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	88	178	0	0.488889	0	A|0.964;G|0.036	0.036	strong	.	FTSJD1	70	.	NM_018348	exon3	c.T2257C	p.F753L	TAATGAAATGCAA	.	PASS	Atlas-SNP
KIF20A	10112	hgsc.bcm.edu	37	5	137520025	137520025	+	Missense_Mutation	SNP	G	G	A	rs142495138	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	107	217	0	0.514423	0	G|1.000;A|0.000	0.000	strong	.	KIF20A	53	.	NM_005733	exon12	c.G1450A	p.V484M	GTCAATGTGAATC	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170724955	170724955	+	Silent	SNP	C	C	T	rs5404	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	55	114	0	0.416667	0	C|0.847;T|0.153	0.153	strong	.	SLC2A2	71	.	NM_000340	exon5	c.G594A	p.T198T	AATGCCCGTGACG	.	PASS	Atlas-SNP
OR8U1	219417	hgsc.bcm.edu	37	11	56143952	56143952	+	Silent	SNP	T	T	C	rs78408319	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	60	114	0	0.48	0	T|0.973;C|0.027	0.027	strong	.	OR8U1	59	.	NM_001005204	exon1	c.T853C	p.L285L	CCCATGTTGAATC	.	PASS	Atlas-SNP
OR7C1	26664	hgsc.bcm.edu	37	19	14910900	14910900	+	Missense_Mutation	SNP	A	A	T	rs149561973	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	31	68	0	0.508197	0	A|0.994;T|0.006	0.006	strong	.	OR7C1	58	.	NM_198944	exon1	c.T49A	p.F17I	CTGAAAATCCCAG	.	PASS	Atlas-SNP
ZMYM6	9204	hgsc.bcm.edu	37	1	35454115	35454115	+	Silent	SNP	A	A	G	rs61745582	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	112	245	0	0.489083	0	A|0.962;G|0.038	0.038	strong	.	ZMYM6	110	.	NM_007167	exon16	c.T2568C	p.Y856Y	TACTAAATATGGT	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161007538	161007538	+	Missense_Mutation	SNP	G	G	C	rs7765803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	96	143	0	0.551724	0	G|0.569;C|0.431	0.431	strong	.	LPA	237	.	NM_005577	exon26	c.C4072G	p.L1358V	TGAGGAGAGTTGA	.	PASS	Atlas-SNP
MC3R	4159	hgsc.bcm.edu	37	20	54824029	54824029	+	Missense_Mutation	SNP	G	G	A	rs3827103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	81	0	1	0	G|0.782;A|0.218	0.218	strong	.	MC3R	83	.	NM_019888	exon1	c.G130A	p.V44I	CCCGAGGTTTTCC	.	PASS	Atlas-SNP
DENND2A	27147	hgsc.bcm.edu	37	7	140227293	140227293	+	Missense_Mutation	SNP	A	A	G	rs6464833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	82	133	0	1	0	A|0.830;G|0.170	0.170	strong	.	DENND2A	132	.	NM_015689	exon13	c.T2330C	p.I777T	GACAGGATGCTGC	.	PASS	Atlas-SNP
CCDC107	203260	hgsc.bcm.edu	37	9	35661057	35661057	+	Missense_Mutation	SNP	C	C	G	rs10441685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	52	119	0	0.448276	0	C|0.929;G|0.071	0.071	strong	.	CCDC107	12	.	NM_174923	exon5	c.C725G	p.S242C	CTACTTCCTGGGA	.	PASS	Atlas-SNP
ELMO3	79767	hgsc.bcm.edu	37	16	67235672	67235672	+	Missense_Mutation	SNP	C	C	T	rs33948247	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	36	82	0	0.5	0	C|0.960;T|0.040	0.040	strong	.	ELMO3	41	.	NM_024712	exon11	c.C1105T	p.R369C	GTCCTACGCCAGG	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79182778	79182778	+	Silent	SNP	T	T	C	rs62075318	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	83	134	0	0.572414	0	T|0.621;C|0.379	0.379	strong	AZI1_ENST00000450824,NS,carcinoma,0,4	AZI1	145	4	NM_014984	exon3	c.A222G	p.R74R	GGATCTTCTAAGG	.	PASS	Atlas-SNP
SQSTM1	8878	hgsc.bcm.edu	37	5	179260661	179260661	+	Silent	SNP	G	G	A	rs10058037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	36	82	0	0.439024	0	G|0.960;A|0.040	0.040	strong	SQSTM1,NS,carcinoma,+1,1	SQSTM1	30	1	NM_003900	exon7	c.G1044A	p.P348P	GGACCCGTCTACA	.	PASS	Atlas-SNP
CRYBA1	1411	hgsc.bcm.edu	37	17	27580756	27580756	+	Silent	SNP	C	C	T	rs1047790	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	40	92	0	0.454545	0	C|0.756;T|0.244	0.244	strong	.	CRYBA1	15	.	NM_005208	exon5	c.C456T	p.G152G	CATGGGCTGGTTC	.	PASS	Atlas-SNP
YARS2	51067	hgsc.bcm.edu	37	12	32908237	32908237	+	Missense_Mutation	SNP	C	C	A	rs11539445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	56	82	0	0.5	0	C|0.856;A|0.144	0.144	strong	.	YARS2	33	.	NM_001040436	exon1	c.G572T	p.G191V	AAGTGACCCCCCA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721817	101721817	+	Missense_Mutation	SNP	T	T	C	rs201076736	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	126	179	0	0.365217	0	.	.	weak	.	PABPC1	76	.	NM_002568	exon8	c.A1115G	p.E372G	CGCTCTTCTTTGC	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124095916	124095916	+	Silent	SNP	C	C	T	rs11825213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	66	191	0	0.39521	0	C|0.927;T|0.073	0.073	strong	.	.	.	.	NM_001007249	exon1	c.C519T	p.T173T	TCACACCGGCTTT	.	PASS	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186052	39186052	+	Silent	SNP	G	G	A	rs150955506	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	85	157	0	0.521472	0	G|0.888;A|0.112	0.112	strong	.	KRTAP1-4	4	.	NM_001257305	exon1	c.C279T	p.A93A	GGCCTCGGCGTGG	.	PASS	Atlas-SNP
TMEM132C	92293	hgsc.bcm.edu	37	12	129189850	129189850	+	Silent	SNP	C	C	T	rs7959567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	23	58	0	0.46	0	C|0.910;T|0.090	0.090	strong	.	TMEM132C	142	.	NM_001136103	exon9	c.C2337T	p.C779C	GGCCTGCCAGAAA	.	PASS	Atlas-SNP
APOBR	55911	hgsc.bcm.edu	37	16	28508447	28508447	+	Silent	SNP	A	A	G	rs40831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	12	45	0	0.333333	0	A|0.584;G|0.416	0.416	strong	.	APOBR	89	.	NM_018690	exon2	c.A2085G	p.A695A	AGAGGCATCTGTC	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	37	9	35714269	35714269	+	Silent	SNP	G	G	A	rs35844106	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	98	0	0.517241	0	G|0.995;A|0.005	0.005	strong	.	TLN1	185	.	NM_006289	exon24	c.C3087T	p.T1029T	CAGCGCGGTGCCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508190	195508190	+	Missense_Mutation	SNP	G	G	C	rs201771865		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	11	263	0	0.0415094	0	.	.	weak	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,+2,3	MUC4	1505	3	NM_018406	exon2	c.C10261G	p.H3421D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
SNRPA	6626	hgsc.bcm.edu	37	19	41263403	41263403	+	Silent	SNP	A	A	G	rs2230694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	167	138	1	0.994048	0.00724638	A|0.811;C|0.000;G|0.189;T|0.000	0.189	strong	.	SNRPA	20	.	NM_004596	exon2	c.A240G	p.K80K	TGACAAACCTATG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235357460	235357460	+	Silent	SNP	A	A	G	rs62000435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	100	181	0	0.52356	0	A|0.992;G|0.008	0.008	strong	.	ARID4B	142	.	NM_016374	exon19	c.T1993C	p.L665L	TGGACAAGCGCCG	.	PASS	Atlas-SNP
CFLAR	8837	hgsc.bcm.edu	37	2	202025375	202025375	+	Silent	SNP	G	G	A	rs33914895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	62	115	0	0.488189	0	G|0.985;A|0.015	0.015	strong	.	CFLAR	37	.	NM_003879	exon9	c.G1014A	p.R338R	CAGGAGGATGTTC	.	PASS	Atlas-SNP
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417642	138417642	+	Missense_Mutation	SNP	C	C	T	rs73730479	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	38	108	0	0.422222	0	C|0.963;T|0.037	0.037	strong	.	ATP6V0A4	93	.	NM_130841	exon16	c.G1888A	p.A630T	GGGGTGCGTTGGA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90424458	90424458	+	Silent	SNP	C	C	T	rs114422841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	35	71	0	0.546875	0	C|0.996;T|0.004	0.004	strong	.	MDN1	478	.	NM_014611	exon46	c.G6873A	p.S2291S	ATCCATCGAGAGG	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55955485	55955485	+	Silent	SNP	A	A	G	rs7921598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	92	0	0.5	0	A|0.756;G|0.244	0.244	strong	.	PCDH15	1715	.	NM_001142763	exon12	c.T1278C	p.T426T	AGGTGAAGTCAAA	.	PASS	Atlas-SNP
FCRL5	83416	hgsc.bcm.edu	37	1	157514685	157514685	+	Silent	SNP	G	G	A	rs11803066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	103	155	0	0.542105	0	G|0.982;A|0.018	0.018	strong	.	FCRL5	177	.	NM_031281	exon4	c.C495T	p.R165R	AGTACAGCGATAT	.	PASS	Atlas-SNP
CRAT	1384	hgsc.bcm.edu	37	9	131866523	131866523	+	Silent	SNP	C	C	G	rs2228304	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	81	139	0	0.663934	0	C|0.852;G|0.148	0.148	strong	.	CRAT	43	.	NM_000755	exon3	c.G354C	p.S118S	TGGGCTCGAGTAG	.	PASS	Atlas-SNP
AFF2	2334	hgsc.bcm.edu	37	X	148035200	148035200	+	Silent	SNP	G	G	A	rs12011040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	415	140	352	0	0.337349	0	0|0.003;A|0.180	0.180	strong	.	AFF2	679	.	NM_002025	exon10	c.G1488A	p.S496S	TGAGTCGGATTCA	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72349040	72349040	+	Silent	SNP	C	C	T	rs9897137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	87	0	0.521277	0	C|0.737;T|0.263	0.263	strong	.	KIF19	102	.	NM_153209	exon15	c.C2061T	p.S687S	ATTGAGCTCTGAT	.	PASS	Atlas-SNP
RAPGEF2	9693	hgsc.bcm.edu	37	4	160273927	160273927	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	3	211	2	0.014218	0.00947867	.	.	none	RAPGEF2,NS,carcinoma,0,2	RAPGEF2	171	2	NM_014247	exon21	c.C3473T	p.S1158L	GCAATTCGTCTTT	.	scavenged	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124821705	124821705	+	Silent	SNP	G	G	A	rs3741512	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	131	252	0	0.486989	0	G|0.966;A|0.034	0.034	strong	.	NCOR2	475	.	NM_006312	exon40	c.C5709T	p.P1903P	GCGAACGGGTGAG	.	PASS	Atlas-SNP
ADCK2	90956	hgsc.bcm.edu	37	7	140374049	140374049	+	Missense_Mutation	SNP	T	T	C	rs1140034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	35	45	0	0.972222	0	T|0.719;C|0.281	0.281	strong	.	ADCK2	37	.	NM_052853	exon1	c.T919C	p.S307P	CTCATCTCCGTGG	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	31	63	0	0.574074	0	A|0.691;G|0.309	0.309	strong	KIAA0649,colon,carcinoma,0,1	.	.	1	NM_014811	exon4	c.A1497G	p.V499V	CCCTGTAGAGGGC	.	PASS	Atlas-SNP
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	28	70	0	0.459016	0	T|0.639;C|0.361	0.361	strong	.	KLRG1	16	.	NM_005810	exon1	c.T66C	p.Y22Y	TGACTATGGACCA	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31729925	31729925	+	Missense_Mutation	SNP	C	C	T	rs1802127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	73	176	0	0.459119	0	C|0.942;T|0.058	0.058	strong	.	MSH5	108	.	NM_172165	exon24	c.C2359T	p.P787S	ATCAAGCCTGTCA	.	PASS	Atlas-SNP
LGI4	163175	hgsc.bcm.edu	37	19	35617270	35617270	+	Silent	SNP	T	T	C	rs1319969	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	66	63	0	0.985075	0	T|0.660;C|0.340	0.340	strong	LGI4,NS,carcinoma,0,1	LGI4	32	1	NM_139284	exon8	c.A1203G	p.T401T	GATGTCTGTGCGT	.	PASS	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62931547	62931547	+	Splice_Site	SNP	T	T	C	rs114205803	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	91	230	0	0.395652	0	T|0.996;C|0.004	0.004	strong	.	SLC22A25	87	.	NM_199352	exon10	c.1395-2A>G	.	TTCCCCTTGGAGT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	164	234	0	0.716157	0	A|0.517;0|0.025	.	strong	.	GPR112	459	.	NM_153834	exon6	c.A828G	p.I276M	ACCTATATTTGCA	.	PASS	Atlas-SNP
GRM3	2913	hgsc.bcm.edu	37	7	86479694	86479694	+	Silent	SNP	G	G	A	rs76035289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	82	162	0	0.525641	0	G|0.985;A|0.015	0.015	strong	.	GRM3	237	.	NM_000840	exon5	c.G2400A	p.T800T	GCAGACGACAACC	.	PASS	Atlas-SNP
CD1E	913	hgsc.bcm.edu	37	1	158325765	158325765	+	Silent	SNP	C	C	T	rs61734677	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	162	296	0	0.517572	0	C|0.978;T|0.022	0.022	strong	.	CD1E	129	.	NM_001042584	exon4	c.C774T	p.D258D	AGGGGACGTCCTG	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29225504	29225504	+	Missense_Mutation	SNP	T	T	C	rs72786179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	72	108	0	0.549618	0	T|0.832;C|0.168	0.168	strong	.	FAM179A	106	.	NM_199280	exon5	c.T530C	p.L177P	TGCCTCTCATCCA	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	120	0	0.992308	0	T|0.540;C|0.460	0.460	strong	.	MPDZ	324	.	NM_003829	exon25	c.A3609G	p.K1203K	TCCAGGTTTCAAG	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263111	80263111	+	Missense_Mutation	SNP	C	C	A	rs34080999	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	105	244	0	0.46875	0	C|0.968;A|0.032	0.032	strong	.	BCL2A1	28	.	NM_001114735	exon1	c.G351T	p.E117D	TGAAATCTCCTTA	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33704346	33704346	+	Silent	SNP	C	C	T	rs114088950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	18	33	0	0.418605	0	C|0.986;T|0.014	0.014	strong	.	STARD13	100	.	NM_178006	exon5	c.G468A	p.V156V	GTCGTCCACACGA	.	PASS	Atlas-SNP
SH2D3A	10045	hgsc.bcm.edu	37	19	6763718	6763718	+	Silent	SNP	A	A	G	rs2305805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	32	73	0	0.410256	0	A|0.742;G|0.258	0.258	strong	.	SH2D3A	53	.	NM_005490	exon2	c.T42C	p.P14P	GTACCAAGGTTGG	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24421950	24421950	+	Missense_Mutation	SNP	C	C	G	rs4319261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	98	87	0	1	0	C|0.542;G|0.458	0.458	strong	.	MYOM3	131	.	NM_152372	exon8	c.G772C	p.D258H	CTGAATCGAAGCC	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183616926	183616926	+	Missense_Mutation	SNP	T	T	C	rs1174657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	116	167	0	0.493617	0	T|0.608;C|0.392	0.392	strong	.	APOBEC4	45	.	NM_203454	exon2	c.A991G	p.K331E	GGTCCTTGGTTTC	.	PASS	Atlas-SNP
TRMT5	57570	hgsc.bcm.edu	37	14	61445981	61445981	+	Missense_Mutation	SNP	C	C	T	rs114005374	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	61	119	0	0.472868	0	C|0.999;T|0.001	0.001	strong	TRMT5,caecum,carcinoma,0,1	TRMT5	44	1	NM_020810	exon2	c.G635A	p.R212Q	TGATCTCGAAGGT	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371034	240371034	+	Silent	SNP	A	A	C	rs150102515		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	7	147	1	0.0348259	0.00680272	A|0.999;C|0.001	0.001	weak	FMN2,NS,carcinoma,0,1	FMN2	451	1	NM_020066	exon5	c.A2922C	p.G974G	AGCAGGAATACCT	.	scavenged	Atlas-SNP
DOCK4	9732	hgsc.bcm.edu	37	7	111462465	111462465	+	Silent	SNP	C	C	T	rs17158877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	34	87	0	0.465753	0	C|0.884;T|0.116	0.116	strong	DOCK4,NS,carcinoma,0,1	DOCK4	365	1	NM_014705	exon27	c.G2883A	p.P961P	CATCTCCGGGCGT	.	PASS	Atlas-SNP
CENPJ	55835	hgsc.bcm.edu	37	13	25480616	25480616	+	Silent	SNP	T	T	A	rs17081368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	88	0	0.508475	0	T|0.950;A|0.050	0.050	strong	.	CENPJ	116	.	NM_018451	exon7	c.A1560T	p.T520T	ACCTTGTGTCTTA	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73461337	73461337	+	Silent	SNP	T	T	A	rs7862440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	461	461	479	1	1	0.00208768	T|0.455;A|0.545	0.545	strong	.	TRPM3	700	.	NM_001007471	exon4	c.A633T	p.A211A	TGTCATTGCTGCT	.	PASS	Atlas-SNP
SLC1A6	6511	hgsc.bcm.edu	37	19	15063757	15063757	+	Silent	SNP	A	A	G	rs2229896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	143	244	0	0.489726	0	T|0.131;G|0.183;C|0.054;A|0.632	0.183	strong	.	SLC1A6	111	.	NM_005071	exon8	c.T1482C	p.I494I	CACGGCAATGATG	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133476629	133476629	+	Missense_Mutation	SNP	A	A	G	rs8177238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	49	93	0	0.49	0	A|0.984;G|0.016	0.016	strong	TF,NS,carcinoma,+1,1	TF	116	1	NM_001063	exon8	c.A887G	p.D296G	GCAAAGACAAATC	.	PASS	Atlas-SNP
S100A3	6274	hgsc.bcm.edu	37	1	153520954	153520954	+	Missense_Mutation	SNP	C	C	T	rs36022742	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	22	45	0	0.458333	0	C|0.861;T|0.139	0.139	strong	.	S100A3	7	.	NM_002960	exon2	c.G8A	p.R3K	AGAGGCCTGGCCA	.	PASS	Atlas-SNP
C2CD5	9847	hgsc.bcm.edu	37	12	22680809	22680809	+	Silent	SNP	T	T	C	rs12322490	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	93	119	0	0.688889	0	T|0.950;C|0.050	0.050	strong	.	.	.	.	NM_014802	exon4	c.A195G	p.L65L	ATCTTGTAAGTCT	.	PASS	Atlas-SNP
OR1A1	8383	hgsc.bcm.edu	37	17	3119767	3119767	+	Missense_Mutation	SNP	C	C	T	rs769427	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	48	89	0	0.475248	0	C|0.608;T|0.392	0.392	strong	OR1A1,NS,carcinoma,0,1	OR1A1	54	1	NM_014565	exon1	c.C853T	p.P285S	TTAAATCCTTTCA	.	PASS	Atlas-SNP
TMEM116	89894	hgsc.bcm.edu	37	12	112375990	112375990	+	Missense_Mutation	SNP	A	A	C	rs3752630	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	95	198	0	0.539773	0	A|0.783;C|0.217	0.217	strong	.	TMEM116	17	.	NM_001193531	exon6	c.T340G	p.C114G	TTTGACAAACTCG	.	PASS	Atlas-SNP
IQCG	84223	hgsc.bcm.edu	37	3	197659160	197659160	+	Missense_Mutation	SNP	C	C	G	rs67877771	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	148	0	0.991304	0	C|0.746;G|0.254	0.254	strong	IQCG,rectum,carcinoma,0,1	IQCG	44	1	NM_032263	exon6	c.G529C	p.D177H	TCACATCGCTGAA	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11736305	11736305	+	Missense_Mutation	SNP	G	G	A	rs36030386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	143	121	0	1	0	G|0.826;A|0.174	0.174	strong	.	GREB1	308	.	NM_014668	exon13	c.G1894A	p.A632T	TCACTCGCTGCCT	.	PASS	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26581981	26581981	+	Silent	SNP	G	G	A	rs34867486	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	58	110	0	0.508772	0	G|0.979;A|0.021	0.021	strong	CEP85,NS,carcinoma,+2,1	CEP85	61	1	NM_022778	exon4	c.G528A	p.A176A	AGAGGCGAGGAAG	.	PASS	Atlas-SNP
HECTD2	143279	hgsc.bcm.edu	37	10	93260363	93260363	+	Silent	SNP	C	C	T	rs34553731	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	29	50	0	0.47541	0	C|0.985;T|0.015	0.015	strong	.	HECTD2	60	.	NM_182765	exon19	c.C2055T	p.D685D	AACGGACTTAACT	.	PASS	Atlas-SNP
SHROOM1	134549	hgsc.bcm.edu	37	5	132159393	132159393	+	Silent	SNP	G	G	A	rs33935150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	37	88	0	0.41573	0	G|0.939;A|0.061	0.061	strong	.	SHROOM1	35	.	NM_133456	exon5	c.C1875T	p.N625N	GGCAGGGTTTTCA	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20432605	20432605	+	Missense_Mutation	SNP	A	A	G	rs59025904	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	59	62	0	0.983333	0	A|0.875;G|0.125	0.125	strong	.	ACSM5	101	.	NM_017888	exon5	c.A649G	p.M217V	AACTGCATGAGGA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744182	54744182	+	Missense_Mutation	SNP	A	A	T	rs374829481	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	63	331	0	0.221053	0	.	.	alt	LILRA6,nipple,malignant_melanoma,0,1	LILRA6	75	1	NM_024318	exon6	c.T1226A	p.F409Y	CTGGGGAAAGACA	.	scavenged	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16364919	16364919	+	Silent	SNP	A	A	C	rs690216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	79	0	1	0	A|0.402;C|0.598	0.598	strong	.	RFTN1	79	.	NM_015150	exon9	c.T1296G	p.P432P	TAGACAAGGTCTC	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	53	95	0	0.535354	0	A|0.545;G|0.455	0.455	strong	ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	NM_001137674	exon2	c.A1391G	p.H464R	CCTTCCATCACAA	.	PASS	Atlas-SNP
KIAA1377	57562	hgsc.bcm.edu	37	11	101829070	101829070	+	Silent	SNP	C	C	T	rs61742070	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	68	0	0.477612	0	C|0.989;T|0.011	0.011	strong	.	KIAA1377	111	.	NM_020802	exon5	c.C678T	p.L226L	ACTCCTCGAAGAT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912315	29912315	+	Missense_Mutation	SNP	A	A	C	rs41554316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	530	173	311	0	0.326415	0	A|0.889;C|0.111	0.111	strong	.	HLA-A	89	.	NM_001242758	exon5	c.A934C	p.I312L	GGCATCATTGCTG	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39234674	39234674	+	Silent	SNP	G	G	A	rs111831826	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	69	0	0.468354	0	G|0.998;A|0.002	0.002	strong	.	CAPN12	43	.	NM_144691	exon1	c.C132T	p.I44I	GAACAGGATCCCC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	40	62	0	1	0	G|0.601;C|0.399	0.399	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G10888C	p.E3630Q	GTGTCTGAGGGGG	.	PASS	Atlas-SNP
ADAMTS10	81794	hgsc.bcm.edu	37	19	8669931	8669931	+	Missense_Mutation	SNP	G	G	C	rs7255721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	128	1	1	0.0078125	G|0.152;C|0.848	0.848	strong	.	ADAMTS10	132	.	NM_030957	exon4	c.C401G	p.T134S	TGGGAGGTGCTGG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79025634	79025634	+	Missense_Mutation	SNP	G	G	A	rs1366271	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	215	219	1	1	0.00456621	G|0.742;A|0.258	0.258	strong	.	CMYA5	643	.	NM_153610	exon2	c.G1046A	p.G349D	GTAGTGGCAGAGC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378358	31378358	+	Missense_Mutation	SNP	T	T	G	rs1063630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	285	326	2	1	0.00613497	C|0.003;G|0.250;T|0.747	0.250	strong	.	MICA	21	.	NM_001177519	exon2	c.T109G	p.W37G	CTGTCCTGGGATG	.	PASS	Atlas-SNP
PDPR	55066	hgsc.bcm.edu	37	16	70180088	70180088	+	Missense_Mutation	SNP	A	A	T	rs2287978	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	91	259	0	0.502762	0	A|0.750;T|0.250	0.250	weak	.	PDPR	66	.	NM_017990	exon16	c.A1919T	p.Y640F	TGTCCTATGCCCC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119894	38119894	+	Missense_Mutation	SNP	G	G	A	rs35105846	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	16	297	1	0.0443213	0.003367	G|0.500;A|0.500	0.500	strong	TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon7	c.G1331A	p.S444N	CTCCCAGTAGAGC	.	scavenged	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16364954	16364954	+	Missense_Mutation	SNP	C	C	T	rs11554130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	38	71	0	0.603175	0	C|0.775;T|0.225	0.225	strong	.	RFTN1	79	.	NM_015150	exon9	c.G1261A	p.V421I	TGGATACACTCCC	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	69104701	69104701	+	Silent	SNP	G	G	A	rs116570374	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	65	0	0.504951	0	G|0.993;A|0.007	0.007	strong	.	PREX2	614	.	NM_024870	exon37	c.G4545A	p.S1515S	TTCCTCGGAGCTG	.	PASS	Atlas-SNP
GABRG2	2566	hgsc.bcm.edu	37	5	161528280	161528280	+	Silent	SNP	C	C	T	rs211037	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	90	0	0.489583	0	C|0.648;T|0.352	0.352	strong	GABRG2,NS,carcinoma,0,1	GABRG2	142	1	NM_198904	exon5	c.C588T	p.N196N	GCACAACTTTCCA	.	PASS	Atlas-SNP
HTR4	3360	hgsc.bcm.edu	37	5	147845463	147845463	+	Missense_Mutation	SNP	G	G	A	rs73266449	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	118	257	0	0.462745	0	G|0.967;A|0.033	0.033	strong	.	HTR4	161	.	NM_199453	exon6	c.C1102T	p.L368F	GCAGGAGGAAGCT	.	PASS	Atlas-SNP
FCRL1	115350	hgsc.bcm.edu	37	1	157771979	157771979	+	Silent	SNP	C	C	T	rs12035302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	65	134	0	0.477941	0	C|0.978;T|0.022	0.022	strong	.	FCRL1	164	.	NM_001159397	exon5	c.G612A	p.P204P	AGACACCGGGACT	.	PASS	Atlas-SNP
PDHX	8050	hgsc.bcm.edu	37	11	34969150	34969150	+	Silent	SNP	C	C	T	rs34582941	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	36	0	0.471429	0	C|0.951;T|0.049	0.049	strong	.	PDHX	40	.	NM_003477	exon3	c.C339T	p.I113I	CAAAATCGTGGTA	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2969689	2969689	+	Missense_Mutation	SNP	T	T	G	rs41515445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	62	111	0	0.504065	0	T|0.972;G|0.028	0.028	strong	.	CARD11	339	.	NM_032415	exon12	c.A1590C	p.E530D	CGTGCCTTCTTCC	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39180263	39180263	+	Missense_Mutation	SNP	G	G	A	rs704959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	155	152	0	1	0	G|0.450;A|0.550	0.550	strong	.	TTC21A	96	.	NM_145755	exon29	c.G3947A	p.R1316K	CCCGAAGGTCCCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684573	100684573	+	Silent	SNP	G	G	A	rs144023476	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	13	141	2	0.0822785	0.0141844	G|0.984;A|0.016	0.016	strong	MUC17,NS,haematopoietic_neoplasm,0,1	MUC17	804	1	NM_001040105	exon3	c.G9876A	p.T3292T	CACAACGGTGGCC	.	scavenged	Atlas-SNP
HK2	3099	hgsc.bcm.edu	37	2	75107671	75107671	+	Silent	SNP	C	C	T	rs28363033	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	62	129	0	0.380368	0	C|0.988;T|0.012	0.012	strong	.	HK2	85	.	NM_000189	exon10	c.C1545T	p.Y515Y	CACCTACGTGTGT	.	PASS	Atlas-SNP
ZNF592	9640	hgsc.bcm.edu	37	15	85326315	85326315	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	80	0	0.467742	0	.	.	none	.	ZNF592	95	.	NM_014630	exon4	c.A409C	p.T137P	TTACCCACCTTCA	.	PASS	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61672235	61672235	+	Silent	SNP	T	T	C	rs174473	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	87	225	0	0.378261	0	T|0.713;C|0.287	0.287	strong	.	RAB3IL1	39	.	NM_013401	exon6	c.A777G	p.T259T	CTGCATTGTGAAG	.	PASS	Atlas-SNP
CAPN6	827	hgsc.bcm.edu	37	X	110494841	110494841	+	Missense_Mutation	SNP	C	C	G	rs12013711	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	344	341	0	0.997101	0	C|0.722;0|0.021	.	strong	.	CAPN6	120	.	NM_014289	exon6	c.G829C	p.V277L	TATACACCTTCTC	.	PASS	Atlas-SNP
ABHD11	83451	hgsc.bcm.edu	37	7	73151643	73151643	+	Missense_Mutation	SNP	C	C	T	rs61745525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	59	0	1	0	C|0.963;T|0.037	0.037	strong	.	ABHD11	11	.	NM_148912	exon4	c.G541A	p.V181M	CTGCCACATAGGT	.	PASS	Atlas-SNP
ZNF420	147923	hgsc.bcm.edu	37	19	37618157	37618157	+	Silent	SNP	T	T	C	rs78427535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	72	141	0	0.486486	0	T|0.984;C|0.016	0.016	strong	.	ZNF420	71	.	NM_144689	exon5	c.T264C	p.D88D	CAGGGATTATTTG	.	PASS	Atlas-SNP
BDNF	627	hgsc.bcm.edu	37	11	27679976	27679976	+	Missense_Mutation	SNP	C	C	T	rs146354977	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	61	139	0	0.465649	0	C|0.999;T|0.001	0.001	strong	.	BDNF	63	.	NM_001143810	exon3	c.G382A	p.V128M	CATTCACGCTCTC	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	491906	491906	+	Silent	SNP	G	G	A	rs6870920	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	43	81	0	0.518072	0	G|0.958;A|0.042	0.042	strong	SLC9A3,head_neck,malignant_melanoma,-1,1	SLC9A3	89	1	NM_004174	exon2	c.C492T	p.G164G	GAAGACGCCGTAG	.	PASS	Atlas-SNP
PITPNM1	9600	hgsc.bcm.edu	37	11	67267636	67267636	+	Silent	SNP	G	G	A	rs59249357	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	13	15	0	0.448276	0	A|0.006;C|0.005;G|0.988	0.006	strong	.	PITPNM1	84	.	NM_001130848	exon6	c.C897T	p.A299A	GGGGGAGGCATCT	.	PASS	Atlas-SNP
HS3ST2	9956	hgsc.bcm.edu	37	16	22826321	22826321	+	Silent	SNP	G	G	A	rs111703383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	106	0	1	0	G|0.949;A|0.051	0.051	strong	.	HS3ST2	59	.	NM_006043	exon1	c.G390A	p.V130V	GGCCGTGCTGGAG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33688865	33688865	+	Silent	SNP	A	A	G	rs7279896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	33	80	0	0.507692	0	A|0.758;G|0.242	0.242	strong	.	URB1	176	.	NM_014825	exon38	c.T6546C	p.A2182A	CTGGGCAGCCACC	.	PASS	Atlas-SNP
IGFALS	3483	hgsc.bcm.edu	37	16	1840777	1840777	+	Missense_Mutation	SNP	G	G	A	rs9282731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	61	103	0	0.559633	0	G|0.909;A|0.091	0.091	strong	.	IGFALS	29	.	NM_001146006	exon2	c.C1756T	p.R586W	AGTCCCGCAGCGC	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9070366	9070366	+	Silent	SNP	T	T	A	rs4883198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	145	187	0	0.517857	0	T|0.310;A|0.690	0.690	strong	.	PHC1	67	.	NM_004426	exon2	c.T93A	p.L31L	GTCACTTTATGAA	.	PASS	Atlas-SNP
SCAMP5	192683	hgsc.bcm.edu	37	15	75305058	75305058	+	Silent	SNP	G	G	T	rs60910940	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	167	164	1	1	0.00609756	G|0.966;T|0.034	0.034	strong	.	SCAMP5	34	.	NM_001178111	exon4	c.G48T	p.P16P	CATCCCGCTGAAG	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	60	51	0	1	0	G|0.789;T|0.211	0.211	strong	.	ARHGAP25	175	.	NM_001007231	exon10	c.G1668T	p.R556S	GCAGAGGATGGTC	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	101	0	0.486486	0	C|0.697;T|0.303	0.303	strong	FAT3_ENST00000409404,colon,carcinoma,0,2	FAT3	1822	2	NM_001008781	exon1	c.C2899T	p.L967L	CTTGGACTGGGGG	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42643529	42643529	+	Missense_Mutation	SNP	T	T	C	rs7181742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	99	0	1	0	T|0.702;C|0.298	0.298	strong	.	GANC	57	.	NM_198141	exon23	c.T2534C	p.F845S	CCAGTTTTGCTGA	.	PASS	Atlas-SNP
SFXN3	81855	hgsc.bcm.edu	37	10	102795819	102795819	+	Missense_Mutation	SNP	A	A	T	rs35361377	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	67	113	0	0.577586	0	A|0.986;T|0.014	0.014	strong	.	SFXN3	19	.	NM_030971	exon5	c.A404T	p.N135I	TTGTTAACTACTC	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52131119	52131119	+	Missense_Mutation	SNP	A	A	G	rs2278831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	70	117	0	0.48951	0	A|0.913;G|0.087	0.087	strong	.	SIGLEC5	67	.	NM_003830	exon5	c.T965C	p.F322S	TGCAGGAAGCCCA	.	PASS	Atlas-SNP
ZRANB1	54764	hgsc.bcm.edu	37	10	126631482	126631482	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	2	76	0	0.0181818	0	.	.	none	ZRANB1,NS,carcinoma,+1,1	ZRANB1	60	1	NM_017580	exon1	c.C420T	p.Y140Y	GGAATACAATGAT	.	scavenged	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36922684	36922684	+	Missense_Mutation	SNP	A	A	C	rs1405069	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	57	74	0	0.612903	0	A|0.456;C|0.544	0.544	strong	.	PI16	50	.	NM_001199159	exon2	c.A148C	p.T50P	TCCCCGACGGCCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152278689	152278689	+	Silent	SNP	C	C	A	rs57672167	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	705	0	1	0	C|0.688;A|0.312	0.312	strong	FLG,NS,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.G8673T	p.V2891V	CTGGCTCACACTG	.	scavenged	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	22	56	0	0.564103	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C3090T	p.D1030D	GAGGGACGAGGAG	.	PASS	Atlas-SNP
ANKRD24	170961	hgsc.bcm.edu	37	19	4216931	4216931	+	Missense_Mutation	SNP	A	A	G	rs61741405	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	16	46	0	0.571429	0	A|0.987;G|0.013	0.013	strong	.	ANKRD24	180	.	NM_133475	exon18	c.A1774G	p.T592A	GAGGCCACAGGAG	.	PASS	Atlas-SNP
OPN4	94233	hgsc.bcm.edu	37	10	88421041	88421041	+	Silent	SNP	C	C	T	rs7478092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	34	67	0	0.472222	0	C|0.934;T|0.066	0.066	strong	.	OPN4	61	.	NM_001030015	exon8	c.C1002T	p.Y334Y	TAGGTACGCACAC	.	PASS	Atlas-SNP
COPA	1314	hgsc.bcm.edu	37	1	160302298	160302298	+	Missense_Mutation	SNP	T	T	C	rs57425682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	29	52	0	0.58	0	T|0.956;C|0.044	0.044	strong	.	COPA	181	.	NM_001098398	exon6	c.A436G	p.T146A	CTTCTGTGGGGTG	.	PASS	Atlas-SNP
CYP4B1	1580	hgsc.bcm.edu	37	1	47280859	47280859	+	Missense_Mutation	SNP	G	G	A	rs2297810	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	77	151	0	0.496774	0	G|0.736;A|0.264	0.264	strong	.	CYP4B1	81	.	NM_001099772	exon8	c.G996A	p.M332I	CTGCATGGCCCTG	.	PASS	Atlas-SNP
CST4	1472	hgsc.bcm.edu	37	20	23666606	23666606	+	Silent	SNP	C	C	T	rs112139500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	93	238	1	0.447115	0.00420168	C|0.873;T|0.127	0.127	strong	.	CST4	37	.	NM_001899	exon3	c.G351A	p.L117L	AGAGCACAACTGT	.	PASS	Atlas-SNP
CAPN3	825	hgsc.bcm.edu	37	15	42681199	42681199	+	Missense_Mutation	SNP	G	G	A	rs1801449	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	107	231	0	0.467249	0	G|0.759;A|0.241	0.241	strong	.	CAPN3	172	.	NM_000070	exon5	c.G706A	p.A236T	GGGGTGGCAGAGT	.	PASS	Atlas-SNP
ELMOD1	55531	hgsc.bcm.edu	37	11	107501428	107501428	+	Missense_Mutation	SNP	A	A	T	rs201717101	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	58	122	0	0.381579	0	.	.	weak	.	ELMOD1	40	.	NM_018712	exon4	c.A166T	p.T56S	ACAGAAACATCAC	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3844787	3844787	+	Silent	SNP	C	C	G	rs1800912	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	65	115	0	0.52	0	C|0.787;G|0.213	0.213	strong	ATP2A3,NS,carcinoma,-2,1	ATP2A3	148	1	NM_174956	exon13	c.G1707C	p.A569A	TGGGGGCGCGTCC	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124949044	124949044	+	Silent	SNP	C	C	T	rs33932952	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	77	161	0	0.553957	0	C|0.814;T|0.186	0.186	strong	SLC37A2,NS,carcinoma,0,1	SLC37A2	105	1	NM_001145290	exon5	c.C351T	p.Y117Y	TTACTACCTCTCA	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5072333	5072333	+	Missense_Mutation	SNP	T	T	G	rs3816913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	121	211	0	0.411565	0	T|0.884;G|0.116	0.116	strong	.	USP6	213	.	NM_004505	exon27	c.T3500G	p.I1167S	CTAACATCAGCAG	.	PASS	Atlas-SNP
DCC	1630	hgsc.bcm.edu	37	18	50705370	50705370	+	Missense_Mutation	SNP	A	A	T	rs116498325	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	78	107	0	0.47561	0	A|0.996;T|0.004	0.004	strong	.	DCC	360	.	NM_005215	exon9	c.A1457T	p.Q486L	CCCTTCAGCTCAC	.	PASS	Atlas-SNP
KCNJ4	3761	hgsc.bcm.edu	37	22	38823895	38823895	+	Silent	SNP	G	G	A	rs105154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	14	23	0	0.4375	0	G|0.921;A|0.079	0.079	strong	.	KCNJ4	74	.	NM_004981	exon2	c.C243T	p.A81A	GAAGAAGGCGATA	.	PASS	Atlas-SNP
ETAA1	54465	hgsc.bcm.edu	37	2	67624739	67624739	+	Silent	SNP	C	C	A	rs182131786	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	23	12	0	0.69697	0	C|0.999;A|0.001	0.001	strong	ETAA1,colon,carcinoma,+2,1	ETAA1	88	1	NM_019002	exon1	c.C159A	p.P53P	GCCTCCCGGGCCA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150946444	150946444	+	Silent	SNP	G	G	A	rs142348925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	98	132	0	0.445455	0	G|0.999;A|0.001	0.001	strong	.	FAT2	465	.	NM_001447	exon1	c.C2049T	p.I683I	GTGGAGGATAGTC	.	PASS	Atlas-SNP
COX7B	1349	hgsc.bcm.edu	37	X	77158147	77158147	+	Missense_Mutation	SNP	C	C	A	rs61752458	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	42	78	0	0.482759	0	C|0.991;A|0.009	0.009	strong	.	COX7B	8	.	NM_001866	exon2	c.C48A	p.S16R	TCGAAGCATTCAG	.	PASS	Atlas-SNP
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126492	19126492	+	Missense_Mutation	SNP	T	T	A	rs8051801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	36	86	0	0.423529	0	T|0.989;A|0.011	0.011	strong	.	ITPRIPL2	40	.	NM_001034841	exon1	c.T709A	p.C237S	GCCTTCTGCGTGG	.	PASS	Atlas-SNP
C20orf144	128864	hgsc.bcm.edu	37	20	32251396	32251396	+	Missense_Mutation	SNP	A	A	G	rs7260921	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	28	42	0	0.424242	0	A|0.881;G|0.119	0.119	strong	.	C20orf144	4	.	NM_080825	exon2	c.A185G	p.Q62R	CTGGGCAACGGAT	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367559	142367559	+	Silent	SNP	G	G	A	rs11785629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	20	17	0	0.666667	0	G|0.364;A|0.636	0.636	strong	.	GPR20	43	.	NM_005293	exon2	c.C465T	p.P155P	GCCTTCGGGCCGC	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95077498	95077498	+	Missense_Mutation	SNP	C	C	T	rs58545014	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	118	178	0	0.732919	0	C|0.972;T|0.028	0.028	strong	.	NOL8	118	.	NM_017948	exon7	c.G1409A	p.G470E	TCACCTCCTTCAG	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38145715	38145715	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	8	113	0	0.0695652	0	.	.	none	.	RPGR	175	.	NM_001034853	exon15	c.A2537G	p.E846G	TCCCCTTCCTCCT	.	PASS	Atlas-SNP
SLC5A6	8884	hgsc.bcm.edu	37	2	27430237	27430237	+	Silent	SNP	T	T	C	rs56970590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	123	191	0	0.574766	0	T|0.952;C|0.048	0.048	strong	.	SLC5A6	63	.	NM_021095	exon3	c.A282G	p.R94R	CCCAAATCGGTAG	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1391362	1391362	+	Silent	SNP	A	A	G	rs75271587	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	24	74	0	0.45283	0	A|0.988;G|0.012	0.012	strong	.	BAIAP3	88	.	NM_003933	exon8	c.A708G	p.A236A	CCGTGCACAGAAG	.	PASS	Atlas-SNP
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	111	96	0	0.991071	0	C|0.688;T|0.312	0.312	strong	.	SLC7A14	110	.	NM_020949	exon7	c.G1173A	p.S391S	GAACCCCGACACG	.	PASS	Atlas-SNP
KDR	3791	hgsc.bcm.edu	37	4	55956183	55956183	+	Silent	SNP	G	G	T	rs145298133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	28	68	0	0.35	0	G|0.999;T|0.001	0.001	strong	.	KDR	307	.	NM_002253	exon23	c.C3132A	p.I1044I	GTCACAGATTTTA	.	PASS	Atlas-SNP
GH2	2689	hgsc.bcm.edu	37	17	61957610	61957610	+	Missense_Mutation	SNP	G	G	T	rs58696130	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	71	82	0	0.537879	0	G|0.983;T|0.017	0.017	strong	.	GH2	73	.	NM_022558	exon5	c.C721A	p.P241T	CTGGTGGGCACTG	.	PASS	Atlas-SNP
C11orf40	143501	hgsc.bcm.edu	37	11	4593411	4593411	+	Missense_Mutation	SNP	G	G	A	rs34097396	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	78	125	0	0.509804	0	G|0.888;A|0.112	0.112	strong	.	C11orf40	37	.	NM_144663	exon3	c.C422T	p.T141M	GAAAGCGTGATAA	.	PASS	Atlas-SNP
GPC3	2719	hgsc.bcm.edu	37	X	132670269	132670269	+	Silent	SNP	T	T	C	rs61754631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	119	172	0	0.61658	0	T|0.927;C|0.073	0.073	strong	.	GPC3	88	.	NM_001164617	exon9	c.A1695G	p.A565A	CGGAGTTGCCTGC	.	PASS	Atlas-SNP
LCN10	414332	hgsc.bcm.edu	37	9	139634495	139634495	+	Nonsense_Mutation	SNP	G	G	A	rs9886752	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	79	94	0	0.675214	0	G|0.818;A|0.182	0.182	strong	.	LCN10	21	.	NM_001001712	exon5	c.C481T	p.Q161X	CATTCTGCCTATC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64057543	64057543	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	21	317	0	0.0610465	0	.	.	none	DPY19L2,caecum,carcinoma,0,1	DPY19L2	97	1	NM_173812	exon3	c.G445A	p.E149K	CCATTTCAGTGCG	.	scavenged	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612064	17612064	+	Missense_Mutation	SNP	A	A	C	rs75253845	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	68	147	0	0.507463	0	A|0.978;C|0.022	0.022	strong	.	MTUS1	144	.	NM_001001924	exon2	c.T1253G	p.M418R	ATGACCATATCAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228461655	228461655	+	Silent	SNP	C	C	T	rs138055037	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	103	185	0	0.559783	0	C|0.996;T|0.004	0.004	strong	.	OBSCN	2142	.	NM_001271223	exon22	c.C6447T	p.H2149H	CACCCACACCCTG	.	PASS	Atlas-SNP
CLGN	1047	hgsc.bcm.edu	37	4	141317068	141317068	+	Missense_Mutation	SNP	G	G	A	rs12513290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	82	159	0	0.44086	0	G|0.909;A|0.091	0.091	strong	.	CLGN	76	.	NM_001130675	exon11	c.C1054T	p.R352W	CAATCCGACATGC	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46856100	46856100	+	Silent	SNP	G	G	A	rs678312	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	241	225	0	1	0	G|0.108;A|0.892	0.892	strong	.	GPR116	133	.	NM_015234	exon4	c.C300T	p.T100T	AATGTCGGTAATT	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50899103	50899103	+	Silent	SNP	G	G	A	rs77064034	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	43	96	0	0.447917	0	G|0.990;A|0.010	0.010	strong	.	SBF1	211	.	NM_002972	exon24	c.C3006T	p.D1002D	GGCGCTGTCAGAC	.	PASS	Atlas-SNP
CETP	1071	hgsc.bcm.edu	37	16	57003846	57003846	+	Missense_Mutation	SNP	C	C	T	rs34716057	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	72	136	0	0.517986	0	C|0.992;T|0.008	0.008	strong	.	CETP	50	.	NM_000078	exon5	c.C460T	p.R154W	AGAGTGCGGACCG	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	285256	285256	+	Silent	SNP	G	G	A	rs144727560	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	36	70	0	0.461538	0	G|0.995;A|0.005	0.005	strong	.	NLRP6	4	.	NM_138329	exon8	c.G2631A	p.A877A	CCCAGCGCTGGAC	.	PASS	Atlas-SNP
PDLIM5	10611	hgsc.bcm.edu	37	4	95539204	95539204	+	Missense_Mutation	SNP	C	C	T	rs141653509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	64	83	0	0.556522	0	C|0.999;T|0.001	0.001	strong	PDLIM5,NS,carcinoma,-1,1	PDLIM5	76	1	NM_001256426	exon12	c.C1057T	p.R353W	TCCACACGGAGCA	.	PASS	Atlas-SNP
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	44	88	0	0.478261	0	T|0.348;G|0.007	0.348	strong	NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	NM_205860	exon8	c.C1569T	p.C523C	CCTGAACGGGGAT	.	PASS	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36927136	36927136	+	Silent	SNP	C	C	T	rs74853487	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	21	0	0.444444	0	C|0.966;T|0.034	0.034	strong	.	PI16	50	.	NM_001199159	exon3	c.C387T	p.Y129Y	CCACTACACGCAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284823	152284823	+	Missense_Mutation	SNP	A	A	G	rs74129459	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	477	23	410	0	0.048218	0	A|0.984;T|0.016	.	alt	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.T2539C	p.S847P	TGCTTGACCCCGG	.	PASS	Atlas-SNP
CXorf64	100130613	hgsc.bcm.edu	37	X	125954900	125954900	+	Silent	SNP	C	C	T	rs41309536	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	118	174	1	0.581281	0.00574713	C|0.878;T|0.122	0.122	strong	.	.	.	.	NM_001122716	exon2	c.C279T	p.Y93Y	CCCCTACGGGCCA	.	PASS	Atlas-SNP
ZFP112	7771	hgsc.bcm.edu	37	19	44831989	44831989	+	Missense_Mutation	SNP	T	T	G	rs2609881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	278	277	232	0	0.996403	0	T|0.766;G|0.234	0.234	strong	.	ZFP112	219	.	NM_001083335	exon5	c.A2339C	p.E780A	CACACCTCACATT	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	46	455	0	0.167273	0	T|0.684;C|0.317	0.317	strong	SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	NM_001040022	exon3	c.T395C	p.V132A	ATGACGTGGAGTT	.	PASS	Atlas-SNP
CPA3	1359	hgsc.bcm.edu	37	3	148601596	148601596	+	Silent	SNP	G	G	A	rs140411214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	67	136	0	0.468531	0	G|0.995;A|0.005	0.005	strong	.	CPA3	75	.	NM_001870	exon9	c.G975A	p.E325E	CCATGAGGACTTG	.	PASS	Atlas-SNP
MYO19	80179	hgsc.bcm.edu	37	17	34858985	34858985	+	Missense_Mutation	SNP	A	A	G	rs61743158	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	65	149	0	0.422078	0	A|0.995;G|0.005	0.005	strong	.	MYO19	130	.	NM_001163735	exon22	c.T2032C	p.C678R	ATGTGCAAGGATG	.	PASS	Atlas-SNP
TPM4	7171	hgsc.bcm.edu	37	19	16186865	16186865	+	Silent	SNP	G	G	A	rs114042568	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	67	108	0	0.489051	0	G|0.989;A|0.011	0.011	strong	.	TPM4	28	.	NM_001145160	exon2	c.G123A	p.E41E	GGAGGAGGAGCTG	.	PASS	Atlas-SNP
FCGRT	2217	hgsc.bcm.edu	37	19	50017191	50017191	+	Silent	SNP	G	G	T	rs11551281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	88	170	0	0.54321	0	G|0.984;T|0.016	0.016	strong	.	FCGRT	23	.	NM_001136019	exon3	c.G126T	p.P42P	TGCCCCGGGGACT	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47462657	47462657	+	Silent	SNP	G	G	A	rs1627232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	63	145	0	0.440559	0	G|0.961;A|0.039	0.039	strong	.	MYO5B	178	.	NM_001080467	exon16	c.C1968T	p.R656R	GATGCAGCGGACA	.	PASS	Atlas-SNP
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917126	32917126	+	Missense_Mutation	SNP	C	C	T	rs9469319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	87	0	0.5	0	C|0.997;T|0.003	0.003	strong	.	HLA-DMA	20	.	NM_006120	exon4	c.G703A	p.V235M	AGGCCACGCCACA	.	PASS	Atlas-SNP
HTR3A	3359	hgsc.bcm.edu	37	11	113857661	113857661	+	Missense_Mutation	SNP	G	G	A	rs35815285	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	69	119	1	0.579832	0.00840336	G|0.965;A|0.035	0.035	strong	HTR3A,NS,carcinoma,+1,1	HTR3A	93	1	NM_213621	exon7	c.G1145A	p.R382H	GGCTGCGTCACCT	.	scavenged	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	37	14	94173098	94173098	+	Missense_Mutation	SNP	G	G	A	rs76642035	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	104	0	0.5	0	G|0.996;A|0.004	0.004	strong	.	UNC79	366	.	NM_020818	exon50	c.G7225A	p.V2409M	AACCACGTGAACC	.	PASS	Atlas-SNP
SOX30	11063	hgsc.bcm.edu	37	5	157078475	157078475	+	Silent	SNP	C	C	G	rs3749797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	196	281	1	0.989899	0.00355872	C|0.825;G|0.175	0.175	strong	SOX30,NS,carcinoma,0,1	SOX30	67	1	NM_178424	exon1	c.G612C	p.P204P	GGCTGCCGGGCTT	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31680334	31680334	+	Missense_Mutation	SNP	C	C	T	rs17122711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	18	49	0	0.461538	0	C|0.960;T|0.040	0.040	strong	.	.	.	.	NM_182519	exon9	c.C1214T	p.P405L	CCAAGCCGATGCC	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860558	16860558	+	Missense_Mutation	SNP	G	G	A	rs61733271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	61	0	1	0	G|0.927;A|0.073	0.073	strong	.	NWD1	303	.	NM_001007525	exon6	c.G1105A	p.V369I	GTGACCGTCCTGC	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42404710	42404710	+	Missense_Mutation	SNP	C	C	T	rs41288297	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	15	48	0	0.365854	0	C|0.947;T|0.053	0.053	strong	.	.	.	.	NM_015058	exon14	c.G1655A	p.R552H	TTTAAACGCATAT	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187078819	187078819	+	Silent	SNP	C	C	G	rs2276923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	24	69	0	0.4	0	C|0.839;G|0.161	0.161	strong	.	FAM149A	52	.	NM_001006655	exon7	c.C675G	p.S225S	CCCGTCCGGACAC	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	37	15	65681648	65681648	+	Missense_Mutation	SNP	A	A	G	rs144676391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	18	79	0	0.36	0	A|0.995;G|0.005	0.005	strong	.	IGDCC4	95	.	NM_020962	exon14	c.T2510C	p.V837A	TCCACCACAGAGC	.	PASS	Atlas-SNP
DNASE1	1773	hgsc.bcm.edu	37	16	3707262	3707262	+	Silent	SNP	G	G	A	rs8176920	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	120	0	1	0	G|0.970;A|0.030	0.030	strong	.	DNASE1	16	.	NM_005223	exon7	c.G624A	p.L208L	CCGCCTGTGGACA	.	PASS	Atlas-SNP
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	116	186	0	0.682353	0	C|0.877;G|0.123	0.123	strong	.	TFDP3	92	.	NM_016521	exon1	c.G58C	p.E20Q	GGTTCTCGTCCAT	.	PASS	Atlas-SNP
C6orf52	347744	hgsc.bcm.edu	37	6	10687325	10687325	+	Silent	SNP	C	C	T	rs144052767	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	53	121	1	0.456897	0.00826446	C|0.990;T|0.010	0.010	strong	C6orf52,caecum,carcinoma,0,1	C6orf52	9	1	NM_001145020	exon3	c.G144A	p.A48A	CTGTCGCGCATAC	.	scavenged	Atlas-SNP
HDAC7	51564	hgsc.bcm.edu	37	12	48185449	48185449	+	Missense_Mutation	SNP	G	G	A	rs73291234	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	79	178	0	0.459302	0	G|0.989;A|0.011	0.011	strong	.	HDAC7	71	.	NM_015401	exon15	c.C1853T	p.S618L	TGGACCGACTGCA	.	PASS	Atlas-SNP
SKIV2L	6499	hgsc.bcm.edu	37	6	31928039	31928039	+	Silent	SNP	C	C	G	rs11541400	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	53	113	0	0.456897	0	C|0.993;G|0.007	0.007	strong	.	SKIV2L	97	.	NM_006929	exon4	c.C279G	p.V93V	GGCTGTCCTGGGA	.	PASS	Atlas-SNP
RPL37	6167	hgsc.bcm.edu	37	5	40834595	40834595	+	Silent	SNP	G	G	A	rs6495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	44	62	0	0.44	0	G|0.996;A|0.004	0.004	strong	.	RPL37	7	.	NM_000997	exon2	c.C117T	p.Y39Y	GGCAGGGTAGCCA	.	PASS	Atlas-SNP
SORBS1	10580	hgsc.bcm.edu	37	10	97174352	97174352	+	Missense_Mutation	SNP	T	T	C	rs2281939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	72	175	0	0.45	0	T|0.860;C|0.140	0.140	strong	SORBS1_ENST00000371247,NS,carcinoma,+2,2	SORBS1	185	2	NM_001034955	exon7	c.A709G	p.T237A	GTGGCGTCTGGCT	.	PASS	Atlas-SNP
MCM2	4171	hgsc.bcm.edu	37	3	127323830	127323830	+	Silent	SNP	C	C	T	rs893293	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	85	177	0	0.518293	0	C|0.348;T|0.652	0.652	strong	.	MCM2	79	.	NM_004526	exon4	c.C504T	p.I168I	GATGATCGAGAGC	.	PASS	Atlas-SNP
NKD2	85409	hgsc.bcm.edu	37	5	1036482	1036482	+	Missense_Mutation	SNP	C	C	A	rs35679233	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	44	72	0	0.52381	0	C|0.994;A|0.006	0.006	strong	.	NKD2	39	.	NM_001271082	exon9	c.C770A	p.T257K	ACTACACGTCCAG	.	PASS	Atlas-SNP
RGR	5995	hgsc.bcm.edu	37	10	86012713	86012713	+	Silent	SNP	C	C	T	rs1042454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	85	0	1	0	C|0.502;T|0.498	0.498	strong	RGR,NS,adenoma,0,2	RGR	42	2	NM_002921	exon4	c.C471T	p.Y157Y	TCACTACGACTAT	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30491311	30491311	+	Silent	SNP	C	C	T	rs2075821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	35	69	0	0.583333	0	C|0.707;T|0.293	0.293	strong	.	NOD1	79	.	NM_006092	exon6	c.G1722A	p.A574A	TTCCCGCGCCGGA	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45799018	45799018	+	Missense_Mutation	SNP	G	G	A	rs45485992	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	38	75	0	0.487179	0	G|0.994;A|0.006	0.006	strong	.	TRPM2	196	.	NM_003307	exon8	c.G1153A	p.V385M	CTGAGCGTGTTCT	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305911	39305911	+	Missense_Mutation	SNP	G	G	A	rs141058010	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	5	146	0	0.0259067	0	.	.	weak	KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	NM_033188	exon1	c.C109T	p.R37C	TGGGGCGGCAGCA	.	scavenged	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18022385	18022385	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	48	53	0	0.571429	0	.	.	none	.	MYO15A	268	.	NM_016239	exon2	c.C271A	p.R91S	CAGATGCGCATGG	.	PASS	Atlas-SNP
STAG1	10274	hgsc.bcm.edu	37	3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	rs34149860	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	87	136	0	0.54375	0	C|0.914;G|0.086	0.086	strong	.	STAG1	135	.	NM_005862	exon30	c.G3396C	p.Q1132H	TTGAATCTGGTCT	.	PASS	Atlas-SNP
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62374096	62374096	+	Silent	SNP	C	C	T	rs7996	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	30	71	0	0.526316	0	C|0.956;T|0.044	0.044	strong	.	SLC2A4RG	20	.	NM_020062	exon7	c.C1005T	p.V335V	GGAGGTCGGAGCC	.	PASS	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129785615	129785615	+	Silent	SNP	C	C	T	rs3734071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	52	125	0	0.448276	0	C|0.823;T|0.177	0.177	strong	.	PRDM10	120	.	NM_020228	exon17	c.G2478A	p.T826T	GGTGCCCGTCAGC	.	PASS	Atlas-SNP
RXFP3	51289	hgsc.bcm.edu	37	5	33937215	33937215	+	Silent	SNP	C	C	T	rs78710898	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	76	111	0	0.546763	0	C|0.989;T|0.011	0.011	strong	.	RXFP3	114	.	NM_016568	exon1	c.C370T	p.L124L	ACCAACCTGGCGC	.	PASS	Atlas-SNP
GAD2	2572	hgsc.bcm.edu	37	10	26559610	26559610	+	Silent	SNP	C	C	T	rs1805397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	80	162	0	0.509554	0	C|0.988;T|0.012	0.012	strong	.	GAD2	116	.	NM_000818	exon10	c.C1017T	p.T339T	AACCACCGTGTAC	.	PASS	Atlas-SNP
RASSF10	644943	hgsc.bcm.edu	37	11	13031846	13031846	+	Silent	SNP	G	G	A	rs12793946	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	92	175	0	0.489362	0	G|0.931;A|0.069	0.069	strong	.	.	.	.	NM_001080521	exon1	c.G723A	p.Q241Q	TCGCCAGCAGGTG	.	PASS	Atlas-SNP
LYRM4	57128	hgsc.bcm.edu	37	6	5260936	5260936	+	Missense_Mutation	SNP	A	A	C	rs2224391	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	14	23	0	0.56	0	A|0.556;C|0.444	0.444	strong	.	LYRM4	5	.	NM_020408	exon1	c.T31G	p.S11A	ACAGAGATAACAC	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136507473	136507473	+	Missense_Mutation	SNP	G	G	A	rs5320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	27	85	0	0.254717	0	G|0.905;A|0.095	0.095	strong	.	DBH	86	.	NM_000787	exon3	c.G631A	p.A211T	TCAGACGCGTGCA	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38189659	38189659	+	Missense_Mutation	SNP	C	C	T	rs34585432	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	47	93	0	0.465347	0	C|0.993;T|0.007	0.007	strong	.	MED24	89	.	NM_014815	exon7	c.G610A	p.A204T	GATTGGCCAGGAT	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	131864657	131864657	+	Silent	SNP	G	G	A	rs374317794		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	26	49	0	0.464286	0	.	.	weak	.	PLXNA4	873	.	NM_020911	exon20	c.C3663T	p.Y1221Y	CGGGGAGTACTCC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	711712	711712	+	Silent	SNP	C	C	T	rs3177415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	50	124	0	0.420168	0	C|0.451;T|0.549	0.549	strong	.	WDR90	107	.	NM_145294	exon31	c.C3789T	p.G1263G	CGCCGGCGAGCTC	.	PASS	Atlas-SNP
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411711	39411711	+	Missense_Mutation	SNP	C	C	G	rs150962386	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	39	0	0.505882	0	C|0.962;G|0.038	0.038	strong	.	KRTAP9-9	24	.	NM_030975	exon1	c.C74G	p.T25S	CTGTGACCACCTG	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52994955	52994955	+	Silent	SNP	G	G	A	rs61747192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	68	0	0.449438	0	G|0.856;A|0.144	0.144	strong	.	KRT72	70	.	NM_001146225	exon1	c.C282T	p.P94P	GCCCCCGGGTGGG	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170469	58170469	+	Silent	SNP	C	C	A	rs11229412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	69	116	1	0.556452	0.00862069	C|0.672;A|0.328	0.328	strong	OR5B3,NS,carcinoma,0,1	OR5B3	65	1	NM_001005469	exon1	c.G414T	p.V138V	AGCACACACAGTT	.	scavenged	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73731012	73731012	+	Silent	SNP	C	C	T	rs151179834	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	58	89	0	0.54717	0	C|0.984;T|0.016	0.016	strong	.	PAPLN	180	.	NM_173462	exon20	c.C2874T	p.R958R	AGGCCGCGACTCC	.	PASS	Atlas-SNP
PHYHD1	254295	hgsc.bcm.edu	37	9	131689361	131689361	+	Silent	SNP	G	G	A	rs751340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	204	172	0	1	0	G|0.615;A|0.385	0.385	strong	PHYHD1,caecum,carcinoma,+1,2	PHYHD1	29	2	NM_001100877	exon2	c.G78A	p.A26A	GTCTGCGGAAGAG	.	PASS	Atlas-SNP
RHNO1	83695	hgsc.bcm.edu	37	12	2994562	2994562	+	Silent	SNP	T	T	C	rs371402573		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	94	178	0	0.580247	0	.	.	weak	.	.	.	.	NM_001257098	exon2	c.T30C	p.P10P	CCAGCCTTCCCAG	.	PASS	Atlas-SNP
IFNA14	3448	hgsc.bcm.edu	37	9	21239589	21239589	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	404	35	329	0	0.0866337	0	.	.	none	IFNA14,NS,haematopoietic_neoplasm,+2,3	IFNA14	29	3	NM_002172	exon1	c.A346C	p.M116L	CATTCATTTGCTG	.	scavenged	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431236	135431236	+	Missense_Mutation	SNP	T	T	C	rs5930932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	170	275	1	0.543131	0.00363636	0|0.015;C|0.499	0.499	strong	.	GPR112	459	.	NM_153834	exon6	c.T5371C	p.F1791L	AATTGCTTTTCTT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92534968	92534968	+	Missense_Mutation	SNP	G	G	A	rs370539148		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	49	98	0	0.544444	0	.	.	weak	.	FAT3	1822	.	NM_001008781	exon9	c.G8789A	p.R2930Q	TGTACCGAGGGAA	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10223697	10223697	+	Missense_Mutation	SNP	G	G	T	rs2074876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	114	0	0.45614	0	G|0.786;T|0.214	0.214	strong	MYH13_ENST00000252172,colon,carcinoma,-1,2	MYH13	533	2	NM_003802	exon25	c.C3228A	p.D1076E	CTGCTTGTCATTT	.	PASS	Atlas-SNP
KIAA1462	57608	hgsc.bcm.edu	37	10	30316872	30316872	+	Silent	SNP	T	T	C	rs3739996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	82	172	0	0.448087	0	T|0.732;C|0.268	0.268	strong	.	KIAA1462	162	.	NM_020848	exon3	c.A2205G	p.A735A	AGGGAATGCTGTG	.	PASS	Atlas-SNP
TACC1	6867	hgsc.bcm.edu	37	8	38677242	38677242	+	Silent	SNP	G	G	A	rs16887780	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	117	225	1	0.508696	0.00444444	G|0.991;A|0.009	0.009	strong	.	TACC1	98	.	NM_006283	exon3	c.G480A	p.T160T	TTCCACGGATATC	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	22	81	0	0.956522	0	G|0.827;A|0.173	0.173	strong	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G152A	p.R51Q	TTGCCCGAGACCT	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44892266	44892266	+	Splice_Site	SNP	T	T	C	rs200167944		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	7	122	3	0.0530303	0.0245902	.	.	weak	ZNF285,colon,carcinoma,0,1	ZNF285	86	1	NM_152354	exon5	c.143-2A>G	.	GTCTCCTAGGAGA	.	scavenged	Atlas-SNP
RERE	473	hgsc.bcm.edu	37	1	8420966	8420966	+	Silent	SNP	G	G	A	rs77608355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	9	10	0	0.818182	0	G|0.972;A|0.028	0.028	strong	.	RERE	129	.	NM_012102	exon19	c.C2601T	p.G867G	TGGGGGGCCTGGG	.	PASS	Atlas-SNP
THRAP3	9967	hgsc.bcm.edu	37	1	36752687	36752687	+	Missense_Mutation	SNP	A	A	G	rs58840555	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	49	115	0	0.404959	0	A|0.946;G|0.054	0.054	strong	.	THRAP3	93	.	NM_005119	exon4	c.A856G	p.T286A	GGCTCAACTCTGC	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	348222	348222	+	Silent	SNP	C	C	T	rs214250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	17	48	0	0.435897	0	C|0.770;T|0.230	0.230	strong	AXIN1,cerebellum,primitive_neuroectodermal_tumour-medulloblastoma,0,1	AXIN1	290	1	NM_181050	exon6	c.G1284A	p.S428S	CCCTGACGATGGA	.	PASS	Atlas-SNP
CYP3A43	64816	hgsc.bcm.edu	37	7	99457605	99457605	+	Missense_Mutation	SNP	C	C	G	rs680055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	54	141	0	0.425197	0	C|0.863;G|0.137	0.137	strong	.	CYP3A43	52	.	NM_057096	exon10	c.C1018G	p.P340A	GTTTTACCCAATA	.	PASS	Atlas-SNP
PIGP	51227	hgsc.bcm.edu	37	21	38444881	38444881	+	Missense_Mutation	SNP	G	G	A	rs73200245	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	29	0	0.444444	0	G|0.789;A|0.211	0.211	strong	.	PIGP	9	.	NM_153681	exon1	c.C7T	p.P3S	TCCGTGGCACCAT	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38412674	38412674	+	Missense_Mutation	SNP	C	C	T	rs16903965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	78	0	0.489583	0	C|0.891;T|0.109	0.109	strong	.	EGFLAM	302	.	NM_001205301	exon11	c.C1418T	p.T473M	GGCACACGGTTAT	.	PASS	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43678796	43678796	+	Missense_Mutation	SNP	C	C	T	rs2435381	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	103	249	0	0.443966	0	C|0.815;T|0.185	0.185	strong	.	CSGALNACT2	67	.	NM_018590	exon8	c.C1435T	p.P479S	CCGGTTCCTGGTC	.	PASS	Atlas-SNP
ACOX1	51	hgsc.bcm.edu	37	17	73944496	73944496	+	Missense_Mutation	SNP	G	G	A	rs35629489	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	12	58	0	0.307692	0	G|0.989;A|0.011	0.011	strong	ACOX1_ENST00000301608,caecum,carcinoma,0,2	ACOX1	85	2	NM_007292	exon13	c.C1771T	p.R591C	TTACACGCTGGTT	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127827598	127827598	+	Silent	SNP	C	C	T	rs61748158	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	67	0	0.5	0	C|0.998;T|0.002	0.002	strong	.	BIN1	85	.	NM_139346	exon5	c.G384A	p.T128T	CAGGTACGTGTCC	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3452262	3452262	+	Silent	SNP	C	C	T	rs8098291	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	14	16	0	0.636364	0	C|0.953;T|0.047	0.047	strong	.	TGIF1	41	.	NM_170695	exon1	c.C285T	p.S95S	CCTCTCCCCGGAG	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88800122	88800122	+	Silent	SNP	C	C	G	rs9928479	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	21	54	0	0.328125	0	C|0.955;G|0.045	0.045	strong	.	PIEZO1	79	.	NM_001142864	exon18	c.G2361C	p.R787R	CAGCAGCCGCTCA	.	PASS	Atlas-SNP
MGP	4256	hgsc.bcm.edu	37	12	15038703	15038703	+	Missense_Mutation	SNP	G	G	A	rs142330429	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	32	52	0	0.516129	0	G|0.994;A|0.006	0.006	strong	.	MGP	16	.	NM_000900	exon1	c.C23T	p.A8V	AGGATGGCAAGAA	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35434238	35434238	+	Missense_Mutation	SNP	A	A	G	rs1811	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	75	91	0	0.986842	0	A|0.410;G|0.590	0.590	strong	.	ZNF30	44	.	NM_001099438	exon5	c.A371G	p.Q124R	AATGTCAGGAATA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	542	86	818	8	0.158672	0.00977995	C|0.897;A|0.103	0.103	strong	FCGBP,mouth,carcinoma,+1,1	FCGBP	416	1	NM_003890	exon10	c.G4847T	p.G1616V	ACCATGCCTTTAC	.	scavenged	Atlas-SNP
LGI3	203190	hgsc.bcm.edu	37	8	22009053	22009053	+	Silent	SNP	G	G	A	rs35142808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	55	96	0	0.486726	0	G|0.968;A|0.032	0.032	strong	.	LGI3	44	.	NM_139278	exon7	c.C778T	p.L260L	ACTTCAGGATGGT	.	PASS	Atlas-SNP
EPHB6	2051	hgsc.bcm.edu	37	7	142563253	142563253	+	Missense_Mutation	SNP	T	T	G	rs8177146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	61	0	0.490909	0	T|0.947;G|0.053	0.053	strong	.	EPHB6	168	.	NM_004445	exon8	c.T970G	p.S324A	TATAAGTCTTCTG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13754394	13754394	+	Silent	SNP	C	C	T	rs2401809	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	251	260	1	0.984314	0.00384615	C|0.669;T|0.331	0.331	strong	.	DNAH5	868	.	NM_001369	exon62	c.G10473A	p.T3491T	GATGAGCGTGGAA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951488	130951488	+	Silent	SNP	A	A	G	rs2443644	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	63	259	0	0.223404	0	A|0.985;G|0.015	0.015	strong	TUBA3E,right_upper_lobe,carcinoma,-1,1	TUBA3E	73	1	NM_207312	exon4	c.T927C	p.H309H	CTTGCCATGGCGA	.	scavenged	Atlas-SNP
NAV3	89795	hgsc.bcm.edu	37	12	78598891	78598891	+	Silent	SNP	G	G	A	rs9971904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	77	69	0	1	0	G|0.427;A|0.573	0.573	strong	.	NAV3	506	.	NM_014903	exon38	c.G6945A	p.P2315P	CATTCCGCAAACT	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159650978	159650978	+	Missense_Mutation	SNP	A	A	G	rs509648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	74	117	0	0.528571	0	A|0.529;G|0.471	0.471	strong	.	FNDC1	250	.	NM_032532	exon10	c.A1312G	p.T438A	CGGGCCACAAACA	.	PASS	Atlas-SNP
PQLC2	54896	hgsc.bcm.edu	37	1	19652063	19652063	+	Silent	SNP	G	G	A	rs11558390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	80	89	0	0.97561	0	G|0.771;A|0.229	0.229	strong	.	PQLC2	34	.	NM_001040125	exon4	c.G369A	p.T123T	CAGGACGCGCCCC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155407595	155407595	+	Missense_Mutation	SNP	C	C	A	rs140554741	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	36	113	0	0.371134	0	C|0.989;A|0.011	0.011	strong	DCHS2_ENST00000443500,NS,carcinoma,0,1	DCHS2	594	1	NM_001142553	exon2	c.G2130T	p.X710Y	GGAAATCTAGGCA	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	121016424	121016424	+	Missense_Mutation	SNP	A	A	G	rs200852252	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	71	189	0	0.473333	0	A|1.000;G|0.000	0.000	strong	.	TECTA	329	.	NM_005422	exon11	c.A3704G	p.N1235S	TGCAGAACAGCAC	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47607281	47607281	+	Missense_Mutation	SNP	C	C	T	rs12564525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	85	164	0	0.518293	0	C|0.715;T|0.285	0.285	strong	.	CYP4A22	60	.	NM_001010969	exon3	c.C376T	p.R126W	GCTCCACGGATTG	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641295	55641295	+	Missense_Mutation	SNP	A	A	G	rs4388990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	74	243	0	0.362745	0	A|0.750;G|0.250	0.250	strong	.	OR6C74	52	.	NM_001005490	exon1	c.A224G	p.Y75C	CTGTCTACATTCC	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	38	78	0	0.447059	0	G|0.640;A|0.360	0.360	strong	TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	NM_014698	exon7	c.C507T	p.D169D	CAGCAAGTCCCCT	.	PASS	Atlas-SNP
MFSD5	84975	hgsc.bcm.edu	37	12	53647373	53647373	+	Silent	SNP	T	T	C	rs10876422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	32	70	0	0.457143	0	T|0.569;C|0.431	0.431	strong	.	MFSD5	40	.	NM_001170790	exon2	c.T1075C	p.L359L	CTGCTGTTGGGCA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124401172	124401172	+	Missense_Mutation	SNP	G	G	A	rs61740383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	83	0	0.530612	0	G|0.957;A|0.043	0.043	strong	.	DNAH10	888	.	NM_207437	exon62	c.G10537A	p.D3513N	CTGGGAGACAAGG	.	PASS	Atlas-SNP
C1orf94	84970	hgsc.bcm.edu	37	1	34663411	34663411	+	Missense_Mutation	SNP	C	C	G	rs1414474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	45	108	0	0.424528	0	C|0.796;G|0.204	0.204	strong	.	C1orf94	156	.	NM_001134734	exon2	c.C906G	p.D302E	TCCTGACAAGCTC	.	PASS	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616401	248616401	+	Silent	SNP	G	G	A	rs77680148	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1155	256	1147	0	0.221645	0	G|0.913;A|0.087	0.087	strong	.	OR2T2	73	.	NM_001004136	exon1	c.G303A	p.Q101Q	AGTTCAGATCTTC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592215	1592215	+	Missense_Mutation	SNP	C	C	G	rs41289057	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	41	200	0	0.136213	0	C|0.624;G|0.376	0.376	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.G221C	p.G74A	TCCCGGCCTGGTC	.	PASS	Atlas-SNP
UBA6	55236	hgsc.bcm.edu	37	4	68534392	68534392	+	Missense_Mutation	SNP	C	C	T	rs10010188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	22	38	0	0.52381	0	C|0.849;T|0.151	0.151	strong	UBA6,colon,carcinoma,+1,1	UBA6	98	1	NM_018227	exon9	c.G670A	p.A224T	GATTTGCCTAAAA	.	PASS	Atlas-SNP
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	101	249	0	0.444934	0	G|0.530;C|0.470	0.470	strong	.	ERO1LB	48	.	NM_019891	exon16	c.C1395G	p.H465Q	CCTACTGTGTTGT	.	PASS	Atlas-SNP
DNPEP	23549	hgsc.bcm.edu	37	2	220250769	220250769	+	Missense_Mutation	SNP	T	T	C	rs6742404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	111	182	0	0.528571	0	T|0.962;C|0.038	0.038	strong	.	DNPEP	40	.	NM_012100	exon6	c.A511G	p.I171V	GAAGAATGGGCCG	.	PASS	Atlas-SNP
KAT7	11143	hgsc.bcm.edu	37	17	47895271	47895271	+	Silent	SNP	T	T	C	rs17853073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	91	162	0	0.522988	0	T|0.965;C|0.035	0.035	strong	.	.	.	.	NM_007067	exon9	c.T1053C	p.Y351Y	CTGGTATCATTCT	.	PASS	Atlas-SNP
TAS2R50	259296	hgsc.bcm.edu	37	12	11139305	11139305	+	Missense_Mutation	SNP	G	G	A	rs142843602	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	93	229	0	0.467337	0	G|0.993;A|0.007	0.007	strong	.	TAS2R50	37	.	NM_176890	exon1	c.C155T	p.A52V	GAGACCGCCAGAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152275559	152275559	+	Missense_Mutation	SNP	A	A	G	rs3126065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	177	1	1	0.00564972	A|0.871;G|0.129	0.129	strong	.	FLG	900	.	NM_002016	exon3	c.T11803C	p.S3935P	CTTGTGAAAGACT	.	PASS	Atlas-SNP
C19orf10	56005	hgsc.bcm.edu	37	19	4658047	4658047	+	Silent	SNP	A	A	G	rs12683	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	28	68	0	0.466667	0	T|0.000;G|0.142;N|0.001;A|0.857	0.142	strong	C19orf10,NS,lymphoid_neoplasm,0,1	C19orf10	9	1	NM_019107	exon6	c.T492C	p.I164I	GGCCACAATCACC	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55178162	55178162	+	Missense_Mutation	SNP	A	A	G	rs11574576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	111	156	0	0.476395	0	A|0.646;C|0.000;G|0.354	0.354	strong	.	LILRB4	86	.	NM_006847	exon10	c.A1003G	p.N335D	GTGAAGAACACAC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376119	52376119	+	Missense_Mutation	SNP	G	G	A	rs10407911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	47	112	0	0.401709	0	G|0.909;A|0.091	0.091	strong	.	ZNF577	63	.	NM_032679	exon7	c.C1124T	p.T375I	ATGTGAGTTTTCT	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256389	24256389	+	Silent	SNP	A	A	T	rs7001097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	51	80	0	0.451327	0	A|0.977;T|0.023	0.023	strong	.	ADAMDEC1	69	.	NM_014479	exon9	c.A765T	p.I255I	ACAGATATATAAC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896100	1896100	+	Silent	SNP	C	C	T	rs6136375	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	48	326	0	0.229665	0	C|0.633;T|0.367	0.367	strong	.	SIRPA	83	.	NM_001040022	exon3	c.C435T	p.R145R	TGTGCGCGGTGAG	.	PASS	Atlas-SNP
MFSD12	126321	hgsc.bcm.edu	37	19	3546340	3546340	+	Silent	SNP	G	G	A	rs11555328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	69	169	0	0.401163	0	G|0.834;A|0.166	0.166	strong	.	MFSD12	22	.	NM_001042680	exon7	c.C1107T	p.Y369Y	CGCTGCGTACACG	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79556305	79556305	+	Missense_Mutation	SNP	C	C	T	rs74140334	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	96	241	0	0.457143	0	C|0.988;T|0.012	0.012	strong	.	DLG5	154	.	NM_004747	exon28	c.G5212A	p.A1738T	TCAGAGCGGTGCA	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94320300	94320300	+	Silent	SNP	C	C	T	rs145516372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	47	119	0	0.379032	0	C|0.992;T|0.008	0.008	strong	.	PIWIL4	70	.	NM_152431	exon7	c.C801T	p.V267V	CAAAGTCCTCCGG	.	PASS	Atlas-SNP
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	38	124	0	0.358491	0	G|0.598;A|0.402	0.402	strong	.	ALDH1A1	98	.	NM_000689	exon3	c.C225T	p.S75S	CCACGGGGATCCA	.	PASS	Atlas-SNP
BPIFA3	128861	hgsc.bcm.edu	37	20	31812949	31812949	+	Silent	SNP	C	C	T	rs147632261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	84	136	0	0.518519	0	C|0.995;T|0.005	0.005	strong	.	.	.	.	NM_178466	exon4	c.C432T	p.I144I	GAGCATCGTTGTG	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30673489	30673489	+	Silent	SNP	G	G	C	rs9295905	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	401	211	359	0	0.526185	0	G|0.944;C|0.056	0.056	strong	.	MDC1	218	.	NM_014641	exon10	c.C3471G	p.T1157T	TTCAGGGGTCTTG	.	PASS	Atlas-SNP
SPANXN3	139067	hgsc.bcm.edu	37	X	142596941	142596941	+	Missense_Mutation	SNP	C	C	G	rs6654212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	138	136	0	0.992806	0	C|0.847;0|0.012	.	strong	.	SPANXN3	49	.	NM_001009609	exon2	c.G129C	p.K43N	TTTTGTCTTCTTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511486	195511486	+	Missense_Mutation	SNP	G	G	T	rs202186297		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	26	113	0	0.230089	0	G|0.996;T|0.005	0.005	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C6965A	p.P2322H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	312	23	264	0	0.073718	0	T|0.996;C|0.004	0.004	strong	ZNF419_ENST00000284020,colon,carcinoma,0,2	ZNF419	134	2	NM_001098494	exon3	c.T96C	p.D32D	TGAGGATGTGGCT	.	scavenged	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80747209	80747209	+	Missense_Mutation	SNP	C	C	G	rs7312569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	42	88	0	0.385321	0	C|0.844;G|0.156	0.156	strong	.	OTOGL	235	.	NM_173591	exon45	c.C5485G	p.L1829V	TTGAATCTAAGAG	.	PASS	Atlas-SNP
OR8H3	390152	hgsc.bcm.edu	37	11	55889918	55889918	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	18	196	0	0.0779221	0	.	.	none	.	OR8H3	92	.	NM_001005201	exon1	c.G70A	p.V24I	GAAGAGGTCCAGA	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45221404	45221404	+	Missense_Mutation	SNP	C	C	T	rs74393756	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	83	150	0	0.448649	0	C|0.978;T|0.022	0.022	strong	.	PRR5-ARHGAP8	53	.	NM_181334	exon10	c.C893T	p.P298L	GGACGCCGCCTCC	.	PASS	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120793296	120793296	+	Silent	SNP	C	C	T	rs7002501	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	57	0	1	0	C|0.713;T|0.287	0.287	strong	.	TAF2	204	.	NM_003184	exon17	c.G2250A	p.Q750Q	TACCTTCTGTAGA	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1537706	1537706	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	37	85	0	0.411111	0	.	.	none	.	PTX4	46	.	NM_001013658	exon2	c.G392A	p.R131Q	CGGGCCCGCTGCT	.	PASS	Atlas-SNP
OR2A7	401427	hgsc.bcm.edu	37	7	143956461	143956461	+	Silent	SNP	T	T	C	rs75809055		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	575	75	347	1	0.130435	0.00288184	T|0.500;C|0.500	0.500	weak	OR2A7_ENST00000493325,NS,carcinoma,0,2	OR2A7	33	2	NM_001005328	exon1	c.A261G	p.P87P	CTTGGCTGGATGC	.	scavenged	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	37	5	175722243	175722243	+	Missense_Mutation	SNP	A	A	G	rs7736723	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	134	321	0	0.414861	0	A|1.000;|0.000	.	weak	.	.	.	.	NM_198567	exon2	c.A340G	p.M114V	GCCTACATGCTTC	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137630361	137630361	+	Silent	SNP	G	G	A	rs61729545	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	100	128	0	0.625	0	G|0.937;A|0.063	0.063	strong	COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	NM_000093	exon10	c.G1431A	p.A477A	CCCCGCGGTGAGT	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73148481	73148481	+	Missense_Mutation	SNP	G	G	A	rs2973566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	85	179	0	0.497076	0	G|0.830;A|0.170	0.170	strong	.	.	.	.	NM_001080479	exon14	c.G1754A	p.R585K	AGCAAAGAGCTTA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268304	1268304	+	Silent	SNP	A	A	G	rs2943503		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	857	33	741	1	0.0385064	0.00134953	G|1.000;|0.000	1.000	weak	MUC5B,NS,lymphoid_neoplasm,0,2	MUC5B	473	2	NM_002458	exon31	c.A10194G	p.T3398T	GATCACAGCCACC	.	scavenged	Atlas-SNP
ARSI	340075	hgsc.bcm.edu	37	5	149677818	149677818	+	Silent	SNP	G	G	A	rs77943970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	48	75	0	0.551724	0	G|0.967;A|0.033	0.033	strong	.	ARSI	65	.	NM_001012301	exon2	c.C669T	p.H223H	AGGGCTGTGGCTG	.	PASS	Atlas-SNP
ATP2B3	492	hgsc.bcm.edu	37	X	152830495	152830495	+	Silent	SNP	T	T	C	rs5986910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	64	185	0	0.329897	0	T|0.920;C|0.080	0.080	strong	.	ATP2B3	552	.	NM_001001344	exon19	c.T3276C	p.H1092H	CGACCATGCCGAG	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262121	39262121	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	17	129	0	0.112583	0	.	.	none	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	NM_001146041	exon1	c.C481T	p.R161C	TGCTGCCGCCCCT	.	scavenged	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	37	11	48166642	48166642	+	Silent	SNP	C	C	T	rs34300475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	100	206	0	0.50505	0	C|0.944;T|0.056	0.056	strong	.	PTPRJ	225	.	NM_002843	exon14	c.C2877T	p.R959R	CAGTCGCTACTCA	.	PASS	Atlas-SNP
ZNF570	148268	hgsc.bcm.edu	37	19	37975400	37975400	+	Silent	SNP	T	T	C	rs78317808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	36	68	0	0.590164	0	T|0.983;C|0.017	0.017	strong	.	ZNF570	58	.	NM_144694	exon5	c.T876C	p.H292H	TCAACATCTGCGA	.	PASS	Atlas-SNP
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67242087	67242087	+	Splice_Site	SNP	G	G	A	rs3816989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	97	214	0	0.5	0	G|0.879;A|0.121	0.121	strong	.	TCTEX1D1	27	.	NM_152665	exon4	c.336+1G>A	.	TCTGAGGTACGTG	.	PASS	Atlas-SNP
EFHD1	80303	hgsc.bcm.edu	37	2	233498669	233498669	+	Silent	SNP	G	G	T	rs2276557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	5	5	0	0.555556	0	G|0.726;T|0.274	0.274	strong	.	EFHD1	28	.	NM_025202	exon1	c.G255T	p.P85P	GTTCCCGGAGTTC	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184573603	184573603	+	Silent	SNP	A	A	G	rs16859356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	69	93	0	0.575	0	A|0.971;G|0.029	0.029	strong	.	VPS8	109	.	NM_001009921	exon13	c.A1140G	p.L380L	TTTTCTATTGGTA	.	PASS	Atlas-SNP
MOAP1	64112	hgsc.bcm.edu	37	14	93649552	93649552	+	Silent	SNP	A	A	G	rs114256363	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	48	118	0	0.432432	0	A|0.982;G|0.018	0.018	strong	.	MOAP1	32	.	NM_022151	exon3	c.T1036C	p.L346L	CTTCCAATATTGC	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38383386	38383386	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	133	225	0	0.53629	0	.	.	none	WDR87,colon,carcinoma,0,1	WDR87	191	1	NM_031951	exon4	c.G2840A	p.R947H	CCTAGACGCTTCA	.	PASS	Atlas-SNP
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712299	140712299	+	Missense_Mutation	SNP	A	A	T	rs62378404	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	159	337	0	0.48773	0	A|0.958;T|0.042	0.042	strong	.	PCDHGA1	397	.	NM_018912	exon1	c.A2048T	p.K683I	CCGCCAAACCCAA	.	PASS	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	37	7	55433880	55433880	+	Silent	SNP	G	G	C	rs2272262	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	38	36	0	0.974359	0	G|0.685;C|0.315	0.315	strong	.	LANCL2	54	.	NM_018697	exon1	c.G162C	p.A54A	CCCGGCGACCACG	.	PASS	Atlas-SNP
ACTRT2	140625	hgsc.bcm.edu	37	1	2938265	2938265	+	Silent	SNP	C	C	T	rs4576609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	64	0	0.439394	0	C|0.804;T|0.196	0.196	strong	.	ACTRT2	69	.	NM_080431	exon1	c.C15T	p.H5H	TCCGCACGCTTTA	.	PASS	Atlas-SNP
ZDHHC23	254887	hgsc.bcm.edu	37	3	113673098	113673098	+	Missense_Mutation	SNP	C	C	T	rs149202494	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	84	151	0	0.5	0	C|1.000;T|0.000	0.000	strong	.	ZDHHC23	38	.	NM_173570	exon3	c.C713T	p.T238I	GCACAACAAAGGA	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	37	11	48166267	48166267	+	Missense_Mutation	SNP	G	G	C	rs4752904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	60	129	0	0.512821	0	G|0.569;C|0.431	0.431	strong	.	PTPRJ	225	.	NM_002843	exon13	c.G2616C	p.E872D	GTATGAGGATTTC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057949	46057949	+	Silent	SNP	C	C	T	rs78352751	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	471	121	297	0	0.2569	0	C|0.982;T|0.018	0.018	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C615T	p.P205P	CGTGCCCGTCCCC	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85432040	85432040	+	Missense_Mutation	SNP	T	T	A	rs7312075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	41	95	0	0.356522	0	T|0.916;A|0.084	0.084	strong	LRRIQ1,NS,carcinoma,0,1	LRRIQ1	512	1	NM_001079910	exon2	c.T86A	p.I29N	AAGACATTGAGAG	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11133642	11133642	+	Silent	SNP	G	G	A	rs61740101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	89	0	0.494624	0	G|0.989;A|0.011	0.011	strong	.	CLEC16A	101	.	NM_015226	exon13	c.G1569A	p.Q523Q	AATCCAGCTCCCC	.	PASS	Atlas-SNP
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	117	212	0	0.50431	0	G|0.650;C|0.000;A|0.350	0.350	strong	.	COX18	20	.	NM_173827	exon4	c.C663T	p.P221P	GGAGTCGGGTGCA	.	PASS	Atlas-SNP
GALNT10	55568	hgsc.bcm.edu	37	5	153783753	153783753	+	Silent	SNP	C	C	T	rs6580076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	67	181	0	0.401198	0	C|0.733;T|0.267	0.267	strong	GALNT10,NS,carcinoma,0,1	GALNT10	70	1	NM_198321	exon8	c.C1146T	p.A382A	CCCGGCCGGAGTC	.	PASS	Atlas-SNP
KCNS1	3787	hgsc.bcm.edu	37	20	43727155	43727155	+	Silent	SNP	C	C	T	rs13043825	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	8	10	0	0.727273	0	C|0.838;T|0.162	0.162	strong	.	KCNS1	30	.	NM_002251	exon4	c.G258A	p.E86E	CGCCTGCTCCTCC	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114156093	114156093	+	Silent	SNP	C	C	T	rs2260080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	50	122	0	0.46729	0	C|0.772;T|0.228	0.228	strong	TMCO3,NS,carcinoma,0,1	TMCO3	77	1	NM_017905	exon5	c.C843T	p.S281S	GCTGTCCTTGCCT	.	PASS	Atlas-SNP
ALDH3A2	224	hgsc.bcm.edu	37	17	19578873	19578873	+	Silent	SNP	A	A	T	rs7216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	62	155	0	0.452555	0	A|0.406;T|0.594	0.594	strong	.	ALDH3A2	41	.	NM_000382	exon10	c.A1446T	p.A482A	CCAGGCAGAATAT	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	37	17	16001756	16001756	+	Silent	SNP	G	G	A	rs79413281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	51	130	0	0.428571	0	G|0.981;A|0.019	0.019	strong	.	NCOR1	240	.	NM_001190440	exon20	c.C2793T	p.L931L	TGAGACGAGTATA	.	PASS	Atlas-SNP
RICTOR	253260	hgsc.bcm.edu	37	5	38950761	38950761	+	Silent	SNP	A	A	G	rs150422546	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	111	207	0	0.528571	0	A|0.999;G|0.001	0.001	strong	.	RICTOR	182	.	NM_152756	exon31	c.T3189C	p.D1063D	ATTGATATCAAGG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107313	55107313	+	Missense_Mutation	SNP	T	T	C	rs36029771	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	201	310	1	0.948113	0.00322581	T|0.849;C|0.151	0.151	strong	.	LILRA1	105	.	NM_006863	exon6	c.T871C	p.Y291H	CGCTCCTACGGGG	.	PASS	Atlas-SNP
ERI1	90459	hgsc.bcm.edu	37	8	8869129	8869129	+	Missense_Mutation	SNP	T	T	G	rs112570397	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	45	51	0	0.6	0	T|0.991;G|0.009	0.009	strong	.	ERI1	20	.	NM_153332	exon3	c.T365G	p.F122C	GCAATTTTGCTGA	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919911	28919911	+	Missense_Mutation	SNP	A	A	G	rs61730306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	43	139	0	0.394495	0	A|0.893;G|0.107	0.107	strong	.	DSG1	176	.	NM_001942	exon11	c.A1610G	p.K537R	GAGCCAAAGATTT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47754541	47754541	+	Silent	SNP	A	A	G	rs61735824	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	111	317	0	0.332335	0	A|0.956;G|0.044	0.044	strong	.	PCNT	283	.	NM_006031	exon3	c.A498G	p.P166P	CCCACCAGAACAG	.	PASS	Atlas-SNP
TCTE1	202500	hgsc.bcm.edu	37	6	44249939	44249939	+	Silent	SNP	G	G	A	rs34405945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	98	135	0	0.535519	0	G|0.988;A|0.012	0.012	strong	.	TCTE1	77	.	NM_182539	exon4	c.C1204T	p.L402L	CAGACAGCTCATT	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112993412	112993412	+	Silent	SNP	C	C	T	rs7615578	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	104	169	0	0.483721	0	C|0.985;T|0.015	0.015	strong	.	BOC	139	.	NM_033254	exon9	c.C1425T	p.P475P	GGCTCCCATCATC	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	336396	336396	+	Missense_Mutation	SNP	G	G	A	rs400037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	102	215	0	0.492754	0	G|0.810;A|0.190	0.190	strong	.	PDIA2	51	.	NM_006849	exon8	c.G1163A	p.R388Q	ATCAGCGGCCAGT	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	91	199	0	0.439614	0	G|0.791;A|0.209	0.209	strong	CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	NM_001168499	exon2	c.G105A	p.P35P	GTGGCCGGAGAAG	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2800096	2800096	+	Missense_Mutation	SNP	C	C	T	rs11984691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	42	52	0	0.591549	0	C|0.939;T|0.061	0.061	strong	.	CSMD1	1469	.	NM_033225	exon69	c.G10433A	p.S3478N	TAATGACTGGAAG	.	PASS	Atlas-SNP
ZNF202	7753	hgsc.bcm.edu	37	11	123600475	123600475	+	Missense_Mutation	SNP	A	A	G	rs1144507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	111	0	1	0	A|0.307;G|0.693	0.693	strong	.	ZNF202	72	.	NM_003455	exon5	c.T461C	p.V154A	GGCTCCACTCCTA	.	PASS	Atlas-SNP
LRP12	29967	hgsc.bcm.edu	37	8	105503401	105503401	+	Missense_Mutation	SNP	T	T	C	rs16871494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	93	170	0	0.492063	0	T|0.957;C|0.043	0.043	strong	.	LRP12	124	.	NM_013437	exon7	c.A2080G	p.S694G	AGGAACTTGCACA	.	PASS	Atlas-SNP
ITGA2B	3674	hgsc.bcm.edu	37	17	42455126	42455126	+	Silent	SNP	C	C	T	rs114232872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	36	69	0	0.521739	0	C|0.995;T|0.005	0.005	strong	.	ITGA2B	88	.	NM_000419	exon21	c.G2127A	p.K709K	ATTCTCCTTCTTC	.	PASS	Atlas-SNP
XPO6	23214	hgsc.bcm.edu	37	16	28123226	28123226	+	Silent	SNP	G	G	A	rs205384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	82	130	0	0.471264	0	A|0.220;C|0.000;G|0.780	0.220	strong	.	XPO6	177	.	NM_015171	exon17	c.C2253T	p.H751H	GCTGGCGTGGTTG	.	PASS	Atlas-SNP
ANKIB1	54467	hgsc.bcm.edu	37	7	92027537	92027537	+	Silent	SNP	C	C	G	rs1861635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	63	112	0	0.525	0	C|0.845;G|0.155	0.155	strong	.	ANKIB1	92	.	NM_019004	exon20	c.C2544G	p.S848S	GAGTTCCTTGGAT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	111	135	0	0.680982	0	0|0.015;C|0.478	0.478	strong	.	GPR112	459	.	NM_153834	exon6	c.T4618C	p.S1540P	AAATCTTCTAAAA	.	PASS	Atlas-SNP
EVA1C	59271	hgsc.bcm.edu	37	21	33867447	33867447	+	Missense_Mutation	SNP	G	G	A	rs61744983	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	88	145	0	0.553459	0	G|0.997;A|0.003	0.003	strong	.	.	.	.	NM_058187	exon5	c.G745A	p.V249M	CCAGGCGTGAAAA	.	PASS	Atlas-SNP
ZBP1	81030	hgsc.bcm.edu	37	20	56189985	56189985	+	Missense_Mutation	SNP	C	C	G	rs16981187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	127	228	0	0.51004	0	C|0.946;G|0.054	0.054	strong	.	ZBP1	65	.	NM_001160419	exon4	c.G460C	p.D154H	CCATGTCCAGAAG	.	PASS	Atlas-SNP
MAK	4117	hgsc.bcm.edu	37	6	10792040	10792040	+	Missense_Mutation	SNP	C	C	A	rs62000445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	73	133	0	0.486667	0	C|0.991;A|0.009	0.009	strong	MAK,NS,carcinoma,-1,1	MAK	47	1	NM_005906	exon10	c.G1184T	p.R395L	CCCCAACGCCTCC	.	PASS	Atlas-SNP
ACAP2	23527	hgsc.bcm.edu	37	3	195027339	195027339	+	Silent	SNP	G	G	A	rs12491026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	70	0	0.470588	0	G|0.957;A|0.043	0.043	strong	.	ACAP2	72	.	NM_012287	exon13	c.C1017T	p.C339C	GAGCATGCAACTT	.	PASS	Atlas-SNP
PPP1R11	6992	hgsc.bcm.edu	37	6	30036471	30036471	+	Silent	SNP	C	C	A	rs2074482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	28	55	0	0.466667	0	C|0.809;A|0.191	0.191	strong	.	PPP1R11	10	.	NM_021959	exon2	c.C174A	p.S58S	CTCATCCAAATGT	.	PASS	Atlas-SNP
HLA-DOA	3111	hgsc.bcm.edu	37	6	32975896	32975896	+	Silent	SNP	A	A	G	rs364950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	78	0	0.443182	0	A|0.906;G|0.094	0.094	strong	.	HLA-DOA	22	.	NM_002119	exon2	c.T225C	p.G75G	AAAGTCACCAAAC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168041152	168041152	+	Splice_Site	SNP	T	T	C	rs16853169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	89	165	0	0.517442	0	T|0.904;C|0.096	0.096	strong	.	XIRP2	914	.	NM_001199143	exon4	c.661+2T>C	.	TATTTGTAAGGTT	.	PASS	Atlas-SNP
KIF1C	10749	hgsc.bcm.edu	37	17	4904564	4904564	+	Silent	SNP	T	T	C	rs17707385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	106	211	0	0.504762	0	C|0.070;N|0.000	0.070	strong	.	KIF1C	70	.	NM_006612	exon5	c.T231C	p.I77I	GGACATTGGAGAA	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	147049868	147049868	+	Silent	SNP	G	G	A	rs3747756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	39	94	0	0.464286	0	G|0.716;A|0.284	0.284	strong	.	ADGB	93	.	NM_024694	exon20	c.G2511A	p.Q837Q	TGCACAGCACTTC	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51227000	51227000	+	Silent	SNP	A	A	G	rs4901055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	20	45	0	0.444444	0	A|0.812;G|0.188	0.188	strong	.	NIN	475	.	NM_020921	exon17	c.T1974C	p.H658H	GTTCTCATGCCTT	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163205	163205	+	Silent	SNP	G	G	C	rs3810870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	146	0	1	0	G|0.419;C|0.581	0.581	strong	PLEKHG4B_ENST00000283426,NS,carcinoma,0,1	PLEKHG4B	167	1	NM_052909	exon11	c.G1950C	p.A650A	ACCTGCGCAACCA	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	17	17	0	0.566667	0	G|0.741;T|0.259	0.259	strong	PRDM6,NS,NS,0,1	PRDM6	26	1	NM_001136239	exon2	c.G123T	p.A41A	CGCCGCGGGTCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511447	195511447	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	7	214	0	0.0588235	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7004T	p.T2335M	AGAGGCGTGGTGT	.	scavenged	Atlas-SNP
CTTN	2017	hgsc.bcm.edu	37	11	70279759	70279759	+	Missense_Mutation	SNP	G	G	A	rs56162978	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	64	121	0	0.463768	0	G|0.941;A|0.059	0.059	strong	.	CTTN	162	.	NM_005231	exon17	c.G1451A	p.S484N	AGGACAGCACCTA	.	PASS	Atlas-SNP
RMND1	55005	hgsc.bcm.edu	37	6	151766822	151766822	+	Missense_Mutation	SNP	C	C	A	rs11550103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	112	0	0.450549	0	C|0.912;A|0.088	0.088	strong	RMND1,lymph_node,lymphoid_neoplasm,0,1	RMND1	32	1	NM_017909	exon2	c.G125T	p.S42I	AGTGTGCTGCATG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	365	171	306	0	0.468493	0	C|0.846;T|0.154	0.154	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C9954T	p.A3318A	CACAGCCACCCCC	.	PASS	Atlas-SNP
CCDC173	129881	hgsc.bcm.edu	37	2	170502509	170502509	+	Missense_Mutation	SNP	G	G	A	rs112720712	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	49	122	0	0.449541	0	G|0.990;A|0.010	0.010	strong	.	.	.	.	NM_001085447	exon9	c.C1501T	p.P501S	CTCCAGGTCCTTC	.	PASS	Atlas-SNP
GLRX	2745	hgsc.bcm.edu	37	5	95152313	95152313	+	Silent	SNP	A	A	G	rs4561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	98	149	0	0.52973	0	T|0.018;G|0.347	0.347	strong	GLRX,NS,carcinoma,-1,1	GLRX	11	1	NM_001243659	exon2	c.T225C	p.I75I	TTTACCAATAAAG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33719400	33719400	+	Silent	SNP	A	A	G	rs9981151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	20	45	0	0.384615	0	A|0.788;G|0.212	0.212	strong	.	URB1	176	.	NM_014825	exon22	c.T3733C	p.L1245L	ACAGCAAGTGGGT	.	PASS	Atlas-SNP
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	37	72	0	0.425287	0	C|0.625;T|0.375	0.375	strong	.	GPR114	52	.	NM_153837	exon9	c.C846T	p.R282R	AACACGCATCCAC	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44368122	44368122	+	Missense_Mutation	SNP	A	A	G	rs3761472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	31	65	0	0.534483	0	A|0.790;G|0.210	0.210	strong	SAMM50,NS,carcinoma,0,1	SAMM50	30	1	NM_015380	exon5	c.A329G	p.D110G	GTGATGACGCACT	.	PASS	Atlas-SNP
MARK3	4140	hgsc.bcm.edu	37	14	103941392	103941392	+	Missense_Mutation	SNP	A	A	G	rs56305318	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	48	86	0	0.564706	0	A|0.958;G|0.042	0.042	strong	.	MARK3	86	.	NM_001128919	exon13	c.A1327G	p.S443G	GCAGATAGTGACC	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11774324	11774324	+	Missense_Mutation	SNP	G	G	A	rs2304402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	234	203	1	0.995745	0.00492611	G|0.556;A|0.444	0.444	strong	.	GREB1	308	.	NM_014668	exon29	c.G5059A	p.D1687N	GCCCCCGACATCA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158647522	158647522	+	Silent	SNP	A	A	G	rs703121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	96	188	0	0.450704	0	A|0.498;G|0.502	0.502	strong	.	SPTA1	720	.	NM_003126	exon7	c.T915C	p.S305S	CTTGTGACTGTGA	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33741716	33741716	+	Silent	SNP	C	C	T	rs17078661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	33	63	0	0.478261	0	C|0.960;T|0.040	0.040	strong	STARD13,NS,carcinoma,-1,1	STARD13	100	1	NM_178006	exon2	c.G213A	p.G71G	CGGGAACCCGGCA	.	PASS	Atlas-SNP
ZNF506	440515	hgsc.bcm.edu	37	19	19906131	19906131	+	Missense_Mutation	SNP	T	T	G	rs16996376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	22	66	0	0.44	0	T|0.935;G|0.065	0.065	strong	.	ZNF506	36	.	NM_001099269	exon4	c.A565C	p.T189P	ATGTAGTACGGGT	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs200527674	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	43	294	0	0.166667	0	T|0.986;G|0.014	0.014	strong	SELPLG_ENST00000550948,NS,haematopoietic_neoplasm,0,1	SELPLG	138	1	NM_001206609	exon2	c.A452C	p.Q151P	ACTGGTTGAGTGG	.	PASS	Atlas-SNP
WNT8B	7479	hgsc.bcm.edu	37	10	102242030	102242030	+	Silent	SNP	G	G	A	rs9420786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	12	17	0	0.413793	0	G|0.978;A|0.022	0.022	strong	.	WNT8B	31	.	NM_003393	exon6	c.G513A	p.A171A	CCAGGCGGTGAAG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106865	55106865	+	Missense_Mutation	SNP	T	T	C	rs373854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	335	323	1	0.997024	0.00309598	T|0.782;C|0.218	0.218	strong	.	LILRA1	105	.	NM_006863	exon5	c.T659C	p.L220P	TGGTCCTAGGTGA	.	PASS	Atlas-SNP
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	73	155	0	0.486667	0	G|0.794;N|0.001	.	strong	.	IL20RA	54	.	NM_014432	exon7	c.C1144T	p.L382F	GGGTGAGAGAAGT	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48256602	48256602	+	Silent	SNP	T	T	C	rs16945974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	193	166	0	1	0	T|0.854;C|0.146	0.146	strong	.	ABCC11	177	.	NM_033151	exon5	c.A684G	p.Q228Q	TGTGCGTTGGTTG	.	PASS	Atlas-SNP
CDC6	990	hgsc.bcm.edu	37	17	38447569	38447569	+	Silent	SNP	T	T	C	rs1130199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	139	154	1	0.992857	0.00649351	T|0.886;C|0.114	0.114	strong	.	CDC6	53	.	NM_001254	exon3	c.T438C	p.C146C	TGCATGTGTGAGA	.	PASS	Atlas-SNP
DNAJB9	4189	hgsc.bcm.edu	37	7	108213545	108213545	+	Silent	SNP	T	T	C	rs376971670		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	83	172	0	0.471591	0	.	.	weak	DNAJB9,NS,carcinoma,+1,1	DNAJB9	25	1	NM_012328	exon3	c.T420C	p.H140H	AAATCATTTCCAG	.	PASS	Atlas-SNP
SELE	6401	hgsc.bcm.edu	37	1	169697218	169697218	+	Silent	SNP	G	G	A	rs5365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	67	0	0.45	0	G|0.982;A|0.018	0.018	strong	.	SELE	84	.	NM_000450	exon8	c.C1260T	p.N420N	CTTCTCGTTGTCC	.	PASS	Atlas-SNP
TMEM14B	81853	hgsc.bcm.edu	37	6	10751379	10751379	+	Silent	SNP	C	C	T	rs1046427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	59	110	0	0.483607	0	C|0.979;T|0.021	0.021	strong	.	TMEM14B	19	.	NM_030969	exon4	c.C114T	p.S38S	GCCGTCCCTGGCT	.	PASS	Atlas-SNP
ZNF560	147741	hgsc.bcm.edu	37	19	9578459	9578459	+	Silent	SNP	C	C	T	rs16980696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	197	202	1	0.99495	0.00495049	C|0.951;T|0.049	0.049	strong	.	ZNF560	162	.	NM_152476	exon10	c.G1164A	p.P388P	GCCTGACGGCACA	.	PASS	Atlas-SNP
SPARC	6678	hgsc.bcm.edu	37	5	151054227	151054227	+	Silent	SNP	T	T	C	rs2304052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	54	94	0	0.54	0	T|0.807;C|0.193	0.193	strong	.	SPARC	38	.	NM_003118	exon3	c.A66G	p.E22E	CAGGGCTTCTTGC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531408	140531408	+	Missense_Mutation	SNP	T	T	G	rs148897759	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	404	16	318	2	0.039604	0.00628931	T|0.997;G|0.003	0.003	strong	PCDHB6,trunk,malignant_melanoma,0,1	PCDHB6	161	1	NM_018939	exon1	c.T1570G	p.S524A	CTGCAGTCTTTCG	.	scavenged	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	109	239	2	0.480176	0.0083682	T|0.627;C|0.373	0.373	strong	CCDC135,NS,carcinoma,0,1	CCDC135	97	1	NM_032269	exon16	c.T2296C	p.C766R	CTAACATGCTGGC	.	scavenged	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52282865	52282865	+	Silent	SNP	C	C	T	rs35851809	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	135	0	0.451613	0	C|0.998;T|0.002	0.002	strong	.	ANKRD33	33	.	NM_182608	exon3	c.C411T	p.V137V	CATGGTCGCATGC	.	PASS	Atlas-SNP
MS4A7	58475	hgsc.bcm.edu	37	11	60161273	60161273	+	Missense_Mutation	SNP	C	C	T	rs372900689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	41	75	0	0.585714	0	.	.	weak	.	MS4A7	38	.	NM_021201	exon7	c.C662T	p.S221L	TTTCCTCGACCCA	.	PASS	Atlas-SNP
TMEM259	91304	hgsc.bcm.edu	37	19	1014454	1014454	+	Missense_Mutation	SNP	C	C	T	rs141314760	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	59	151	0	0.472	0	C|0.999;T|0.001	0.001	strong	.	.	.	.	NM_033420	exon2	c.G244A	p.V82I	CCAGGACGAAGAG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	40	114	0	0.300752	0	C|0.778;T|0.222	0.222	strong	.	TYW1	71	.	NM_018264	exon14	c.C1743T	p.N581N	ATGGAACGTGGAC	.	PASS	Atlas-SNP
ELMO3	79767	hgsc.bcm.edu	37	16	67234134	67234134	+	Missense_Mutation	SNP	A	A	G	rs8058861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	34	93	0	0.435897	0	A|0.847;G|0.153	0.153	strong	.	ELMO3	41	.	NM_024712	exon5	c.A442G	p.N148D	CAGAGTAACAGTC	.	PASS	Atlas-SNP
HSPB3	8988	hgsc.bcm.edu	37	5	53751818	53751818	+	Missense_Mutation	SNP	G	G	A	rs35258119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	144	139	0	0.986301	0	G|0.992;A|0.008	0.008	strong	.	HSPB3	17	.	NM_006308	exon1	c.G199A	p.G67S	CGAGAAGGCAAAT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27804690	27804690	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	13	171	0	0.0822785	0	.	.	none	.	C2orf16	357	.	NM_032266	exon1	c.C5251T	p.H1751Y	AGACATCACAGTC	.	PASS	Atlas-SNP
ARSA	410	hgsc.bcm.edu	37	22	51064039	51064039	+	Missense_Mutation	SNP	G	G	C	rs743616	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	70	150	0	0.393258	0	G|0.545;C|0.455	0.455	strong	.	ARSA	19	.	NM_001085426	exon8	c.C1178G	p.T393S	TTTCCAGTCCGCA	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493188	33493188	+	Missense_Mutation	SNP	T	T	A	rs193179333	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	5	176	1	0.0248756	0.00568182	T|0.902;A|0.097	0.097	strong	RHPN2,colon,carcinoma,0,9	RHPN2	107	9	NM_033103	exon9	c.A1070T	p.H357L	AAGTAGTGGGCCA	.	scavenged	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76195833	76195833	+	Missense_Mutation	SNP	A	A	G	rs143470231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	13	33	0	0.464286	0	A|0.987;G|0.013	0.013	strong	LMO7_ENST00000357063,colon,carcinoma,-2,2	LMO7	334	2	NM_005358	exon1	c.A4G	p.K2E	GCTATGAAGAAAA	.	PASS	Atlas-SNP
OR51I2	390064	hgsc.bcm.edu	37	11	5474894	5474894	+	Missense_Mutation	SNP	T	T	C	rs74049540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	64	125	0	0.474074	0	T|0.937;C|0.063	0.063	strong	.	OR51I2	76	.	NM_001004754	exon1	c.T176C	p.M59T	AGCCCATGTACTA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10470794	10470794	+	Missense_Mutation	SNP	G	G	C	rs77833234	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	9	33	0	0.428571	0	G|0.993;C|0.007	0.007	strong	.	RP1L1	453	.	NM_178857	exon4	c.C814G	p.P272A	GCCGTGGCGTGCT	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	103	161	1	0.52551	0.00621118	A|0.685;G|0.315	0.315	strong	CPO,NS,carcinoma,+2,1	CPO	42	1	NM_173077	exon9	c.A948G	p.T316T	TGGAACATATGGG	.	scavenged	Atlas-SNP
CHSY3	337876	hgsc.bcm.edu	37	5	129520679	129520679	+	Missense_Mutation	SNP	G	G	A	rs10068403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	27	62	0	0.380282	0	G|0.878;A|0.122	0.122	strong	CHSY3,right_upper_lobe,carcinoma,+1,2	CHSY3	92	2	NM_175856	exon3	c.G1844A	p.G615E	TGGGAGGGCACAA	.	PASS	Atlas-SNP
SAP130	79595	hgsc.bcm.edu	37	2	128775464	128775464	+	Silent	SNP	A	A	G	rs6430968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	98	0	1	0	A|0.965;G|0.035	0.035	strong	.	SAP130	169	.	NM_001145928	exon3	c.T216C	p.S72S	GACTTCAGAATCT	.	PASS	Atlas-SNP
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	6	111	0	0.0857143	0	.	.	weak	.	SHROOM4	171	.	NM_020717	exon6	c.C3391G	p.Q1131E	CCTCCTGTTGCTT	.	PASS	Atlas-SNP
EMR3	84658	hgsc.bcm.edu	37	19	14740942	14740942	+	Missense_Mutation	SNP	G	G	A	rs78700925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	56	126	0	0.478632	0	G|0.984;A|0.016	0.016	strong	.	EMR3	99	.	NM_032571	exon14	c.C1721T	p.P574L	GCAGCTGGACCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512686	195512686	+	Missense_Mutation	SNP	G	G	T	rs79043683	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	96	402	0	0.333333	0	G|0.992;T|0.008	0.008	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5765A	p.P1922H	GTGACAGGAAGAG	.	PASS	Atlas-SNP
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297352	179297352	+	Silent	SNP	A	A	G	rs384668	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	56	119	0	0.466667	0	A|0.890;G|0.110	0.110	strong	.	TBC1D9B	157	.	NM_198868	exon16	c.T2628C	p.C876C	GGAGCCACAGGCC	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54895682	54895682	+	Silent	SNP	C	C	T	rs2229505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	43	94	0	0.443299	0	C|0.962;T|0.038	0.038	strong	.	SPTBN1	378	.	NM_003128	exon36	c.C7071T	p.F2357F	GCGGTTCAGCCTT	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44019305	44019305	+	Silent	SNP	C	C	T	rs6684279	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	41	89	0	0.506173	0	C|0.964;T|0.036	0.036	strong	.	PTPRF	172	.	NM_002840	exon4	c.C234T	p.F78F	GCGCTTCGAGGTG	.	PASS	Atlas-SNP
GPR55	9290	hgsc.bcm.edu	37	2	231775371	231775371	+	Missense_Mutation	SNP	C	C	T	rs80290067	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	20	43	0	0.425532	0	C|0.971;T|0.029	0.029	strong	.	GPR55	46	.	NM_005683	exon2	c.G307A	p.V103I	TGCTGACGAAGTA	.	PASS	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147901	93147901	+	Silent	SNP	C	C	T	rs74784157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	72	140	0	0.470588	0	C|0.947;T|0.053	0.053	strong	.	PLEKHG7	38	.	NM_001004330	exon6	c.C351T	p.H117H	GCTCCACGTGCCA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744772	54744772	+	Missense_Mutation	SNP	T	T	G	rs77717986	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	475	64	382	0	0.134737	0	.	.	weak	.	LILRA6	75	.	NM_024318	exon5	c.A890C	p.Y297S	GCACCATAGCACC	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27709812	27709812	+	Silent	SNP	C	C	T	rs61740294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	18	29	0	0.428571	0	C|0.978;T|0.022	0.022	strong	.	KIAA0556	348	.	NM_015202	exon9	c.C1104T	p.S368S	AGCCAGCCCACTG	.	PASS	Atlas-SNP
CDC42BPB	9578	hgsc.bcm.edu	37	14	103434985	103434985	+	Silent	SNP	G	G	A	rs55659700	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	47	106	0	0.479592	0	G|0.992;A|0.008	0.008	strong	.	CDC42BPB	123	.	NM_006035	exon15	c.C2064T	p.S688S	CAGCTCGGATTTG	.	PASS	Atlas-SNP
PRAMEF12	390999	hgsc.bcm.edu	37	1	12837634	12837634	+	Silent	SNP	T	T	A	rs848578	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	572	571	533	0	0.998252	0	T|0.287;C|0.001;A|0.713	0.713	strong	.	PRAMEF12	69	.	NM_001080830	exon3	c.T1344A	p.I448I	CAAGATTATTGTG	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837053	43837053	+	Missense_Mutation	SNP	G	G	T	rs2233887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	85	151	0	0.512048	0	G|0.984;T|0.016	0.016	strong	SEMG1,bladder,carcinoma,+1,3	SEMG1	71	3	NM_003007	exon2	c.G1115T	p.R372L	CCCAACGCAGTAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268528	1268528	+	Missense_Mutation	SNP	C	C	T	rs202008769	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	657	250	462	0	0.380518	0	.	.	weak	MUC5B,colon,carcinoma,0,4	MUC5B	473	4	NM_002458	exon31	c.C10418T	p.S3473L	GGACTTCGGCCAC	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	37	15	65676726	65676726	+	Missense_Mutation	SNP	C	C	T	rs33918653	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	17	20	0	0.708333	0	C|0.807;T|0.193	0.193	strong	.	IGDCC4	95	.	NM_020962	exon20	c.G3374A	p.C1125Y	TTCCTGCAGGCTG	.	PASS	Atlas-SNP
ARID5B	84159	hgsc.bcm.edu	37	10	63829539	63829539	+	Silent	SNP	C	C	T	rs76296217	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	30	64	0	0.375	0	C|0.954;T|0.046	0.046	strong	.	ARID5B	125	.	NM_032199	exon8	c.C1182T	p.T394T	TTGTACCCGCAGA	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448940	4448940	+	Missense_Mutation	SNP	G	G	A	rs899440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	75	184	0	0.40107	0	G|0.935;A|0.065	0.065	strong	.	MYBBP1A	69	.	NM_014520	exon15	c.C2038T	p.H680Y	TCAGGTGGGAGCA	.	PASS	Atlas-SNP
FOXRED2	80020	hgsc.bcm.edu	37	22	36902259	36902259	+	Missense_Mutation	SNP	G	G	A	rs56767103	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	93	0	0.526882	0	G|0.974;A|0.026	0.026	strong	.	FOXRED2	48	.	NM_001102371	exon2	c.C211T	p.R71C	GGTAGCGTGTGAA	.	PASS	Atlas-SNP
SCNN1D	6339	hgsc.bcm.edu	37	1	1226063	1226063	+	Missense_Mutation	SNP	G	G	A	rs13306651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	91	0	0.423077	0	G|0.984;A|0.016	0.016	strong	.	SCNN1D	60	.	NM_001130413	exon15	c.G1906A	p.A636T	CCTTCCGCCAAGT	.	PASS	Atlas-SNP
KIAA1328	57536	hgsc.bcm.edu	37	18	34647323	34647323	+	Silent	SNP	T	T	A	rs3747896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	190	164	0	0.989583	0	A|0.237;G|0.031;T|0.732	0.237	strong	.	KIAA1328	39	.	NM_020776	exon7	c.T1047A	p.G349G	TGGTGGTGGGGCA	.	PASS	Atlas-SNP
C9orf171	389799	hgsc.bcm.edu	37	9	135285802	135285802	+	Silent	SNP	G	G	A	rs111465967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	60	65	0	0.714286	0	G|0.959;A|0.041	0.041	strong	.	C9orf171	53	.	NM_207417	exon1	c.G144A	p.E48E	GAACGAGCGGCTG	.	PASS	Atlas-SNP
MRTO4	51154	hgsc.bcm.edu	37	1	19583636	19583636	+	Silent	SNP	C	C	T	rs1126682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	60	115	0	0.382166	0	C|0.842;T|0.158	0.158	strong	MRTO4,NS,carcinoma,0,1	MRTO4	17	1	NM_016183	exon4	c.C270T	p.H90H	CCTGCACCAGGTA	.	PASS	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	136904783	136904783	+	Silent	SNP	G	G	A	rs78692210	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	113	223	0	0.453815	0	G|0.988;A|0.012	0.012	strong	.	MAP3K5	136	.	NM_005923	exon24	c.C3321T	p.A1107A	TGTGGTGGCTATG	.	PASS	Atlas-SNP
CSTA	1475	hgsc.bcm.edu	37	3	122060390	122060390	+	Missense_Mutation	SNP	G	G	T	rs34021626	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	48	83	0	0.55814	0	G|0.984;T|0.016	0.016	strong	.	CSTA	11	.	NM_005213	exon3	c.G273T	p.K91N	AAACAAGGATGAC	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9074259	9074259	+	Silent	SNP	C	C	T	rs76479220		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	128	287	0	0.422442	0	.	.	weak	.	PHC1	67	.	NM_004426	exon5	c.C369T	p.P123P	CTCTCCCAGTGCT	.	PASS	Atlas-SNP
NXPE1	120400	hgsc.bcm.edu	37	11	114393757	114393757	+	Missense_Mutation	SNP	C	C	T	rs79538449	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	99	145	0	0.596386	0	C|0.997;T|0.003	0.003	strong	.	NXPE1	8	.	NM_152315	exon5	c.G526A	p.G176S	TATAACCACCAGG	.	PASS	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150667016	150667016	+	Missense_Mutation	SNP	T	T	C	rs978012	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	123	136	1	0.991935	0.00735294	T|0.484;C|0.515	0.515	strong	.	SLC36A3	54	.	NM_001145017	exon7	c.A622G	p.K208E	GGGCTTTTTCCAC	.	PASS	Atlas-SNP
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	208	196	1	0.985782	0.00510204	T|0.731;C|0.269	0.269	strong	ZNF653,NS,carcinoma,0,2	ZNF653	48	2	NM_138783	exon4	c.A795G	p.P265P	GCCTGCTGGGTTG	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56435080	56435080	+	Missense_Mutation	SNP	G	G	C	rs9652855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	55	111	1	0.544554	0.00900901	G|0.886;C|0.114	0.114	strong	RNF43,lower_third,carcinoma,+1,1	RNF43	157	1	NM_017763	exon9	c.C2057G	p.P686R	ACACTGGGGGTGT	.	scavenged	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	31998612	31998612	+	Missense_Mutation	SNP	G	G	A	rs2006771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	121	187	0	0.562791	0	G|0.614;A|0.386	0.386	strong	.	SFI1	78	.	NM_001007467	exon17	c.G1646A	p.R549Q	CAGAGCGACAGCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677519	100677519	+	Missense_Mutation	SNP	C	C	T	rs148817224	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	36	132	0	0.160714	0	C|0.993;T|0.007	0.007	strong	.	MUC17	804	.	NM_001040105	exon3	c.C2822T	p.A941V	CTGAGGCTAGAAC	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43243218	43243218	+	Silent	SNP	A	A	G	rs12185497	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	210	283	0	0.985915	0	A|0.407;G|0.593	0.593	strong	PSG3,NS,carcinoma,0,1	PSG3	82	1	NM_021016	exon2	c.T88C	p.L30L	TAGGCAAGTTCCA	.	PASS	Atlas-SNP
ANAPC15	25906	hgsc.bcm.edu	37	11	71821236	71821236	+	Silent	SNP	A	A	G	rs17161980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	96	182	0	0.505263	0	A|0.864;G|0.136	0.136	strong	.	.	.	.	NM_014042	exon5	c.T216C	p.D72D	CTCATCATCTTCA	.	PASS	Atlas-SNP
FAM73B	84895	hgsc.bcm.edu	37	9	131804785	131804785	+	Missense_Mutation	SNP	T	T	C	rs11544968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	28	0	1	0	T|0.791;C|0.209	0.209	strong	.	FAM73B	37	.	NM_032809	exon3	c.T299C	p.V100A	CTTCAGTGAAGAA	.	PASS	Atlas-SNP
EVX2	344191	hgsc.bcm.edu	37	2	176948445	176948445	+	Silent	SNP	C	C	G	rs61731351	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	54	72	0	0.519231	0	C|0.930;G|0.070	0.070	strong	EVX2,NS,carcinoma,0,1	EVX2	51	1	NM_001080458	exon1	c.G60C	p.T20T	GCCCGCCGTAGGG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	52	68	0	0.619048	0	A|0.863;G|0.137	0.137	strong	.	NCOA3	156	.	NM_181659	exon15	c.A2880G	p.T960T	TCCCACATTGCCT	.	PASS	Atlas-SNP
ZNF7	7553	hgsc.bcm.edu	37	8	146067054	146067054	+	Missense_Mutation	SNP	G	G	A	rs1735169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	28	70	0	0.4375	0	G|0.515;A|0.485	0.485	strong	.	ZNF7	62	.	NM_003416	exon5	c.G562A	p.G188R	AGTCAGGGAGAGA	.	PASS	Atlas-SNP
TNFRSF17	608	hgsc.bcm.edu	37	16	12061626	12061626	+	Silent	SNP	G	G	A	rs2017662	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	67	0	0.485294	0	G|0.872;A|0.128	0.128	strong	TNFRSF17,colon,carcinoma,+1,1	TNFRSF17	16	1	NM_001192	exon3	c.G477A	p.T159T	CACCACGAAAACG	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6304087	6304087	+	Silent	SNP	A	A	G	rs1046316	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	80	1	1	0.0125	A|0.271;G|0.729	0.729	strong	WFS1,NS,carcinoma,0,2	WFS1	71	2	NM_001145853	exon8	c.A2565G	p.S855S	GCTCTCACCCACC	.	scavenged	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5427652	5427652	+	Silent	SNP	G	G	A	rs4720623	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	59	62	0	0.983333	0	G|0.633;A|0.367	0.367	strong	.	TNRC18	311	.	NM_001080495	exon5	c.C1803T	p.A601A	GCGCACGGCCACG	.	PASS	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	37	2	171715387	171715387	+	Missense_Mutation	SNP	G	G	A	rs769402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	61	111	0	0.516949	0	G|0.935;A|0.065	0.065	strong	.	GAD1	79	.	NM_000817	exon16	c.G1595A	p.R532Q	AACGACGGGAAAA	.	PASS	Atlas-SNP
COL4A6	1288	hgsc.bcm.edu	37	X	107417730	107417730	+	Silent	SNP	G	G	A	rs5973851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	58	94	0	0.384106	0	G|0.712;A|0.288	0.288	strong	.	COL4A6	270	.	NM_001847	exon31	c.C3081T	p.G1027G	AGGTAAGCCCCGG	.	PASS	Atlas-SNP
IL18BP	10068	hgsc.bcm.edu	37	11	71711438	71711438	+	Missense_Mutation	SNP	G	G	A	rs376290357		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	44	91	0	0.517647	0	.	.	weak	.	IL18BP	15	.	NM_001145057	exon3	c.G70A	p.V24I	CACGTCGTCACTC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880822	39880822	+	Missense_Mutation	SNP	A	A	G	rs2292305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	73	1	0.522388	0.0136986	A|0.756;G|0.244	0.244	strong	THBS1,NS,carcinoma,0,1	THBS1	106	1	NM_003246	exon10	c.A1567G	p.T523A	AACCCCACACCCC	.	scavenged	Atlas-SNP
RRS1	23212	hgsc.bcm.edu	37	8	67342077	67342077	+	Silent	SNP	G	G	A	rs3739337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	14	35	0	0.424242	0	G|0.918;A|0.082	0.082	strong	.	RRS1	13	.	NM_015169	exon1	c.G711A	p.E237E	TCAGGAGCGCCTC	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110376861	110376861	+	Silent	SNP	G	G	A	rs7008687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	9	23	0	0.5625	0	G|0.774;A|0.226	0.226	strong	.	PKHD1L1	522	.	NM_177531	exon2	c.G159A	p.G53G	AAGAGGGGAAGGT	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18025527	18025527	+	Missense_Mutation	SNP	A	A	G	rs76468019	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	52	106	0	0.460177	0	A|0.957;G|0.043	0.043	strong	MYO15A,NS,carcinoma,+1,1	MYO15A	268	1	NM_016239	exon2	c.A3413G	p.Q1138R	AGCCTCAAGTCCA	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242003487	242003487	+	Silent	SNP	C	C	T	rs17852471	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	78	119	0	0.481481	0	C|0.733;T|0.267	0.267	strong	.	SNED1	76	.	NM_001080437	exon19	c.C2544T	p.G848G	CGGCGGCGGGGCC	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101683929	101683929	+	Silent	SNP	C	C	T	rs703715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	29	87	0	0.426471	0	C|0.346;T|0.654	0.654	strong	UTP20,NS,malignant_melanoma,+1,1	UTP20	222	1	NM_014503	exon7	c.C612T	p.N204N	TAAAAACGCACTT	.	PASS	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	37	20	41408886	41408886	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	20	52	1	0.307692	0.0192308	.	.	none	PTPRT,NS,carcinoma,0,2	PTPRT	372	2	NM_007050	exon4	c.C540T	p.D180D	GACCTCGTCCACG	.	scavenged	Atlas-SNP
GINS2	51659	hgsc.bcm.edu	37	16	85722496	85722496	+	Silent	SNP	A	A	C	rs80063963	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	20	37	0	1	0	A|0.865;C|0.135	0.135	strong	.	GINS2	15	.	NM_016095	exon1	c.T9G	p.A3A	CTCGGCAGCGTCC	.	PASS	Atlas-SNP
MADD	8567	hgsc.bcm.edu	37	11	47306585	47306585	+	Missense_Mutation	SNP	G	G	A	rs1051006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	42	62	0	0.591549	0	G|0.733;A|0.267	0.267	strong	.	MADD	172	.	NM_130474	exon13	c.G2251A	p.V751M	TCGAACGTGGACA	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26620761	26620761	+	Missense_Mutation	SNP	T	T	C	rs6695966	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	36	97	0	0.467532	0	T|0.974;C|0.026	0.026	strong	.	UBXN11	54	.	NM_183008	exon9	c.A494G	p.E165G	TTGCTCTCTGAGT	.	PASS	Atlas-SNP
HERC6	55008	hgsc.bcm.edu	37	4	89319296	89319296	+	Missense_Mutation	SNP	T	T	C	rs17014118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	75	161	0	0.477707	0	T|0.490;C|0.510	0.510	strong	.	HERC6	104	.	NM_017912	exon8	c.T1027C	p.F343L	TTAGACTTCGTGG	.	PASS	Atlas-SNP
SYNPO	11346	hgsc.bcm.edu	37	5	149998128	149998128	+	Missense_Mutation	SNP	G	G	A	rs6579797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	235	202	2	0.995763	0.00990099	G|0.850;A|0.150	0.150	strong	SYNPO_ENST00000394243,colon,carcinoma,0,1	SYNPO	147	1	NM_001166209	exon2	c.G199A	p.D67N	GGGGACGACTCTG	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	59	94	0	0.584158	0	G|0.681;A|0.319	0.319	strong	.	YTHDC2	118	.	NM_022828	exon14	c.G1955A	p.S652N	CTGACAGTACACA	.	PASS	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095573	90095573	+	Missense_Mutation	SNP	C	C	T	rs77382359	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	22	267	0	0.0912863	0	C|0.500;T|0.500	0.500	weak	C16orf3,rectum,carcinoma,0,1	C16orf3	14	1	NM_001214	exon1	c.G178A	p.V60I	AGGCTACGGGGCA	.	PASS	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7628027	7628027	+	Silent	SNP	C	C	T	rs11255206	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	41	77	0	0.427083	0	C|0.983;T|0.017	0.017	strong	.	ITIH5	343	.	NM_001001851	exon8	c.G945A	p.K315K	GGCATCCTTGGTC	.	PASS	Atlas-SNP
RBPJL	11317	hgsc.bcm.edu	37	20	43945487	43945487	+	Missense_Mutation	SNP	T	T	C	rs34078698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	24	66	0	0.421053	0	T|0.986;C|0.014	0.014	strong	RBPJL,colon,carcinoma,+1,1	RBPJL	67	1	NM_014276	exon12	c.T1442C	p.V481A	ACAGCGTGCGGCC	.	PASS	Atlas-SNP
WIPF3	644150	hgsc.bcm.edu	37	7	29924002	29924002	+	Missense_Mutation	SNP	C	C	A	rs371924598		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	69	117	0	0.492857	0	.	.	weak	.	WIPF3	46	.	NM_001080529	exon5	c.C892A	p.P298T	CTCCCCCCTTATG	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16899852	16899852	+	Missense_Mutation	SNP	G	G	T	rs140602425		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	55	113	0	0.436508	0	G|1.000;T|0.000	0.000	weak	.	NWD1	303	.	NM_001007525	exon13	c.G2791T	p.D931Y	TCAAAGGATTACA	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66364749	66364749	+	Silent	SNP	T	T	C	rs1558877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	121	0	1	0	T|0.481;C|0.519	0.519	strong	.	ARSG	55	.	NM_001267727	exon7	c.T765C	p.P255P	CTTACCTGTGACT	.	PASS	Atlas-SNP
FUS	2521	hgsc.bcm.edu	37	16	31193948	31193948	+	Silent	SNP	C	C	T	rs61733962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	94	193	0	0.513661	0	C|0.965;T|0.035	0.035	strong	.	FUS	52	.	NM_001170634	exon3	c.C153T	p.G51G	CTATGGCCAGAGC	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55339652	55339652	+	Nonsense_Mutation	SNP	C	C	T	rs1459101	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	79	168	1	0.481707	0.00595238	C|0.759;T|0.241	0.241	strong	OR4C16,NS,carcinoma,-2,1	OR4C16	104	1	NM_001004701	exon1	c.C49T	p.Q17X	TTGACACAGGATC	.	scavenged	Atlas-SNP
OR6C4	341418	hgsc.bcm.edu	37	12	55945258	55945258	+	Missense_Mutation	SNP	T	T	C	rs11835716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	56	127	0	0.459016	0	T|0.905;C|0.095	0.095	strong	.	OR6C4	34	.	NM_001005494	exon1	c.T248C	p.M83T	CCAGCATGACAAC	.	PASS	Atlas-SNP
C22orf23	84645	hgsc.bcm.edu	37	22	38341124	38341124	+	Missense_Mutation	SNP	T	T	G	rs35562630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	163	348	0	0.442935	0	T|0.946;G|0.054	0.054	strong	.	C22orf23	21	.	NM_032561	exon5	c.A406C	p.M136L	CCTCCATGTCCTT	.	PASS	Atlas-SNP
NTRK1	4914	hgsc.bcm.edu	37	1	156838432	156838432	+	Missense_Mutation	SNP	C	C	T	rs55909005	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	53	93	0	0.514563	0	C|0.987;T|0.013	0.013	strong	.	NTRK1	287	.	NM_001012331	exon6	c.C710T	p.T237M	CAGCCACGGTGAT	.	PASS	Atlas-SNP
SCGB1D1	10648	hgsc.bcm.edu	37	11	61959636	61959636	+	Missense_Mutation	SNP	C	C	T	rs116188604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	88	151	0	0.533333	0	C|0.982;T|0.018	0.018	strong	SCGB1D1,NS,carcinoma,0,1	SCGB1D1	18	1	NM_006552	exon2	c.C164T	p.A55V	TGGAAGCTGTTGC	.	PASS	Atlas-SNP
SIGLEC8	27181	hgsc.bcm.edu	37	19	51960940	51960940	+	Missense_Mutation	SNP	A	A	G	rs10409962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	56	99	0	0.538462	0	A|0.783;G|0.217	0.217	strong	SIGLEC8,colon,carcinoma,+1,2	SIGLEC8	130	2	NM_014442	exon2	c.T508C	p.S170P	TCCTGGAGTGGCC	.	PASS	Atlas-SNP
SULT1C4	27233	hgsc.bcm.edu	37	2	108994808	108994808	+	Missense_Mutation	SNP	C	C	G	rs1402467	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	122	0	1	0	C|0.602;G|0.398	0.398	strong	.	SULT1C4	41	.	NM_006588	exon1	c.C15G	p.D5E	ACACGACATGGAG	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73240431	73240431	+	Silent	SNP	T	T	G	rs73451725	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	88	184	0	0.606897	0	T|0.873;G|0.127	0.127	strong	.	TRPM3	700	.	NM_206945	exon13	c.A1176C	p.R392R	ATACTCTCGCTTG	.	PASS	Atlas-SNP
ILDR1	286676	hgsc.bcm.edu	37	3	121712098	121712098	+	Missense_Mutation	SNP	G	G	A	rs34284625	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	81	152	0	0.468208	0	G|0.956;A|0.044	0.044	strong	.	ILDR1	120	.	NM_001199799	exon7	c.C1498T	p.H500Y	GGGAGTGCGAGCC	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25672880	25672880	+	Missense_Mutation	SNP	T	T	C	rs34732786	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	51	160	0	0.421488	0	T|0.980;C|0.020	0.020	strong	.	IFLTD1	121	.	NM_001145728	exon7	c.A928G	p.T310A	TAGCTGTAGATGC	.	PASS	Atlas-SNP
C6orf118	168090	hgsc.bcm.edu	37	6	165715673	165715673	+	Silent	SNP	A	A	G	rs9459356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	83	173	0	0.434555	0	A|0.802;G|0.198	0.198	strong	.	C6orf118	116	.	NM_144980	exon2	c.T138C	p.N46N	AAGCCGATTCAGA	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	75	158	0	0.465839	0	A|0.634;G|0.366	0.366	strong	.	DIP2A	332	.	NM_206891	exon3	c.A174G	p.P58P	AGACCCATCTCTG	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78014024	78014024	+	Silent	SNP	G	G	A	rs2885349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	56	0	0.5	0	G|0.968;A|0.032	0.032	strong	CCDC40_ENST00000374877,rectum,carcinoma,+1,2	CCDC40	198	2	NM_017950	exon3	c.G507A	p.S169S	CCCGTCGGAGCAA	.	PASS	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153475556	153475556	+	Missense_Mutation	SNP	T	T	C	rs11897929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	93	181	0	0.540698	0	T|0.920;C|0.080	0.080	strong	.	FMNL2	75	.	NM_052905	exon14	c.T1511C	p.M504T	TGTCCATGGGGTC	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242352768	242352768	+	Missense_Mutation	SNP	A	A	C	rs16843643	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	32	50	0	0.551724	0	A|0.960;C|0.040	0.040	strong	.	FARP2	92	.	NM_014808	exon7	c.A555C	p.K185N	CCTCAAAGTGAAC	.	PASS	Atlas-SNP
ZNF385C	201181	hgsc.bcm.edu	37	17	40183707	40183707	+	Silent	SNP	G	G	C	rs75049227	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	358	172	352	0	0.480447	0	G|0.994;C|0.006	0.006	strong	.	ZNF385C	7	.	NM_001242704	exon4	c.C369G	p.A123A	ATCCTGGGCCTGG	.	PASS	Atlas-SNP
NECAB2	54550	hgsc.bcm.edu	37	16	84027966	84027966	+	Missense_Mutation	SNP	C	C	T	rs79514285	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	50	100	0	0.50505	0	C|0.996;T|0.004	0.004	strong	.	NECAB2	36	.	NM_019065	exon7	c.C656T	p.P219L	CCACTCCCGCCTC	.	PASS	Atlas-SNP
RRM2	6241	hgsc.bcm.edu	37	2	10263874	10263874	+	Silent	SNP	C	C	G	rs5030743	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	30	42	0	0.535714	0	C|0.969;G|0.031	0.031	strong	.	RRM2	63	.	NM_001165931	exon4	c.C510G	p.S170S	CCTCTCCAAGGAC	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7963948	7963948	+	Missense_Mutation	SNP	G	G	A	rs3745379	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	65	0	0.486486	0	G|0.950;A|0.050	0.050	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.G541A	p.E181K	GCCACCGAACGGG	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	100	0	0.5	0	G|0.928;A|0.072	0.072	strong	.	FRMD4B	90	.	NM_015123	exon9	c.C708T	p.L236L	TCGAGTGAGACCT	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31256546	31256546	+	Missense_Mutation	SNP	G	G	A	rs1046457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	85	165	0	0.518293	0	G|0.494;A|0.506	0.506	strong	.	DDX11	188	.	NM_030653	exon26	c.G2572A	p.V858I	GCCAGCGTAGTGC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036999	33036999	+	Missense_Mutation	SNP	T	T	C	rs199711661		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	152	0	1	0	.	.	weak	.	HLA-DPA1	20	.	NM_033554	exon3	c.A425G	p.K142R	AAGAACTTGTCAA	.	PASS	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19087154	19087154	+	Silent	SNP	T	T	C	rs7875404	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	59	86	0	0.437037	0	T|0.849;C|0.151	0.151	strong	.	HAUS6	66	.	NM_017645	exon6	c.A585G	p.Q195Q	TGATAATCTGCAA	.	PASS	Atlas-SNP
MTMR10	54893	hgsc.bcm.edu	37	15	31234064	31234064	+	Missense_Mutation	SNP	C	C	T	rs6493352	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	113	190	0	0.533019	0	C|0.844;T|0.156	0.156	strong	.	MTMR10	74	.	NM_017762	exon16	c.G1943A	p.R648H	GAGACACGTGGCA	.	PASS	Atlas-SNP
RBM33	155435	hgsc.bcm.edu	37	7	155534653	155534653	+	Silent	SNP	C	C	G	rs73167165	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	54	94	0	0.415385	0	C|0.931;G|0.069	0.069	strong	.	RBM33	157	.	NM_053043	exon13	c.C2190G	p.P730P	CACGCCCTCAGCA	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102487643	102487643	+	Missense_Mutation	SNP	T	T	C	rs61730848	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	91	222	0	0.408072	0	T|0.998;C|0.002	0.002	strong	.	MMP20	52	.	NM_004771	exon2	c.A274G	p.M92V	CGTTCATTGTGGT	.	PASS	Atlas-SNP
DNAJA4	55466	hgsc.bcm.edu	37	15	78567853	78567853	+	Silent	SNP	G	G	T	rs967821	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	46	111	0	0.393162	0	G|0.788;T|0.212	0.212	strong	.	DNAJA4	63	.	NM_018602	exon6	c.G747T	p.G249G	AGATGGGCAAAAG	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	37	15	86182670	86182670	+	Silent	SNP	G	G	A	rs16942564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	41	37	0	0.561644	0	G|0.944;A|0.056	0.056	strong	.	AKAP13	394	.	NM_007200	exon9	c.G4227A	p.K1409K	TTCCAAGCAGAGC	.	PASS	Atlas-SNP
PPP1R12C	54776	hgsc.bcm.edu	37	19	55623871	55623871	+	Missense_Mutation	SNP	T	T	G	rs116840455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	38	122	0	0.408602	0	T|0.990;G|0.010	0.010	strong	.	PPP1R12C	46	.	NM_017607	exon3	c.A535C	p.M179L	CCTCCATGGCGTC	.	PASS	Atlas-SNP
PRPSAP1	5635	hgsc.bcm.edu	37	17	74307737	74307737	+	Silent	SNP	T	T	C	rs10459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	80	126	0	0.526316	0	T|0.766;C|0.234	0.234	strong	.	PRPSAP1	32	.	NM_002766	exon10	c.A1044G	p.Q348Q	GGGACATTGCAGC	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786833	75786833	+	Silent	SNP	G	G	A	rs139448820	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	43	41	0	0.472527	0	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.C1941T	p.Y647Y	ACATACGTAAGGT	.	PASS	Atlas-SNP
SLITRK4	139065	hgsc.bcm.edu	37	X	142717383	142717383	+	Silent	SNP	A	A	G	rs73577386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	168	199	1	1	0.00502513	A|0.836;G|0.164	0.164	strong	.	SLITRK4	162	.	NM_001184750	exon2	c.T1542C	p.S514S	GACCCCACTGACA	.	PASS	Atlas-SNP
RPS6KA2	6196	hgsc.bcm.edu	37	6	166912062	166912062	+	Silent	SNP	C	C	T	rs2230732	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	39	93	0	0.448276	0	C|0.805;T|0.194	0.194	strong	.	RPS6KA2	212	.	NM_001006932	exon9	c.G705A	p.A235A	CTCGGGCGCCATG	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744209	54744209	+	Missense_Mutation	SNP	T	T	A	rs8105096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	304	113	320	0	0.371711	0	C|0.155;T|0.845	.	strong	.	LILRA6	75	.	NM_024318	exon6	c.A1199T	p.Y400F	GAGCTGTATGAGC	.	PASS	Atlas-SNP
GPR68	8111	hgsc.bcm.edu	37	14	91700319	91700319	+	Missense_Mutation	SNP	A	A	G	rs151219229	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	11	46	0	0.261905	0	A|0.995;G|0.005	0.005	strong	.	GPR68	32	.	NM_001177676	exon2	c.T1076C	p.F359S	GTGGGGAACCCGC	.	PASS	Atlas-SNP
MTMR7	9108	hgsc.bcm.edu	37	8	17206588	17206588	+	Silent	SNP	G	G	A	rs2285291	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	36	34	0	1	0	G|0.923;A|0.077	0.077	strong	.	MTMR7	75	.	NM_004686	exon5	c.C471T	p.V157V	GTCACAGACCTGT	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52320786	52320786	+	Missense_Mutation	SNP	G	G	A	rs74731075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	40	68	0	0.493827	0	G|0.973;A|0.027	0.027	strong	.	PXDNL	414	.	NM_144651	exon17	c.C3398T	p.A1133V	ACGGCCGCAGAAT	.	PASS	Atlas-SNP
PAG1	55824	hgsc.bcm.edu	37	8	81897200	81897200	+	Silent	SNP	C	C	T	rs7006101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	371	183	384	0	0.493261	0	C|0.853;T|0.147	0.147	strong	.	PAG1	39	.	NM_018440	exon7	c.G687A	p.S229S	GTCCACCGAGGCA	.	PASS	Atlas-SNP
MAPK7	5598	hgsc.bcm.edu	37	17	19285392	19285392	+	Silent	SNP	G	G	A	rs2233079	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	114	144	0	0.57	0	G|0.959;A|0.041	0.041	strong	.	MAPK7	72	.	NM_002749	exon5	c.G1776A	p.A592A	CCCAGCGCCAACG	.	PASS	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55904422	55904422	+	Missense_Mutation	SNP	A	A	G	rs114758947	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	127	183	0	0.538136	0	A|0.983;G|0.017	0.017	strong	.	OR8J3	112	.	NM_001004064	exon1	c.T773C	p.M258T	AAATACATAAATA	.	PASS	Atlas-SNP
GPR124	25960	hgsc.bcm.edu	37	8	37690615	37690615	+	Silent	SNP	G	G	A	rs61738775	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	15	14	0	0.882353	0	G|0.934;A|0.066	0.066	strong	.	GPR124	85	.	NM_032777	exon9	c.G1185A	p.P395P	TGCCCCGGGCACC	.	PASS	Atlas-SNP
RRP1	8568	hgsc.bcm.edu	37	21	45220483	45220483	+	Missense_Mutation	SNP	A	A	G	rs915770	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	91	0	0.508065	0	A|0.767;G|0.233	0.233	strong	RRP1,NS,carcinoma,0,1	RRP1	23	1	NM_003683	exon10	c.A977G	p.K326R	TCTACAAAGTGAT	.	PASS	Atlas-SNP
USP50	373509	hgsc.bcm.edu	37	15	50836846	50836846	+	Silent	SNP	G	G	C	rs114737323	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	43	53	0	0.5	0	G|0.957;C|0.043	0.043	strong	.	USP50	24	.	NM_203494	exon2	c.C186G	p.L62L	GCTGCAGAGACAC	.	PASS	Atlas-SNP
PJA1	64219	hgsc.bcm.edu	37	X	68381912	68381912	+	Silent	SNP	G	G	A	rs3761646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	49	74	0	0.485149	0	G|0.863;0|0.003	.	strong	.	PJA1	106	.	NM_145119	exon2	c.C1170T	p.G390G	GCTTTCGCCACTG	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71658541	71658541	+	Missense_Mutation	SNP	C	C	T	rs11542286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	199	208	0	1	0	T|0.085;G|0.166	0.085	strong	ZNF638,NS,carcinoma,-1,1	ZNF638	179	1	NM_014497	exon26	c.C5735T	p.A1912V	CAGTGGCGTCTGA	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156936364	156936364	+	Missense_Mutation	SNP	T	T	C	rs1422795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	48	95	0	0.428571	0	T|0.592;C|0.408	0.408	strong	.	ADAM19	216	.	NM_033274	exon9	c.A850G	p.S284G	TCCAACTGAGAAA	.	PASS	Atlas-SNP
SERPINF2	5345	hgsc.bcm.edu	37	17	1657653	1657653	+	Missense_Mutation	SNP	G	G	A	rs1057335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	79	155	0	0.503185	0	G|0.814;A|0.186	0.186	strong	.	SERPINF2	33	.	NM_000934	exon10	c.G1301A	p.R434K	GCGTGAGGAACCC	.	PASS	Atlas-SNP
SLC36A2	153201	hgsc.bcm.edu	37	5	150696540	150696540	+	Silent	SNP	C	C	T	rs431240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	167	127	1	1	0.00787402	C|0.410;T|0.590	0.590	strong	.	SLC36A2	71	.	NM_181776	exon10	c.G1290A	p.T430T	GTAGAACGTGGTG	.	PASS	Atlas-SNP
PPFIBP1	8496	hgsc.bcm.edu	37	12	27829369	27829369	+	Silent	SNP	T	T	C	rs35150305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	71	93	0	0.546154	0	T|0.978;C|0.022	0.022	strong	.	PPFIBP1	153	.	NM_177444	exon18	c.T1470C	p.A490A	CAGAGCTCCGGCA	.	PASS	Atlas-SNP
DRD3	1814	hgsc.bcm.edu	37	3	113890789	113890789	+	Silent	SNP	T	T	C	rs3732783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	54	80	0	0.524272	0	T|0.920;C|0.080	0.080	strong	.	DRD3	76	.	NM_033663	exon2	c.A51G	p.A17A	GTTCTCTGCCCCA	.	PASS	Atlas-SNP
OAS1	4938	hgsc.bcm.edu	37	12	113357209	113357209	+	Missense_Mutation	SNP	G	G	A	rs1131476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	67	67	0	1	0	A|0.746;C|0.000;G|0.253;N|0.000;T|0.000	0.746	strong	.	OAS1	128	.	NM_016816	exon6	c.G1054A	p.A352T	AACAGTGCAGACG	.	PASS	Atlas-SNP
KIAA0895L	653319	hgsc.bcm.edu	37	16	67210855	67210855	+	Missense_Mutation	SNP	G	G	C	rs61733789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	99	0	0.521277	0	G|0.923;C|0.077	0.077	strong	.	KIAA0895L	32	.	NM_001040715	exon7	c.C1275G	p.H425Q	CCGCAGGTGGTCC	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25312689	25312689	+	Silent	SNP	A	A	G	rs4748997	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	48	60	0	1	0	A|0.746;G|0.254	0.254	strong	.	THNSL1	70	.	NM_024838	exon3	c.A537G	p.G179G	TTCTGGAACATCT	.	PASS	Atlas-SNP
OAS2	4939	hgsc.bcm.edu	37	12	113424893	113424893	+	Silent	SNP	C	C	G	rs2072138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	91	128	0	0.52	0	C|0.753;G|0.247	0.247	strong	OAS2_ENST00000449768,NS,carcinoma,+1,1	OAS2	86	1	NM_002535	exon2	c.C228G	p.T76T	TGGTACCCTTGTC	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102965016	102965016	+	Missense_Mutation	SNP	A	A	G	rs140337324	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	26	56	0	0.433333	0	A|0.999;G|0.001	0.001	strong	.	BANK1	95	.	NM_017935	exon11	c.A1921G	p.R641G	ACAGCCAGAAGAC	.	PASS	Atlas-SNP
NIM1	0	hgsc.bcm.edu	37	5	43277283	43277283	+	Silent	SNP	G	G	A	rs61734291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	58	79	0	0.517857	0	G|0.965;A|0.035	0.035	strong	.	.	.	.	NM_153361	exon3	c.G417A	p.V139V	CGAAGTGGTGGAG	.	PASS	Atlas-SNP
PSRC1	84722	hgsc.bcm.edu	37	1	109824361	109824361	+	Silent	SNP	A	A	C	rs11800211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	83	126	0	0.568493	0	A|0.938;C|0.062	0.062	strong	.	PSRC1	12	.	NM_001032291	exon4	c.T399G	p.S133S	CGTCAAAGAGTTC	.	PASS	Atlas-SNP
KLHL26	55295	hgsc.bcm.edu	37	19	18778879	18778879	+	Silent	SNP	C	C	T	rs79044993	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	32	41	0	0.450704	0	C|0.988;T|0.012	0.012	strong	.	KLHL26	43	.	NM_018316	exon3	c.C672T	p.I224I	CGAGATCGACCTG	.	PASS	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	433056	433056	+	Missense_Mutation	SNP	G	G	T	rs2303738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	95	0	0.46	0	G|0.971;T|0.029	0.029	strong	.	AHRR	67	.	NM_020731	exon11	c.G1172T	p.G391V	AGGGGGGCTCAGG	.	PASS	Atlas-SNP
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914000	31914000	+	Silent	SNP	T	T	A	rs1023364	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	82	0	0.483516	0	T|0.271;A|0.729	0.729	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.A153T	p.G51G	TCCATATCCTTCA	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233271852	233271852	+	Silent	SNP	C	C	T	rs61730280	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	54	93	0	0.465517	0	C|0.990;T|0.010	0.010	strong	.	ALPPL2	36	.	NM_031313	exon2	c.C153T	p.A51A	GACAGCCGCCAAG	.	PASS	Atlas-SNP
OR2T6	254879	hgsc.bcm.edu	37	1	248551560	248551560	+	Silent	SNP	C	C	T	rs954474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	141	281	0	0.484536	0	C|0.780;T|0.220	0.220	strong	OR2T6,rectum,carcinoma,+1,2	OR2T6	101	2	NM_001005471	exon1	c.C651T	p.S217S	TGCATCCTACACC	.	PASS	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52090671	52090671	+	Missense_Mutation	SNP	T	T	A	rs60097262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	56	99	0	0.430769	0	T|0.983;A|0.017	0.017	strong	.	ZNF175	65	.	NM_007147	exon5	c.T1087A	p.Y363N	AAGCCCTATAAAT	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	37	14	45711594	45711594	+	Silent	SNP	T	T	C	rs1266209	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	54	133	0	0.406015	0	T|0.738;C|0.262	0.262	strong	.	MIS18BP1	92	.	NM_018353	exon4	c.A786G	p.K262K	TTTGGATTTAGTG	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124863136	124863136	+	Silent	SNP	C	C	A	rs7951202	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	21	56	0	0.381818	0	C|0.719;A|0.281	0.281	strong	.	CCDC15	134	.	NM_025004	exon11	c.C2211A	p.P737P	AGTGCCCTTGGTA	.	PASS	Atlas-SNP
OR2B2	81697	hgsc.bcm.edu	37	6	27879093	27879093	+	Silent	SNP	G	G	A	rs73392698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	31	59	0	0.563636	0	G|0.984;A|0.016	0.016	strong	.	OR2B2	54	.	NM_033057	exon1	c.C1005T	p.S335S	ACTTGCGGAGAAG	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	rs61734899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	24	71	0	0.393443	0	G|0.983;A|0.017	0.017	strong	.	PGLYRP2	116	.	NM_052890	exon4	c.C1390T	p.H464Y	CCCAGTGCCAGCC	.	PASS	Atlas-SNP
SLC4A11	83959	hgsc.bcm.edu	37	20	3209254	3209254	+	Silent	SNP	G	G	A	rs139086376	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	72	184	0	0.470588	0	G|0.994;A|0.006	0.006	strong	.	SLC4A11	188	.	NM_001174090	exon18	c.C2421T	p.P807P	GGGCTTGGGGATC	.	PASS	Atlas-SNP
PDE3B	5140	hgsc.bcm.edu	37	11	14810762	14810762	+	Silent	SNP	A	A	G	rs4757268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	28	81	0	0.394366	0	A|0.362;G|0.638	0.638	strong	PDE3B,NS,carcinoma,0,1	PDE3B	98	1	NM_000922	exon4	c.A1389G	p.R463R	CAAAAGACCTCAC	.	PASS	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	37	4	148575601	148575601	+	Missense_Mutation	SNP	T	T	C	rs17023638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	43	68	0	0.421569	0	T|0.963;C|0.037	0.037	strong	.	PRMT10	68	.	NM_138364	exon9	c.A1447G	p.S483G	TAAAACTTTTTGC	.	PASS	Atlas-SNP
CCDC14	64770	hgsc.bcm.edu	37	3	123633665	123633665	+	Silent	SNP	T	T	C	rs13319634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	82	167	0	0.416244	0	T|0.970;C|0.030	0.030	strong	.	CCDC14	97	.	NM_022757	exon12	c.A2700G	p.R900R	CTGGAGTCTAGCT	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579419	55579419	+	Silent	SNP	T	T	C	rs34948392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	489	236	402	0	0.482618	0	T|0.896;C|0.104	0.104	strong	OR5L1,NS,carcinoma,+2,3	OR5L1	145	3	NM_001004738	exon1	c.T477C	p.H159H	GATTCATTTGTGC	.	PASS	Atlas-SNP
ISOC2	79763	hgsc.bcm.edu	37	19	55967848	55967848	+	Silent	SNP	C	C	T	rs11555784	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	26	80	0	0.382353	0	C|0.939;T|0.061	0.061	strong	.	ISOC2	16	.	NM_001136202	exon2	c.G6A	p.A2A	GGCAGCCGCCATT	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15904914	15904914	+	Missense_Mutation	SNP	C	C	T	rs150835909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	86	146	0	0.480447	0	C|0.990;T|0.010	0.010	strong	.	OR10H5	49	.	NM_001004466	exon1	c.C56T	p.A19V	TCTCTGCCTTCCC	.	PASS	Atlas-SNP
NOC2L	26155	hgsc.bcm.edu	37	1	889421	889421	+	Missense_Mutation	SNP	C	C	T	rs3828050	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	143	288	1	0.52	0.00347222	C|0.999;T|0.001	0.001	strong	NOC2L,NS,carcinoma,0,1	NOC2L	42	1	NM_015658	exon7	c.G740A	p.R247H	TCCACACGAAGCT	.	PASS	Atlas-SNP
AGBL4	84871	hgsc.bcm.edu	37	1	49005351	49005351	+	Missense_Mutation	SNP	C	C	T	rs60977321	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	57	109	0	0.44186	0	C|0.961;T|0.039	0.039	strong	.	AGBL4	54	.	NM_032785	exon12	c.G1327A	p.V443M	CAACCACGGGGTT	.	PASS	Atlas-SNP
AMPD3	272	hgsc.bcm.edu	37	11	10503756	10503756	+	Silent	SNP	G	G	A	rs16907852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	25	59	0	0.480769	0	G|0.846;A|0.154	0.154	strong	.	AMPD3	68	.	NM_000480	exon4	c.G600A	p.P200P	ACCTCCGGAAGAG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37115116	37115116	+	Missense_Mutation	SNP	C	C	T	rs7702892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	64	0	0.527027	0	C|0.970;T|0.030	0.030	strong	C5orf42_ENST00000425232,bladder,carcinoma,+1,2	C5orf42	422	2	NM_023073	exon50	c.G9184A	p.G3062R	TGGCTCCACCAGC	.	PASS	Atlas-SNP
IFT43	112752	hgsc.bcm.edu	37	14	76543004	76543004	+	Missense_Mutation	SNP	G	G	A	rs17783366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	34	72	0	0.365591	0	G|0.774;A|0.226	0.226	strong	.	IFT43	63	.	NM_052873	exon4	c.G280A	p.D94N	CACAGAGATTTGG	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6303022	6303022	+	Silent	SNP	C	C	T	rs1801214	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	84	0	1	0	A|0.000;C|0.334;G|0.000;T|0.666	0.666	strong	.	WFS1	71	.	NM_001145853	exon8	c.C1500T	p.N500N	CCTCAACGTCAGC	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59480952	59480952	+	Nonsense_Mutation	SNP	G	G	A	rs499037	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	26	64	0	0.376812	0	G|0.953;A|0.047	0.047	strong	.	OR10V1	40	.	NM_001005324	exon1	c.C367T	p.Q123X	TAAACTGGTCATA	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	213	190	0	0.986111	0	C|0.365;N|0.001	.	strong	.	KLHL33	37	.	NM_001109997	exon4	c.G1546A	p.A516T	GCACAGCGGGCAG	.	PASS	Atlas-SNP
TRIM33	51592	hgsc.bcm.edu	37	1	114948309	114948309	+	Silent	SNP	A	A	G	rs56056367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	145	299	0	0.512367	0	A|0.985;G|0.015	0.015	strong	.	TRIM33	115	.	NM_033020	exon15	c.T2491C	p.L831L	TTGCCAATGCATC	.	PASS	Atlas-SNP
NIPBL	25836	hgsc.bcm.edu	37	5	36985751	36985751	+	Silent	SNP	A	A	G	rs293756	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	101	169	0	0.545946	0	A|0.961;G|0.039	0.039	strong	.	NIPBL	513	.	NM_015384	exon10	c.A2469G	p.K823K	ACAAAAATCAGAT	.	PASS	Atlas-SNP
ATPBD4	89978	hgsc.bcm.edu	37	15	35830665	35830665	+	Missense_Mutation	SNP	C	C	T	rs34907758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	49	117	0	0.475728	0	C|0.972;T|0.028	0.028	strong	.	ATPBD4	30	.	NM_001141972	exon3	c.G122A	p.G41E	TCAGACCCCACTG	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86838497	86838497	+	Silent	SNP	C	C	T	rs9630451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	73	69	0	1	0	C|0.819;T|0.181	0.181	strong	.	AGBL1	151	.	NM_152336	exon16	c.C2094T	p.D698D	TCTTGACATCCTG	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49937813	49937813	+	Silent	SNP	A	A	G	rs1150057	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	122	1	0.991304	0.00819672	A|0.729;G|0.271	0.271	strong	.	KCNH3	88	.	NM_012284	exon6	c.A939G	p.A313A	CATCGCAGCGCTG	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12856856	12856856	+	Missense_Mutation	SNP	A	A	G	rs2305398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	264	191	0	1	0	G|0.597;N|0.001	0.597	strong	.	CAND2	138	.	NM_001162499	exon8	c.A1223G	p.Q408R	AAACACAGCCCCC	.	PASS	Atlas-SNP
OR7D2	162998	hgsc.bcm.edu	37	19	9297196	9297196	+	Missense_Mutation	SNP	G	G	A	rs61739064	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	66	0	0.471429	0	G|0.983;A|0.017	0.017	strong	.	OR7D2	55	.	NM_175883	exon1	c.G739A	p.V247I	CTCTCCGTCGTTT	.	PASS	Atlas-SNP
UPP2	151531	hgsc.bcm.edu	37	2	158977928	158977928	+	Silent	SNP	A	A	C	rs10186677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	185	382	0	0.610561	0	A|0.980;C|0.020	0.020	strong	.	UPP2	60	.	NM_001135098	exon7	c.A633C	p.A211A	GATTGCACCAGGG	.	PASS	Atlas-SNP
IGSF5	150084	hgsc.bcm.edu	37	21	41142958	41142958	+	Silent	SNP	C	C	T	rs61737685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	30	47	0	0.566038	0	C|0.957;T|0.043	0.043	strong	.	IGSF5	62	.	NM_001080444	exon4	c.C534T	p.L178L	GGAGCTCGGTCTC	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30795419	30795419	+	Silent	SNP	C	C	T	rs35221354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	30	78	0	0.422535	0	C|0.947;T|0.053	0.053	strong	INMT,NS,carcinoma,+1,1	INMT	38	1	NM_006774	exon3	c.C744T	p.A248A	TGCTGCCAACAAT	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140237094	140237094	+	Silent	SNP	C	C	G	rs60872775	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	309	157	365	0	0.508091	0	C|0.989;G|0.011	0.011	strong	.	PCDHA10	358	.	NM_031859	exon1	c.C1461G	p.A487A	GAACGCCCTGGTG	.	PASS	Atlas-SNP
ZNF714	148206	hgsc.bcm.edu	37	19	21300964	21300964	+	Silent	SNP	T	T	C	rs111456417	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	16	35	0	0.5	0	T|0.935;C|0.065	0.065	strong	.	ZNF714	121	.	NM_182515	exon5	c.T1494C	p.H498H	TAAACATAGGAAA	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34725116	34725116	+	Silent	SNP	G	G	A	rs62547038	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	492	138	447	0	0.280488	0	G|0.858;A|0.142	0.142	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C2121T	p.V707V	TGCCAGGACCCCA	.	PASS	Atlas-SNP
SYCP2	10388	hgsc.bcm.edu	37	20	58496438	58496438	+	Missense_Mutation	SNP	A	A	G	rs61730337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	101	165	0	0.523316	0	A|0.979;G|0.021	0.021	strong	.	SYCP2	204	.	NM_014258	exon3	c.T95C	p.I32T	ATATCAATTTGCA	.	PASS	Atlas-SNP
UBTF	7343	hgsc.bcm.edu	37	17	42284951	42284951	+	Silent	SNP	A	A	G	rs113823176	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	118	177	0	0.529148	0	A|0.990;G|0.010	0.010	strong	.	UBTF	65	.	NM_014233	exon20	c.T2040C	p.D680D	TTCATCATCCTCC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26687761	26687761	+	Missense_Mutation	SNP	G	G	A	rs17005371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	109	260	0	0.486607	0	G|0.841;A|0.159	0.159	strong	.	OTOF	524	.	NM_194248	exon39	c.C4936T	p.P1646S	CAGAGGGCCCAGT	.	PASS	Atlas-SNP
KIAA0146	23514	hgsc.bcm.edu	37	8	48511729	48511729	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	41	102	0	0.405941	0	.	.	none	.	KIAA0146	64	.	NM_001080394	exon10	c.C1515T	p.S505S	GGCCAGCTCAGGA	.	PASS	Atlas-SNP
PNMAL1	55228	hgsc.bcm.edu	37	19	46973981	46973981	+	Silent	SNP	G	G	A	rs4803960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	66	55	0	1	0	G|0.732;A|0.268	0.268	strong	.	PNMAL1	87	.	NM_018215	exon2	c.C312T	p.A104A	AAACTCGGCATCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506460	195506460	+	Missense_Mutation	SNP	G	G	C	rs113130007	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	10	116	2	0.10989	0.0172414	C|0.994;G|0.006	0.994	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11991G	p.H3997Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677714	100677714	+	Missense_Mutation	SNP	C	C	T	rs79432420	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	61	168	0	0.211073	0	C|0.989;T|0.011	0.011	strong	.	MUC17	804	.	NM_001040105	exon3	c.C3017T	p.T1006I	CAACAACTCCTGT	.	PASS	Atlas-SNP
ZSCAN25	221785	hgsc.bcm.edu	37	7	99226981	99226981	+	Missense_Mutation	SNP	C	C	G	rs10239632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	35	52	0	0.603448	0	C|0.966;G|0.034	0.034	strong	.	.	.	.	NM_145115	exon8	c.C973G	p.P325A	GGGCTTCCTCCTC	.	PASS	Atlas-SNP
BMX	660	hgsc.bcm.edu	37	X	15555339	15555339	+	Silent	SNP	G	G	A	rs376617024	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	100	177	0	0.460829	0	.	.	weak	.	BMX	73	.	NM_001721	exon14	c.G1305A	p.K435K	GGGCAAGTGGAAG	.	PASS	Atlas-SNP
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	30	48	0	0.652174	0	C|0.642;T|0.358	0.358	strong	.	MEGF11	70	.	NM_032445	exon4	c.G284A	p.S95N	TCTCCGCTCTCAT	.	PASS	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52089982	52089982	+	Missense_Mutation	SNP	C	C	G	rs61736479	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	82	159	0	0.5	0	C|0.885;G|0.115	0.115	strong	.	ZNF175	65	.	NM_007147	exon5	c.C398G	p.S133C	GGTGTTCCATTTT	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	37	6	46977894	46977894	+	Missense_Mutation	SNP	C	C	T	rs115292676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	100	180	0	0.561798	0	C|0.989;T|0.011	0.011	strong	GPR110,colon,carcinoma,-1,2	GPR110	102	2	NM_153840	exon11	c.G1277A	p.R426Q	AATTTCCGAGAAA	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103124207	103124207	+	Silent	SNP	T	T	C	rs1062831	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	59	139	0	0.440298	0	T|0.807;C|0.193	0.193	strong	.	RELN	593	.	NM_173054	exon62	c.A10074G	p.A3358A	CAGCACTGCCTTG	.	PASS	Atlas-SNP
SLC26A11	284129	hgsc.bcm.edu	37	17	78201686	78201686	+	Silent	SNP	C	C	T	rs61011315	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	23	39	0	0.511111	0	C|0.944;T|0.056	0.056	strong	.	SLC26A11	60	.	NM_173626	exon7	c.C663T	p.H221H	GGACCACGTGCCT	.	PASS	Atlas-SNP
RACGAP1	29127	hgsc.bcm.edu	37	12	50384542	50384542	+	Missense_Mutation	SNP	T	T	C	rs140590023	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	67	159	0	0.401198	0	T|0.998;C|0.002	0.002	strong	.	RACGAP1	36	.	NM_013277	exon18	c.A1748G	p.H583R	AGCTGATGTTCAG	.	PASS	Atlas-SNP
TSPAN2	10100	hgsc.bcm.edu	37	1	115601528	115601528	+	Silent	SNP	C	C	G	rs3738702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	68	123	0	0.482269	0	C|0.901;G|0.099	0.099	strong	TSPAN2,NS,malignant_melanoma,-1,1	TSPAN2	37	1	NM_005725	exon5	c.G420C	p.G140G	GAGTGTCCCATTG	.	PASS	Atlas-SNP
KRT78	196374	hgsc.bcm.edu	37	12	53240584	53240584	+	Silent	SNP	A	A	G	rs2682342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	29	46	0	1	0	A|0.737;G|0.263	0.263	strong	KRT78,caecum,carcinoma,-1,1	KRT78	41	1	NM_173352	exon3	c.T624C	p.R208R	TGTGGCACGCCTG	.	PASS	Atlas-SNP
OR2A2	442361	hgsc.bcm.edu	37	7	143807304	143807304	+	Missense_Mutation	SNP	T	T	C	rs10252253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	65	102	0	0.560345	0	T|0.806;C|0.194	0.194	strong	OR2A2,colon,carcinoma,0,1	OR2A2	48	1	NM_001005480	exon1	c.T629C	p.L210P	GGCCTCTTTCCTT	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011406	46011406	+	Silent	SNP	G	G	T	rs374116165		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	46	362	0	0.178295	0	.	.	weak	.	KRTAP10-6	57	.	NM_198688	exon1	c.C960A	p.V320V	GGAGGGGACGGGC	.	PASS	Atlas-SNP
AKIRIN2	55122	hgsc.bcm.edu	37	6	88385579	88385579	+	Silent	SNP	G	G	A	rs63749091	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	61	107	0	0.458647	0	G|0.968;A|0.032	0.032	strong	.	AKIRIN2	13	.	NM_018064	exon4	c.C600T	p.S200S	CTTACAGCTAGCA	.	PASS	Atlas-SNP
TOX	9760	hgsc.bcm.edu	37	8	59727966	59727966	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	166	274	0	0.497006	0	.	.	none	.	TOX	83	.	NM_014729	exon7	c.G1323A	p.M441I	CTGCTGCATGGTG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149489048	149489048	+	Missense_Mutation	SNP	C	C	T	rs893602	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	60	0	0.480519	0	C|0.979;T|0.021	0.021	strong	.	.	.	.	NM_198455	exon35	c.C5389T	p.R1797C	AGCACCCGCCAGA	.	PASS	Atlas-SNP
ZNF645	158506	hgsc.bcm.edu	37	X	22291732	22291732	+	Silent	SNP	C	C	T	rs6629461	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	76	134	0	0.531469	0	C|0.774;T|0.226	0.226	strong	.	ZNF645	67	.	NM_152577	exon1	c.C624T	p.I208I	GGATATCCAGGCT	.	PASS	Atlas-SNP
CNTROB	116840	hgsc.bcm.edu	37	17	7847955	7847955	+	Missense_Mutation	SNP	C	C	A	rs11650083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	55	86	0	0.470085	0	C|0.491;A|0.509	0.509	strong	CNTROB,colon,carcinoma,0,1	CNTROB	61	1	NM_001037144	exon12	c.C1733A	p.P578Q	ACCCTCCAGTACG	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13649665	13649665	+	Silent	SNP	C	C	T	rs13327200	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	38	69	0	0.426966	0	C|0.911;T|0.089	0.089	strong	.	FBLN2	137	.	NM_001998	exon3	c.C1410T	p.N470N	GGACAACGTCTGC	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12409327	12409327	+	Missense_Mutation	SNP	C	C	T	rs17165910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	103	271	0	0.371841	0	C|0.841;T|0.159	0.159	strong	.	VWDE	123	.	NM_001135924	exon12	c.G2605A	p.E869K	TCCCCTCCTCCAC	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16337448	16337448	+	Silent	SNP	C	C	A	rs28707654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	48	0	0.551282	0	C|0.978;A|0.022	0.022	strong	.	NRIP1	103	.	NM_003489	exon4	c.G3066T	p.G1022G	TCTAGACCCTGCA	.	PASS	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60585282	60585282	+	Missense_Mutation	SNP	G	G	A	rs144345462	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	148	294	1	0.458204	0.00340136	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_022495	exon6	c.G1112A	p.R371Q	TTCCCCGACCTAT	.	PASS	Atlas-SNP
SLC23A2	9962	hgsc.bcm.edu	37	20	4843470	4843470	+	Silent	SNP	C	C	A	rs34073337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	14	50	0	0.378378	0	C|0.930;A|0.070	0.070	strong	SLC23A2,caecum,carcinoma,0,2	SLC23A2	62	2	NM_203327	exon14	c.G1440T	p.A480A	AAGGGACGCAAAG	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7580958	7580958	+	Missense_Mutation	SNP	A	A	G	rs2076299	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	17	76	0	0.447368	0	A|0.840;C|0.001	.	strong	.	DSP	306	.	NM_004415	exon23	c.A4535G	p.Y1512C	TCCAGTATGACCT	.	PASS	Atlas-SNP
KCNK17	89822	hgsc.bcm.edu	37	6	39267315	39267315	+	Missense_Mutation	SNP	C	C	T	rs2758910	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	80	151	0	0.484848	0	C|0.989;T|0.011	0.011	strong	KCNK17,NS,carcinoma,-1,1	KCNK17	61	1	NM_031460	exon5	c.G887A	p.R296Q	GGCTCCCGGTCAG	.	PASS	Atlas-SNP
FAM161A	84140	hgsc.bcm.edu	37	2	62069358	62069358	+	Missense_Mutation	SNP	T	T	C	rs11125895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	63	122	0	0.434483	0	T|0.833;C|0.167	0.167	strong	.	FAM161A	200	.	NM_032180	exon2	c.A321G	p.I107M	AGTTTCTATGTGG	.	PASS	Atlas-SNP
CYP11B1	1584	hgsc.bcm.edu	37	8	143961102	143961102	+	Missense_Mutation	SNP	C	C	T	rs4534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	84	126	0	0.506024	0	C|0.920;T|0.080	0.080	strong	.	CYP11B1	128	.	NM_000497	exon1	c.G128A	p.R43Q	GGACGCCGGGGCA	.	PASS	Atlas-SNP
CORO2B	10391	hgsc.bcm.edu	37	15	69006909	69006909	+	Silent	SNP	C	C	T	rs17852399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	84	127	0	0.515337	0	C|0.955;T|0.045	0.045	strong	.	CORO2B	68	.	NM_006091	exon7	c.C777T	p.S259S	CCTCTCCATGCCC	.	PASS	Atlas-SNP
CEACAM4	1089	hgsc.bcm.edu	37	19	42132193	42132193	+	Missense_Mutation	SNP	T	T	C	rs3848568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	132	201	0	0.556962	0	T|0.883;C|0.117	0.117	strong	.	CEACAM4	42	.	NM_001817	exon2	c.A206G	p.K69R	TTCCCCTTGTGCC	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168709385	168709385	+	Missense_Mutation	SNP	T	T	C	rs6925614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	38	0	1	0	T|0.628;C|0.372	0.372	strong	DACT2_ENST00000366795,NS,carcinoma,-1,1	DACT2	46	1	NM_214462	exon4	c.A1052G	p.E351G	TCTCCCTCGCTAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512565	195512565	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	3	402	0	0.0111524	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.C5886T	p.P1962P	ACCTGTGGGTACT	.	scavenged	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52365223	52365223	+	Missense_Mutation	SNP	G	G	A	rs55931436	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	91	150	0	0.469072	0	G|0.984;A|0.016	0.016	strong	.	DNAH1	534	.	NM_015512	exon7	c.G931A	p.D311N	GACTACGACGAGG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113259152	113259152	+	Missense_Mutation	SNP	T	T	G	rs10817033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	117	177	0	0.625668	0	T|0.887;G|0.113	0.113	strong	.	SVEP1	326	.	NM_153366	exon8	c.A1743C	p.Q581H	AGAATCTTGCTGT	.	PASS	Atlas-SNP
TTBK1	84630	hgsc.bcm.edu	37	6	43252029	43252029	+	Missense_Mutation	SNP	T	T	C	rs3800298	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	14	37	0	0.538462	0	T|0.667;C|0.333	0.333	strong	TTBK1,NS,carcinoma,0,1	TTBK1	124	1	NM_032538	exon14	c.T3551C	p.L1184S	CAGCATTGGACAC	.	PASS	Atlas-SNP
MBL2	4153	hgsc.bcm.edu	37	10	54528236	54528236	+	Silent	SNP	G	G	A	rs35805975	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	27	51	0	0.465517	0	G|0.981;A|0.019	0.019	strong	.	MBL2	55	.	NM_000242	exon4	c.C408T	p.N136N	GAACTTGTTCCCA	.	PASS	Atlas-SNP
OGFOD1	55239	hgsc.bcm.edu	37	16	56496469	56496469	+	Missense_Mutation	SNP	G	G	A	rs147797412	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	95	0	0.482143	0	G|1.000;A|0.000	0.000	weak	.	OGFOD1	31	.	NM_018233	exon4	c.G371A	p.R124Q	ATTTCCGGTCCTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272246	1272246	+	Silent	SNP	G	G	A	rs115045504	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	520	253	551	2	0.486538	0.00362976	G|0.988;A|0.012	0.012	strong	MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon31	c.G14136A	p.T4712T	CAGCACGGCCACC	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	rs201335235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	8	91	0	0.0720721	0	.	.	weak	.	ZNF799	111	.	NM_001080821	exon4	c.A1057C	p.K353Q	GACTTTTCAGTGA	.	PASS	Atlas-SNP
FAM221B	392307	hgsc.bcm.edu	37	9	35826038	35826038	+	Missense_Mutation	SNP	T	T	C	rs13294245	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	40	118	0	0.392157	0	T|0.758;C|0.242	0.242	strong	.	FAM221B	38	.	NM_001012446	exon2	c.A121G	p.K41E	AAGGCTTCAAGAA	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657583	49657583	+	Silent	SNP	G	G	A	rs144793394		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	65	187	0	0.282609	0	G|0.999;A|0.001	0.001	weak	.	HRC	85	.	NM_002152	exon1	c.C912T	p.D304D	ATCATTGTCATCT	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38147170	38147170	+	Missense_Mutation	SNP	C	C	T	rs1801688	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	140	268	0	0.520446	0	0|0.003;T|0.102	0.102	strong	.	RPGR	175	.	NM_001034853	exon14	c.G1697A	p.G566E	AAAATCCCTTGTG	.	PASS	Atlas-SNP
UQCC	55245	hgsc.bcm.edu	37	20	33971876	33971876	+	Missense_Mutation	SNP	T	T	C	rs114745625	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	104	217	0	0.477064	0	T|0.997;C|0.003	0.003	strong	.	UQCC	41	.	NM_018244	exon3	c.A190G	p.I64V	GCTGTATGTCTAT	.	PASS	Atlas-SNP
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	110	186	1	0.56701	0.00537634	G|0.762;A|0.238	0.238	strong	.	SNX7	76	.	NM_015976	exon6	c.G1011A	p.E337E	ACATGAGTACGTG	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44157797	44157797	+	Silent	SNP	G	G	T	rs112463030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	81	0	0.515789	0	G|0.994;T|0.006	0.006	strong	.	LOXHD1	367	.	NM_144612	exon14	c.C1843A	p.R615R	CATTCCGCATGGT	.	PASS	Atlas-SNP
GHRHR	2692	hgsc.bcm.edu	37	7	31009576	31009576	+	Missense_Mutation	SNP	G	G	T	rs4988498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	61	119	0	0.60396	0	G|0.919;T|0.081	0.081	strong	.	GHRHR	55	.	NM_000823	exon4	c.G363T	p.E121D	GGCTGAGGAGGTA	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12315848	12315848	+	Silent	SNP	C	C	T	rs1493952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	16	31	0	0.615385	0	C|0.576;T|0.424	0.424	strong	.	MICALCL	59	.	NM_032867	exon3	c.C870T	p.G290G	TGAAGGCGGGAAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179430224	179430224	+	Missense_Mutation	SNP	G	G	T	rs79926414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	90	199	1	0.596026	0.00502513	G|0.976;T|0.024	0.024	strong	.	TTN	18412	.	NM_001267550	exon326	c.C80635A	p.Q26879K	TAGGCTGTATAGT	.	PASS	Atlas-SNP
FOXRED2	80020	hgsc.bcm.edu	37	22	36886178	36886178	+	Silent	SNP	A	A	G	rs73409777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	39	68	0	0.481481	0	A|0.975;G|0.025	0.025	strong	.	FOXRED2	48	.	NM_001102371	exon9	c.T1932C	p.Y644Y	GGGGGCATAGTCC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863320	144863320	+	Missense_Mutation	SNP	T	T	C	rs139822181	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	419	132	463	0	0.315036	0	T|0.967;C|0.033	0.033	strong	.	PDE4DIP	817	.	NM_014644	exon37	c.A6083G	p.K2028R	ATACCTTTCAGCC	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009491	46009491	+	Silent	SNP	C	C	T	rs3796376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	79	139	0	0.509677	0	C|0.825;T|0.175	0.175	strong	.	FYCO1	115	.	NM_024513	exon8	c.G1335A	p.L445L	GCGCTCCAGGCTG	.	PASS	Atlas-SNP
IPO13	9670	hgsc.bcm.edu	37	1	44422367	44422367	+	Silent	SNP	A	A	G	rs36061711	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	83	129	0	0.506098	0	A|0.964;G|0.036	0.036	strong	.	IPO13	86	.	NM_014652	exon4	c.A1098G	p.T366T	GTACACACTGCAG	.	PASS	Atlas-SNP
SPAG8	26206	hgsc.bcm.edu	37	9	35811749	35811749	+	Silent	SNP	C	C	T	rs79261709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	44	80	0	0.578947	0	C|0.988;T|0.012	0.012	strong	.	SPAG8	67	.	NM_001039592	exon2	c.G294A	p.A98A	GGGTCCCGCACAG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036950	33036950	+	Silent	SNP	C	C	T	rs2308931	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	52	138	0	0.468468	0	C|0.869;T|0.131	0.131	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.G474A	p.L158L	AGTGACCAGCTCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276583	152276583	+	Missense_Mutation	SNP	C	C	G	rs12083389	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	643	596	633	0	0.926905	0	C|0.820;G|0.180	0.180	strong	.	FLG	900	.	NM_002016	exon3	c.G10779C	p.E3593D	GGAGCTCTCTGCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677378	100677378	+	Missense_Mutation	SNP	C	C	A	rs143956720	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	35	120	0	0.212121	0	C|0.958;A|0.042	0.042	strong	MUC17,NS,lymphoid_neoplasm,0,1	MUC17	804	1	NM_001040105	exon3	c.C2681A	p.T894K	CCAGCACACCTGT	.	PASS	Atlas-SNP
CPPED1	55313	hgsc.bcm.edu	37	16	12798724	12798724	+	Missense_Mutation	SNP	C	C	T	rs145004672	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	94	1	0.542169	0.0106383	C|0.988;T|0.012	0.012	strong	CPPED1,rectum,carcinoma,0,1	CPPED1	41	1	NM_018340	exon3	c.G472A	p.V158I	ACAGGACGCCCCC	.	scavenged	Atlas-SNP
ZNF326	284695	hgsc.bcm.edu	37	1	90486412	90486412	+	Silent	SNP	T	T	G	rs2816881	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	137	301	0	0.498182	0	T|0.355;G|0.645	0.645	strong	.	ZNF326	60	.	NM_182976	exon10	c.T1236G	p.V412V	CAGTGTTTATATC	.	PASS	Atlas-SNP
CASS4	57091	hgsc.bcm.edu	37	20	55033420	55033420	+	Missense_Mutation	SNP	C	C	T	rs35031530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	101	120	0	0.990196	0	C|0.905;T|0.095	0.095	strong	CASS4,NS,carcinoma,-1,1	CASS4	121	1	NM_020356	exon6	c.C1978T	p.P660S	CCTCAGCCTTCGA	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170291	58170291	+	Missense_Mutation	SNP	T	T	C	rs11229410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	58	0	0.483871	0	C|0.321;T|0.679	0.321	strong	.	OR5B3	65	.	NM_001005469	exon1	c.A592G	p.I198V	CATAAATAAGAAC	.	PASS	Atlas-SNP
PRKD3	23683	hgsc.bcm.edu	37	2	37543544	37543544	+	Missense_Mutation	SNP	T	T	C	rs11896614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	65	146	0	0.454545	0	T|0.960;C|0.040	0.040	strong	.	PRKD3	170	.	NM_005813	exon1	c.A124G	p.N42D	TTCCATTAGAGAG	.	PASS	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	68	106	0	0.60177	0	C|0.919;T|0.081	0.081	strong	AMPH,NS,carcinoma,-1,1	AMPH	157	1	NM_001635	exon19	c.G1716A	p.A572A	AGGAGCCGCGTCC	.	PASS	Atlas-SNP
ABCB8	11194	hgsc.bcm.edu	37	7	150730712	150730712	+	Missense_Mutation	SNP	G	G	A	rs6975981	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	49	118	0	0.457944	0	G|0.973;A|0.027	0.027	strong	.	ABCB8	65	.	NM_007188	exon2	c.G116A	p.S39N	ACCGCAGCTCCTC	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64461914	64461914	+	Silent	SNP	A	A	G	rs34001379	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	78	171	0	0.493671	0	A|0.995;G|0.005	0.005	strong	SYNE2,rectum,carcinoma,+2,1	SYNE2	577	1	NM_182914	exon23	c.A2934G	p.E978E	CAAAGAACATGAG	.	PASS	Atlas-SNP
CLEC1A	51267	hgsc.bcm.edu	37	12	10251445	10251445	+	Missense_Mutation	SNP	C	C	G	rs2306894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	172	178	0	1	0	C|0.179;G|0.819	0.819	strong	CLEC1A,colon,carcinoma,0,2	CLEC1A	48	2	NM_016511	exon1	c.G77C	p.G26A	GCAGAGCCTTGAG	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12229655	12229655	+	Silent	SNP	T	T	G	rs2279390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	160	213	0	0.987654	0	G|0.341;N|0.000	0.341	strong	.	MICAL2	114	.	NM_014632	exon5	c.T558G	p.V186V	GAAGGTTCTAGAG	.	PASS	Atlas-SNP
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	94	185	0	0.439252	0	C|0.701;T|0.299	0.299	strong	SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	NM_144644	exon4	c.G630A	p.A210A	GAACTCCGCTTTA	.	PASS	Atlas-SNP
ERO1L	30001	hgsc.bcm.edu	37	14	53133134	53133134	+	Silent	SNP	A	A	G	rs34388088	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	84	230	0	0.422111	0	A|0.985;G|0.015	0.015	strong	.	ERO1L	35	.	NM_014584	exon7	c.T588C	p.A196A	TTTCCAAGCATCT	.	PASS	Atlas-SNP
KLC3	147700	hgsc.bcm.edu	37	19	45848946	45848946	+	Silent	SNP	G	G	A	rs114640964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	22	42	0	0.52381	0	G|0.990;A|0.010	0.010	strong	.	KLC3	37	.	NM_177417	exon2	c.G147A	p.A49A	CCTGGCGGAGGCC	.	PASS	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681130	55681130	+	Missense_Mutation	SNP	A	A	T	rs34573569	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	17	53	0	0.447368	0	A|0.877;T|0.123	0.123	strong	.	OR5W2	112	.	NM_001001960	exon1	c.T929A	p.F310Y	CCTTAAAATAAAA	.	PASS	Atlas-SNP
C17orf64	124773	hgsc.bcm.edu	37	17	58508618	58508618	+	Silent	SNP	T	T	C	rs3760332	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	22	68	0	0.349206	0	T|0.702;C|0.298	0.298	strong	.	C17orf64	19	.	NM_181707	exon6	c.T702C	p.T234T	AGAGACTGAACCG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124374487	124374487	+	Silent	SNP	T	T	C	rs55750661	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	67	138	0	0.478571	0	T|0.998;C|0.002	0.002	strong	.	KALRN	556	.	NM_001024660	exon39	c.T5832C	p.Y1944Y	AGACTATGTCAAG	.	PASS	Atlas-SNP
FAM207A	85395	hgsc.bcm.edu	37	21	46396659	46396659	+	Missense_Mutation	SNP	G	G	C	rs3737075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	23	37	0	0.511111	0	G|0.835;C|0.165	0.165	strong	.	.	.	.	NM_058190	exon6	c.G634C	p.V212L	CCCCTGGTGGCCA	.	PASS	Atlas-SNP
KIAA0226L	80183	hgsc.bcm.edu	37	13	46919719	46919719	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	25	48	0	0.531915	0	.	.	none	.	KIAA0226L	63	.	NM_025113	exon13	c.G1648A	p.E550K	CCTGCTCGAACTC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14816829	14816829	+	Missense_Mutation	SNP	G	G	C	rs7041710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	16	25	0	0.516129	0	G|0.856;C|0.144	0.144	strong	.	FREM1	261	.	NM_144966	exon16	c.C2587G	p.L863V	CCAAGAGTAGGTC	.	PASS	Atlas-SNP
TREM1	54210	hgsc.bcm.edu	37	6	41243926	41243926	+	Missense_Mutation	SNP	G	G	C	rs2234245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	90	0	0.470588	0	G|0.979;C|0.021	0.021	strong	.	TREM1	38	.	NM_018643	exon4	c.C642G	p.F214L	ACTCAGGAATCCA	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	37	20	47841660	47841660	+	Missense_Mutation	SNP	G	G	T	rs11553387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	94	172	0	0.447619	0	A|0.001;C|0.006;G|0.814;T|0.179	0.179	strong	.	DDX27	74	.	NM_017895	exon6	c.G617T	p.G206V	CAGGAGGATTTTT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	501	101	501	1	0.201597	0.00199601	G|0.995;C|0.005	0.005	strong	FLG,NS,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.C10702G	p.Q3568E	GCTCCTGAGCAGA	.	scavenged	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536117	1536117	+	Silent	SNP	G	G	A	rs58192896	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	36	73	0	0.455696	0	G|0.941;A|0.059	0.059	strong	.	PTX4	46	.	NM_001013658	exon3	c.C1245T	p.F415F	CCCCACGAAGGCC	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	389	9	352	2	0.0231362	0.00568182	.	.	weak	LILRB4,NS,carcinoma,0,1	LILRB4	86	1	NM_006847	exon12	c.T1254G	p.F418L	CAGCTTTACCCTC	.	scavenged	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7060092	7060092	+	Missense_Mutation	SNP	A	A	G	rs16921697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	29	59	0	0.54717	0	A|0.957;G|0.043	0.043	strong	NLRP14_ENST00000299481,NS,carcinoma,0,2	NLRP14	187	2	NM_176822	exon2	c.A275G	p.K92R	GAGCGAAAGAAGA	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5067984	5067984	+	Missense_Mutation	SNP	A	A	G	rs2500016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	145	265	1	0.498282	0.00377358	A|0.493;G|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.A229G	p.T77A	CTTTCTACAACCT	.	PASS	Atlas-SNP
AGRP	181	hgsc.bcm.edu	37	16	67517179	67517179	+	Silent	SNP	C	C	T	rs34123523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	54	108	0	0.574468	0	C|0.877;T|0.123	0.123	strong	.	AGRP	8	.	NM_001138	exon2	c.G123A	p.E41E	TGGGAGCTCTGGG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26168333	26168333	+	Silent	SNP	C	C	T	rs185388626	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	53	82	0	0.56383	0	C|0.998;T|0.002	0.002	strong	.	MYO18B	322	.	NM_032608	exon7	c.C1725T	p.D575D	CGAGGACCTGGCC	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46501308	46501308	+	Silent	SNP	T	T	C	rs61740461	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	65	135	0	0.541667	0	T|0.931;C|0.069	0.069	strong	.	LTF	98	.	NM_002343	exon2	c.A45G	p.G15G	ACACAGTCCTGGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179666982	179666982	+	Missense_Mutation	SNP	C	C	A	rs35683768	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	72	97	0	0.580645	0	C|0.975;A|0.025	0.025	strong	.	TTN	18412	.	NM_001267550	exon3	c.G178T	p.D60Y	GGCCATCGCTAAA	.	PASS	Atlas-SNP
GPR148	344561	hgsc.bcm.edu	37	2	131486765	131486765	+	Missense_Mutation	SNP	C	C	G	rs80008074	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	106	194	0	0.486239	0	C|0.932;G|0.068	0.068	strong	.	GPR148	54	.	NM_207364	exon1	c.C41G	p.A14G	CTACAGCTTGGCC	.	PASS	Atlas-SNP
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	228	232	0	0.991304	0	T|0.613;C|0.387	0.387	strong	.	RNASE11	44	.	NM_145250	exon3	c.A375G	p.T125T	CACTTCTGTGGAG	.	PASS	Atlas-SNP
ULK1	8408	hgsc.bcm.edu	37	12	132404110	132404110	+	Silent	SNP	C	C	T	rs113954208	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	41	90	0	0.594203	0	C|0.994;T|0.006	0.006	strong	.	ULK1	92	.	NM_003565	exon25	c.C2778T	p.L926L	CAAGCTCTGCCTG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	8996460	8996460	+	Missense_Mutation	SNP	A	A	C	rs115933306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	204	0	1	0	A|0.974;C|0.026	0.026	strong	.	MUC16	4315	.	NM_024690	exon61	c.T41112G	p.D13704E	GATGGCATCCACT	.	PASS	Atlas-SNP
CXCR2	3579	hgsc.bcm.edu	37	2	218999798	218999798	+	Silent	SNP	T	T	C	rs142747099	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	109	249	1	0.457983	0.00401606	T|0.999;C|0.001	0.001	strong	.	CXCR2	54	.	NM_001168298	exon4	c.T274C	p.L92L	CTAGCCTTGGCCG	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21952884	21952884	+	Silent	SNP	G	G	A	rs1130564	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	25	52	0	0.403226	0	G|0.955;A|0.045	0.045	strong	.	RAP1GAP	119	.	NM_001145658	exon3	c.C87T	p.S29S	CCCATCGCTCCTC	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92548785	92548785	+	Missense_Mutation	SNP	C	C	T	rs1048755	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	84	169	0	0.444444	0	C|0.699;T|0.301	0.301	strong	.	ATXN3	46	.	NM_004993	exon8	c.G634A	p.V212M	CTAACACTCGTTC	.	PASS	Atlas-SNP
FSCN1	6624	hgsc.bcm.edu	37	7	5643145	5643145	+	Silent	SNP	T	T	C	rs1640233	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	108	128	0	0.990826	0	T|0.793;C|0.207	0.207	strong	.	FSCN1	29	.	NM_003088	exon3	c.T1008C	p.F336F	CTACTTTGACATC	.	PASS	Atlas-SNP
GPR108	56927	hgsc.bcm.edu	37	19	6737516	6737516	+	Silent	SNP	C	C	T	rs11539591	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	10	12	0	0.588235	0	C|0.900;T|0.100	0.100	strong	.	GPR108	35	.	NM_001080452	exon1	c.G72A	p.V24V	CAGCAGCACCAGA	.	PASS	Atlas-SNP
PPP1R3F	89801	hgsc.bcm.edu	37	X	49142987	49142987	+	Missense_Mutation	SNP	C	C	T	rs372361395		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	54	89	0	0.490909	0	.	.	weak	.	PPP1R3F	56	.	NM_033215	exon4	c.C1835T	p.T612M	TAGCCACGATGGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677516	100677516	+	Missense_Mutation	SNP	A	A	G	rs58478927	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	38	130	0	0.168142	0	A|0.995;G|0.005	0.005	strong	.	MUC17	804	.	NM_001040105	exon3	c.A2819G	p.E940G	GTTCTGAGGCTAG	.	PASS	Atlas-SNP
ADAMTS1	9510	hgsc.bcm.edu	37	21	28214238	28214238	+	Silent	SNP	T	T	C	rs77718820	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	67	146	0	0.51145	0	T|0.990;C|0.010	0.010	strong	.	ADAMTS1	131	.	NM_006988	exon3	c.A1149G	p.R383R	GCAGCTTCTGCTC	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860001	16860001	+	Missense_Mutation	SNP	A	A	T	rs76739123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	79	115	0	0.552448	0	A|0.975;T|0.025	0.025	strong	.	NWD1	303	.	NM_001007525	exon6	c.A548T	p.Q183L	GGGAACAGGGAGC	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18566386	18566386	+	Missense_Mutation	SNP	G	G	A	rs143643706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	137	390	0	0.388102	0	G|0.945;A|0.055	0.055	strong	.	ZNF286B	75	.	NM_001145045	exon5	c.C433T	p.R145W	TATTCCGTGTCAG	.	PASS	Atlas-SNP
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709935	31709935	+	Missense_Mutation	SNP	G	G	A	rs149814034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	94	192	0	0.445498	0	G|0.997;A|0.003	0.003	strong	.	KRTAP27-1	53	.	NM_001077711	exon1	c.C52T	p.L18F	CAGAGAGTGGTGG	.	PASS	Atlas-SNP
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	43	94	0	0.443299	0	C|0.969;T|0.031	0.031	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.G134A	p.R45H	GATGGGCGGCAGC	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	107	208	1	0.477679	0.00480769	A|0.384;G|0.616	0.616	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon35	c.A5526G	p.S1842S	CATGTCACCTGGG	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78506181	78506181	+	Silent	SNP	C	C	A	rs34813806	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	77	74	0	0.740385	0	C|0.990;A|0.010	0.010	strong	.	PCSK5	329	.	NM_006200	exon1	c.C84A	p.P28P	GCTCCCCGTGTGT	.	PASS	Atlas-SNP
GMPR	2766	hgsc.bcm.edu	37	6	16279097	16279097	+	Silent	SNP	T	T	C	rs739473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	101	83	0	1	0	T|0.909;C|0.091	0.091	strong	.	GMPR	44	.	NM_006877	exon6	c.T630C	p.H210H	TGCCCATGGCCTG	.	PASS	Atlas-SNP
VNN1	8876	hgsc.bcm.edu	37	6	133013576	133013576	+	Missense_Mutation	SNP	G	G	T	rs34535050	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	33	63	0	0.492537	0	G|0.975;T|0.025	0.025	strong	.	VNN1	69	.	NM_004666	exon5	c.C974A	p.A325E	GAGAGCGCTTCTA	.	PASS	Atlas-SNP
DPCD	25911	hgsc.bcm.edu	37	10	103368654	103368654	+	Missense_Mutation	SNP	T	T	C	rs7006	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	36	97	0	0.387097	0	T|0.720;C|0.280	0.280	strong	.	DPCD	15	.	NM_015448	exon5	c.T467C	p.L156S	ACGCCTTGCTGAG	.	PASS	Atlas-SNP
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	100	197	0	0.507614	0	G|0.691;A|0.309	0.309	strong	.	ZDHHC4	36	.	NM_018106	exon4	c.G157A	p.V53M	AGAGCCGTGCATG	.	PASS	Atlas-SNP
PDE4C	5143	hgsc.bcm.edu	37	19	18330144	18330144	+	Missense_Mutation	SNP	C	C	T	rs34503849	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	55	81	0	0.585106	0	C|0.982;T|0.018	0.018	strong	.	PDE4C	80	.	NM_000923	exon9	c.G866A	p.R289Q	CTGATCCGGGACA	.	PASS	Atlas-SNP
PAN3	255967	hgsc.bcm.edu	37	13	28750683	28750683	+	Silent	SNP	A	A	G	rs142608239	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	72	86	0	0.585366	0	A|0.995;G|0.005	0.005	strong	.	PAN3	123	.	NM_175854	exon3	c.A606G	p.P202P	CAAGCCATATTCA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151945215	151945215	+	Silent	SNP	T	T	C	rs75129488	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	484	24	440	0	0.0495868	0	T|0.750;C|0.250	0.250	strong	MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	2	NM_170606	exon14	c.A2304G	p.S768S	AAATGATGACTCT	.	scavenged	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6293696	6293696	+	Silent	SNP	C	C	G	rs1801213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	254	204	0	0.996078	0	C|0.294;G|0.706	0.706	strong	WFS1,NS,carcinoma,0,1	WFS1	71	1	NM_001145853	exon6	c.C684G	p.R228R	GAGGCGCATGCTG	.	PASS	Atlas-SNP
ECHDC3	79746	hgsc.bcm.edu	37	10	11797484	11797484	+	Silent	SNP	A	A	G	rs34878615	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	53	104	0	0.53	0	A|0.981;G|0.019	0.019	strong	.	ECHDC3	12	.	NM_024693	exon4	c.A468G	p.Q156Q	CTGTCAACTGGTT	.	PASS	Atlas-SNP
GPD2	2820	hgsc.bcm.edu	37	2	157425931	157425931	+	Missense_Mutation	SNP	A	A	C	rs35096779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	55	85	0	0.458333	0	A|0.963;C|0.037	0.037	strong	.	GPD2	59	.	NM_001083112	exon11	c.A1357C	p.K453Q	GCTGTCAAAACTC	.	PASS	Atlas-SNP
HEPACAM	220296	hgsc.bcm.edu	37	11	124794763	124794763	+	Silent	SNP	T	T	G	rs36089266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	57	127	0	0.513514	0	T|0.994;G|0.006	0.006	strong	HEPACAM,NS,carcinoma,-1,4	HEPACAM	64	4	NM_152722	exon2	c.A288C	p.R96R	ACGGTCTCGATAG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110489620	110489620	+	Silent	SNP	A	A	T	rs1783148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	62	0	0.517857	0	A|0.634;T|0.366	0.366	strong	.	PKHD1L1	522	.	NM_177531	exon53	c.A9084T	p.T3028T	AGCCACATATAAG	.	PASS	Atlas-SNP
BCAT1	586	hgsc.bcm.edu	37	12	25031515	25031515	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	9	112	0	0.0849057	0	.	.	none	.	BCAT1	44	.	NM_001178093	exon5	c.A495G	p.P165P	TGAATATGGGACC	.	PASS	Atlas-SNP
TMEM18	129787	hgsc.bcm.edu	37	2	677295	677295	+	Silent	SNP	C	C	T	rs3210390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	21	43	0	0.538462	0	C|0.864;T|0.136	0.136	strong	.	TMEM18	22	.	NM_152834	exon1	c.G51A	p.V17V	CGTGAGCACGGCT	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31362352	31362352	+	Missense_Mutation	SNP	C	C	T	rs2241493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	60	189	0	0.431655	0	C|0.189;T|0.811	0.811	strong	.	TRPM1	183	.	NM_001252020	exon3	c.G212A	p.S71N	TGTTTGCTTTCCT	.	PASS	Atlas-SNP
CST4	1472	hgsc.bcm.edu	37	20	23669488	23669488	+	Missense_Mutation	SNP	T	T	C	rs73902130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	144	217	0	0.525547	0	T|0.964;C|0.036	0.036	strong	CST4,colon,carcinoma,-1,1	CST4	37	1	NM_001899	exon1	c.A119G	p.N40S	TCATCATTGAGGT	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120575112	120575112	+	Silent	SNP	G	G	A	rs61740048	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	61	101	0	0.504132	0	G|0.997;A|0.003	0.003	strong	ENPP2_ENST00000522826,colon,carcinoma,0,7	ENPP2	254	7	NM_006209	exon25	c.C2562T	p.N854N	CTCCTCGTTGTCA	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29445425	29445425	+	Silent	SNP	G	G	A	rs56146053	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	57	125	0	0.413043	0	G|0.970;A|0.030	0.030	strong	ALK,colon,carcinoma,0,1	ALK	533	1	NM_004304	exon21	c.C3408T	p.S1136S	CATTCCGGACACC	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	125900104	125900104	+	Silent	SNP	A	A	T	rs143188464	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	81	157	0	0.519231	0	A|0.994;T|0.006	0.006	strong	.	TMEM132B	207	.	NM_052907	exon3	c.A972T	p.I324I	GAAGATAACGGCA	.	PASS	Atlas-SNP
AGFG1	3267	hgsc.bcm.edu	37	2	228398422	228398422	+	Silent	SNP	A	A	G	rs13015491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	83	123	0	0.560811	0	A|0.931;G|0.069	0.069	strong	AGFG1,NS,carcinoma,0,1	AGFG1	80	1	NM_001135187	exon8	c.A1044G	p.A348A	GACTGCAGACAAA	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69550080	69550080	+	Silent	SNP	A	A	G	rs5936873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	134	251	0	0.50566	0	A|0.938;0|0.003	.	strong	.	KIF4A	118	.	NM_012310	exon9	c.A969G	p.T323T	GGAAACATTAAAT	.	PASS	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	37	5	156742033	156742033	+	Silent	SNP	C	C	T	rs17054446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	49	116	0	0.471154	0	C|0.993;T|0.007	0.007	strong	.	CYFIP2	354	.	NM_001037332	exon13	c.C1287T	p.G429G	TCCTGGCACCGCG	.	PASS	Atlas-SNP
BTK	695	hgsc.bcm.edu	37	X	100617218	100617218	+	Silent	SNP	A	A	G	rs148358153	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	46	126	0	0.455446	0	A|0.993;G|0.007	0.007	strong	.	BTK	87	.	NM_000061	exon7	c.T531C	p.P177P	ACTCCCAGGTTTT	.	PASS	Atlas-SNP
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	120	0	0.504951	0	C|0.828;T|0.172	0.172	strong	.	GPD1L	25	.	NM_015141	exon4	c.C408T	p.D136D	TTCTGACATCATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513425	195513425	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	468	61	523	0	0.130342	0	.	.	none	MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G5026C	p.G1676R	CGTGACCGGTGGA	.	scavenged	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22847084	22847084	+	Missense_Mutation	SNP	G	G	T	rs71236901	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	465	330	526	2	0.709677	0.00380228	G|0.500;T|0.500	0.500	strong	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G613T	p.A205S	GGAAAAGCCTTTA	.	scavenged	Atlas-SNP
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117746	46117746	+	Silent	SNP	C	C	T	rs112431728	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	44	83	0	0.54321	0	C|0.994;T|0.006	0.006	strong	.	KRTAP10-12	21	.	NM_198699	exon1	c.C630T	p.P210P	CGTGCCCGTCCCC	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	406	192	431	0	0.472906	0	C|0.800;G|0.200	0.200	strong	.	CR1	354	.	NM_000651	exon41	c.C6830G	p.P2277R	GTGACCCTCAAGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413223	105413223	+	Silent	SNP	A	A	G	rs55797226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	282	262	3	0.989474	0.0114504	A|0.492;G|0.508	0.508	strong	AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.T8565C	p.D2855D	CTTAAGATCCCCT	.	scavenged	Atlas-SNP
SEC14L3	266629	hgsc.bcm.edu	37	22	30857448	30857448	+	Silent	SNP	A	A	G	rs5749104	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	61	132	0	0.432624	0	A|0.276;G|0.724	0.724	strong	.	SEC14L3	46	.	NM_174975	exon11	c.T930C	p.D310D	CGCACCATCAGAT	.	PASS	Atlas-SNP
R3HDM1	23518	hgsc.bcm.edu	37	2	136393658	136393658	+	Missense_Mutation	SNP	A	A	G	rs961360	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	36	121	0	0.4	0	A|0.689;G|0.311	0.311	strong	R3HDM1,NS,carcinoma,-2,1	R3HDM1	84	1	NM_015361	exon11	c.A808G	p.M270V	CTGTAGATGAGAA	.	PASS	Atlas-SNP
NIPBL	25836	hgsc.bcm.edu	37	5	36986297	36986297	+	Silent	SNP	A	A	G	rs1669445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	22	33	0	0.488889	0	A|0.961;G|0.039	0.039	strong	.	NIPBL	513	.	NM_015384	exon10	c.A3015G	p.L1005L	TGTGCTACAAAAA	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152732998	152732998	+	Missense_Mutation	SNP	C	C	T	rs140912923	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	55	72	0	0.5	0	C|0.994;T|0.006	0.006	strong	KPRP,NS,carcinoma,0,3	KPRP	152	3	NM_001025231	exon2	c.C934T	p.R312C	CCTCGCCGCCCCA	.	PASS	Atlas-SNP
KCTD19	146212	hgsc.bcm.edu	37	16	67324827	67324827	+	Silent	SNP	A	A	G	rs8053912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	92	0	0.46	0	A|0.834;G|0.166	0.166	strong	.	KCTD19	82	.	NM_001100915	exon15	c.T2628C	p.D876D	CCGGTCATCCTTG	.	PASS	Atlas-SNP
ZNF839	55778	hgsc.bcm.edu	37	14	102808273	102808273	+	Missense_Mutation	SNP	C	C	A	rs1053019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	183	0	0.480263	0	C|0.920;A|0.080	0.080	strong	.	ZNF839	41	.	NM_018335	exon8	c.C2541A	p.F847L	CCGGTTCCCCTGT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130095598	130095598	+	Missense_Mutation	SNP	A	A	G	rs115250607	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	73	165	0	0.417143	0	A|0.983;G|0.017	0.017	strong	.	COL6A5	205	.	NM_153264	exon3	c.A586G	p.S196G	GACCTCAGCACAT	.	PASS	Atlas-SNP
GPKOW	27238	hgsc.bcm.edu	37	X	48970655	48970655	+	Silent	SNP	C	C	T	rs34057359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	102	231	0	0.492754	0	C|0.873;T|0.127	0.127	strong	.	GPKOW	38	.	NM_015698	exon11	c.G1335A	p.R445R	CAAAGCCCGGCTC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100105782	100105782	+	Missense_Mutation	SNP	C	C	G	rs2061634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	52	97	0	0.565217	0	C|0.698;G|0.302	0.302	strong	.	.	.	.	NM_020893	exon19	c.C2567G	p.S856C	ACACTTCCAGTGC	.	PASS	Atlas-SNP
POC5	134359	hgsc.bcm.edu	37	5	75001590	75001590	+	Missense_Mutation	SNP	T	T	A	rs77025299	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	19	67	0	0.345455	0	T|0.965;A|0.035	0.035	strong	.	POC5	82	.	NM_001099271	exon4	c.A246T	p.E82D	TGCAGTTTCTCTT	.	PASS	Atlas-SNP
PTGIR	5739	hgsc.bcm.edu	37	19	47124742	47124742	+	Missense_Mutation	SNP	G	G	C	rs28590598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	59	114	0	0.513043	0	G|0.973;C|0.027	0.027	strong	.	PTGIR	31	.	NM_000960	exon3	c.C956G	p.S319W	GTCTGCGAGTCTC	.	PASS	Atlas-SNP
METAP2	10988	hgsc.bcm.edu	37	12	95879734	95879734	+	Silent	SNP	C	C	T	rs2305293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	72	0	0.528571	0	C|0.954;T|0.046	0.046	strong	.	METAP2	28	.	NM_006838	exon4	c.C405T	p.C135C	AGAATGCGAATAC	.	PASS	Atlas-SNP
UPK2	7379	hgsc.bcm.edu	37	11	118827655	118827655	+	Missense_Mutation	SNP	G	G	T	rs3886020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	57	82	0	0.6	0	A|0.000;C|0.008	.	strong	.	UPK2	12	.	NM_006760	exon2	c.G139T	p.A47S	CTGGTTGCCTTGC	.	PASS	Atlas-SNP
IFNA10	3446	hgsc.bcm.edu	37	9	21206919	21206919	+	Missense_Mutation	SNP	G	G	C	rs28368144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	324	340	1	0.993865	0.00294118	G|0.959;C|0.041	0.041	strong	IFNA10,NS,carcinoma,0,1	IFNA10	29	1	NM_002171	exon1	c.C178G	p.R60G	GGATTCGGAAATC	.	PASS	Atlas-SNP
TMPRSS12	283471	hgsc.bcm.edu	37	12	51236802	51236802	+	Missense_Mutation	SNP	T	T	C	rs10876100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	120	0	0.508475	0	T|0.715;C|0.285	0.285	strong	.	TMPRSS12	33	.	NM_182559	exon1	c.T55C	p.Y19H	CACTTATACTCAG	.	PASS	Atlas-SNP
ZNF224	7767	hgsc.bcm.edu	37	19	44611957	44611957	+	Silent	SNP	T	T	C	rs3746322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	72	160	1	0.566929	0.00625	T|0.850;C|0.150	0.150	strong	ZNF224,NS,carcinoma,0,1	ZNF224	70	1	NM_013398	exon6	c.T1644C	p.S548S	GAAGAGTTTTGGC	.	scavenged	Atlas-SNP
SOWAHC	65124	hgsc.bcm.edu	37	2	110372688	110372688	+	Missense_Mutation	SNP	C	C	G	rs72938294	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	40	68	0	0.481928	0	C|0.983;G|0.017	0.017	strong	.	.	.	.	NM_023016	exon1	c.C622G	p.L208V	CGTGACCTGGTGA	.	PASS	Atlas-SNP
UCP3	7352	hgsc.bcm.edu	37	11	73717263	73717263	+	Silent	SNP	G	G	A	rs2229706	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	39	66	0	0.557143	0	G|0.991;A|0.009	0.009	strong	.	UCP3	31	.	NM_003356	exon3	c.C288T	p.I96I	GAGGCCGATGCGG	.	PASS	Atlas-SNP
KIAA0226L	80183	hgsc.bcm.edu	37	13	46946157	46946157	+	Missense_Mutation	SNP	C	C	T	rs1408184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	88	197	0	0.511628	0	T|0.432;G|0.002	0.432	strong	.	KIAA0226L	63	.	NM_025113	exon3	c.G454A	p.G152R	AAATCCCAGGGCT	.	PASS	Atlas-SNP
DPY19L4	286148	hgsc.bcm.edu	37	8	95746883	95746883	+	Silent	SNP	G	G	A	rs113391412	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	67	90	0	0.587719	0	G|0.988;A|0.012	0.012	strong	.	DPY19L4	60	.	NM_181787	exon3	c.G153A	p.K51K	TGCAAAGATTTTC	.	PASS	Atlas-SNP
LRRC73	221424	hgsc.bcm.edu	37	6	43475195	43475195	+	Silent	SNP	G	G	A	rs61746927	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	25	50	0	0.480769	0	G|0.980;A|0.020	0.020	strong	.	.	.	.	NM_001012974	exon5	c.C879T	p.S293S	CTTACCGCTGGGG	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7880585	7880585	+	Silent	SNP	A	A	T	rs17031601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	113	183	0	0.530516	0	A|0.985;T|0.015	0.015	strong	.	PER3	95	.	NM_016831	exon15	c.A1818T	p.I606I	GTCCATAGACACA	.	PASS	Atlas-SNP
MARVELD2	153562	hgsc.bcm.edu	37	5	68715576	68715576	+	Missense_Mutation	SNP	G	G	A	rs140764671	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	43	69	0	0.488636	0	G|0.995;A|0.005	0.005	strong	.	MARVELD2	49	.	NM_001244734	exon2	c.G364A	p.A122T	TCTCCAGCAAGAC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057943	46057943	+	Silent	SNP	C	C	T	rs77446663	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	456	117	293	0	0.256579	0	C|0.982;T|0.018	0.018	strong	KRTAP10-10,NS,carcinoma,+2,1	KRTAP10-10	37	1	NM_181688	exon1	c.C609T	p.C203C	CTGCTGCGTGCCC	.	PASS	Atlas-SNP
APP	351	hgsc.bcm.edu	37	21	27326977	27326977	+	Silent	SNP	A	A	G	rs45537238	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	81	140	0	0.529412	0	A|0.977;G|0.023	0.023	strong	.	APP	90	.	NM_000484	exon13	c.T1614C	p.Y538Y	GCGCTCATAAATC	.	PASS	Atlas-SNP
PCDHA5	56143	hgsc.bcm.edu	37	5	140202418	140202418	+	Missense_Mutation	SNP	C	C	A	rs61735511	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	86	161	0	0.511905	0	C|0.940;A|0.060	0.060	strong	PCDHA5_ENST00000529859,NS,carcinoma,-1,2	PCDHA5	361	2	NM_018908	exon1	c.C1058A	p.T353N	TAACCACCCTTTT	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	56423968	56423968	+	Missense_Mutation	SNP	A	A	C	rs11004439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	39	61	0	0.541667	0	A|0.797;C|0.203	0.203	strong	.	PCDH15	1715	.	NM_001142763	exon2	c.T55G	p.S19A	AGAGAGAGCCCAG	.	PASS	Atlas-SNP
GGN	199720	hgsc.bcm.edu	37	19	38876944	38876944	+	Missense_Mutation	SNP	C	C	T	rs151268424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	10	33	0	0.3125	0	C|0.996;T|0.004	0.004	strong	.	GGN	50	.	NM_152657	exon3	c.G958A	p.E320K	ACCCTTCGCCGTC	.	PASS	Atlas-SNP
FAM45A	404636	hgsc.bcm.edu	37	10	120883045	120883045	+	Missense_Mutation	SNP	A	A	G	rs74157632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	97	0	1	0	A|0.934;G|0.066	0.066	strong	.	FAM45A	30	.	NM_207009	exon6	c.A658G	p.N220D	CACCTCAACGCCG	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136521749	136521749	+	Silent	SNP	G	G	A	rs78516399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	18	52	0	0.580645	0	G|0.993;A|0.007	0.007	strong	.	DBH	86	.	NM_000787	exon10	c.G1539A	p.Q513Q	CCTGCAGAAGTAC	.	PASS	Atlas-SNP
OTOL1	131149	hgsc.bcm.edu	37	3	161221262	161221262	+	Silent	SNP	T	T	A	rs113998122	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	60	108	0	0.560748	0	T|0.990;A|0.010	0.010	strong	.	OTOL1	63	.	NM_001080440	exon4	c.T966A	p.T322T	CCCCACTGGGAAG	.	PASS	Atlas-SNP
PROK2	60675	hgsc.bcm.edu	37	3	71821933	71821933	+	Missense_Mutation	SNP	G	G	T	rs60239864	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	94	121	0	0.618421	0	G|0.994;T|0.006	0.006	strong	.	PROK2	13	.	NM_001126128	exon4	c.C332A	p.P111Q	AAGCCTGGCAGAC	.	PASS	Atlas-SNP
ZNF425	155054	hgsc.bcm.edu	37	7	148801337	148801337	+	Silent	SNP	T	T	C	rs12704061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	39	87	0	0.397959	0	T|0.773;C|0.227	0.227	strong	.	ZNF425	99	.	NM_001001661	exon4	c.A1626G	p.T542T	GTGCTCTGTGAGA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103386496	103386496	+	Silent	SNP	T	T	G	rs7988702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	129	227	0	0.490494	0	T|0.974;G|0.026	0.026	strong	.	.	.	.	NM_001146197	exon4	c.A16551C	p.P5517P	TGACATTGGTGAA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152660451	152660451	+	Silent	SNP	G	G	A	rs71575926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	41	81	0	0.650794	0	G|0.895;A|0.105	0.105	strong	.	SYNE1	3227	.	NM_182961	exon75	c.C12276T	p.L4092L	GCAAAGGAGATCT	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	711396	711396	+	Missense_Mutation	SNP	C	C	G	rs28374506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	73	90	0	0.5	0	C|0.902;G|0.098	0.098	strong	.	KANK1	231	.	NM_001256876	exon7	c.C630G	p.H210Q	CAAGCACCAGCTT	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	19	62	0	0.463415	0	T|0.708;C|0.292	0.292	strong	KIF26A,NS,carcinoma,0,1	KIF26A	84	1	NM_015656	exon12	c.T2487C	p.G829G	CAAGGGTCCCCGA	.	PASS	Atlas-SNP
SLC22A5	6584	hgsc.bcm.edu	37	5	131729935	131729935	+	Missense_Mutation	SNP	C	C	T	rs11568525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	55	168	0	0.395683	0	C|0.972;T|0.028	0.028	strong	.	SLC22A5	34	.	NM_003060	exon10	c.C1645T	p.P549S	GAAAGGCCCACAA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228473959	228473959	+	Missense_Mutation	SNP	T	T	G	rs202022683	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	101	192	2	0.495098	0.0104167	.	.	weak	OBSCN_ENST00000570156,NS,haematopoietic_neoplasm,0,4	OBSCN	2142	4	NM_001271223	exon39	c.T10472G	p.V3491G	ACCACGTGCTGAC	.	scavenged	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30795412	30795412	+	Missense_Mutation	SNP	A	A	G	rs6970210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	45	85	0	0.584416	0	A|0.954;G|0.046	0.046	strong	.	INMT	38	.	NM_006774	exon3	c.A737G	p.N246S	TCACCAATGCTGC	.	PASS	Atlas-SNP
FBP2	8789	hgsc.bcm.edu	37	9	97349591	97349591	+	Silent	SNP	G	G	T	rs2280301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	55	78	0	0.611111	0	G|0.890;T|0.110	0.110	strong	.	FBP2	26	.	NM_003837	exon2	c.C331A	p.R111R	GCACCCGCTTCTC	.	PASS	Atlas-SNP
TBC1D10A	83874	hgsc.bcm.edu	37	22	30700607	30700607	+	Silent	SNP	T	T	G	rs4823089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	53	99	0	0.456897	0	T|0.801;G|0.199	0.199	strong	.	TBC1D10A	49	.	NM_001204240	exon2	c.A243C	p.V81V	CAGGGGTACTTCC	.	PASS	Atlas-SNP
NIPAL4	348938	hgsc.bcm.edu	37	5	156899925	156899925	+	Missense_Mutation	SNP	C	C	T	rs61743233	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	22	37	0	0.478261	0	C|0.922;T|0.078	0.078	strong	.	NIPAL4	48	.	NM_001099287	exon6	c.C1358T	p.S453L	GCACCTCATCACC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376207	52376207	+	Missense_Mutation	SNP	G	G	A	rs9807842	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	89	0	0.506024	0	G|0.891;A|0.109	0.109	strong	ZNF577,NS,lymphoid_neoplasm,+1,1	ZNF577	63	1	NM_032679	exon7	c.C1036T	p.R346C	GAGTACGCTGATG	.	PASS	Atlas-SNP
PLK4	10733	hgsc.bcm.edu	37	4	128808620	128808620	+	Silent	SNP	A	A	T	rs112831813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	482	238	406	0	0.493776	0	A|0.993;T|0.007	0.007	strong	.	PLK4	65	.	NM_014264	exon6	c.A1428T	p.V476V	AACCGTACAACAG	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	37	22	28193097	28193097	+	Silent	SNP	C	C	T	rs45471598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	18	22	0	0.473684	0	C|0.962;T|0.038	0.038	strong	MN1,colon,carcinoma,0,1	MN1	122	1	NM_002430	exon1	c.G3435A	p.P1145P	GGGTGGCGGGGCG	.	PASS	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	37	13	33016660	33016660	+	Missense_Mutation	SNP	C	C	T	rs17077568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	45	129	0	0.432692	0	C|0.928;T|0.072	0.072	strong	.	N4BP2L2	90	.	NM_033111	exon7	c.G2014A	p.E672K	GTTCTTCCCATCT	.	PASS	Atlas-SNP
CASP10	843	hgsc.bcm.edu	37	2	202074098	202074098	+	Missense_Mutation	SNP	G	G	A	rs13010627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	79	131	0	0.560284	0	G|0.963;A|0.037	0.037	strong	.	CASP10	95	.	NM_032977	exon9	c.G1228A	p.V410I	CCTTCCGTATCCA	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30795448	30795448	+	Missense_Mutation	SNP	G	G	A	rs6970605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	18	43	0	0.486486	0	G|0.956;A|0.044	0.044	strong	.	INMT	38	.	NM_006774	exon3	c.G773A	p.R258H	TGGCTCGCAAGAA	.	PASS	Atlas-SNP
PTPLAD1	51495	hgsc.bcm.edu	37	15	65856653	65856653	+	Silent	SNP	G	G	A	rs11539008	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	82	146	0	0.503067	0	G|0.872;A|0.128	0.128	strong	.	PTPLAD1	23	.	NM_016395	exon7	c.G633A	p.T211T	CACTACGTCACCG	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	712066	712066	+	Silent	SNP	A	A	C	rs34680571	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	50	93	0	0.390625	0	T|0.000;C|0.069;A|0.931	0.069	strong	.	KANK1	231	.	NM_001256876	exon7	c.A1300C	p.R434R	GAGATGAGAAATT	.	PASS	Atlas-SNP
CHD7	55636	hgsc.bcm.edu	37	8	61765560	61765560	+	Silent	SNP	G	G	A	rs2068096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	132	229	0	0.505747	0	G|0.886;A|0.114	0.114	strong	.	CHD7	534	.	NM_017780	exon31	c.G6276A	p.E2092E	GTGGGAGTGTGGA	.	PASS	Atlas-SNP
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	31	18	0	1	0	T|0.727;C|0.273	0.273	strong	.	ADAT3	15	.	NM_138422	exon2	c.T888C	p.T296T	GTGCACTGGCTAC	.	PASS	Atlas-SNP
DPF2	5977	hgsc.bcm.edu	37	11	65113459	65113459	+	Silent	SNP	G	G	T	rs61736579	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	51	78	0	0.495146	0	G|0.989;T|0.011	0.011	strong	.	DPF2	54	.	NM_006268	exon8	c.G834T	p.G278G	CCTGGGGGACTCA	.	PASS	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31414851	31414851	+	Missense_Mutation	SNP	T	T	C	rs7587515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	59	127	0	0.433824	0	T|0.900;C|0.100	0.100	strong	.	CAPN14	36	.	NM_001145122	exon11	c.A1228G	p.R410G	GGCACCTGTGCCT	.	PASS	Atlas-SNP
SMAD6	4091	hgsc.bcm.edu	37	15	67073549	67073549	+	Silent	SNP	C	C	T	rs12591946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	31	35	0	0.525424	0	C|0.982;T|0.018	0.018	strong	.	SMAD6	14	.	NM_005585	exon4	c.C1167T	p.F389F	CGGCTTCGGCATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508367	195508367	+	Missense_Mutation	SNP	G	G	A	rs55917029	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	387	85	453	0	0.219638	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C10084T	p.P3362S	TGACAGGAAGAGG	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22575504	22575504	+	Missense_Mutation	SNP	C	C	G	rs116270361	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	152	280	0	0.529617	0	C|0.976;G|0.024	0.024	strong	.	ZNF98	230	.	NM_001098626	exon4	c.G533C	p.G178A	TTCTTTCCAGTAT	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124174062	124174062	+	Silent	SNP	C	C	T	rs61747979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	108	0	0.490385	0	C|0.969;T|0.031	0.031	strong	.	KALRN	556	.	NM_003947	exon22	c.C3585T	p.A1195A	GCTGGCCGATAGC	.	PASS	Atlas-SNP
ADARB2	105	hgsc.bcm.edu	37	10	1405835	1405835	+	Silent	SNP	G	G	A	rs35398040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	74	0	0.991304	0	G|0.981;A|0.019	0.019	strong	.	ADARB2	95	.	NM_018702	exon3	c.C465T	p.V155V	CGCGAAGACCGGG	.	PASS	Atlas-SNP
AMHR2	269	hgsc.bcm.edu	37	12	53823307	53823307	+	Silent	SNP	G	G	A	rs784890	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	142	113	0	1	0	G|0.856;A|0.144	0.144	strong	.	AMHR2	61	.	NM_020547	exon8	c.G1038A	p.S346S	TGGATCGTGTGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505774	195505774	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	10	238	2	0.0478469	0.00840336	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12677A	p.P4226H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs7260508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	36	0	1	0	C|0.620;T|0.380	0.380	strong	PSG8_ENST00000404209,NS,carcinoma,-1,2	PSG8	101	2	NM_001130168	exon1	c.G35A	p.R12H	GTGATGCGCTGTG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2162887	2162887	+	Silent	SNP	A	A	G	rs2369068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	19	49	0	0.372549	0	A|0.796;G|0.204	0.204	strong	.	PKD1	184	.	NM_000296	exon13	c.T3063C	p.G1021G	CTGCAGACCCTGC	.	PASS	Atlas-SNP
SYNGR3	9143	hgsc.bcm.edu	37	16	2042086	2042086	+	Missense_Mutation	SNP	G	G	A	rs199784173	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	10	5	0	0.909091	0	G|0.994;A|0.006	0.006	strong	.	SYNGR3	10	.	NM_004209	exon2	c.G211A	p.G71S	CGCTTCGGCGTCG	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239162182	239162182	+	Missense_Mutation	SNP	C	C	T	rs55704277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	57	88	0	0.59375	0	C|0.962;T|0.038	0.038	strong	.	PER2	85	.	NM_022817	exon19	c.G2482A	p.A828T	CTGTGGCGTTCAA	.	PASS	Atlas-SNP
C17orf64	124773	hgsc.bcm.edu	37	17	58506785	58506785	+	Silent	SNP	G	G	T	rs9913666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	62	104	0	0.488189	0	G|0.912;T|0.088	0.088	strong	.	C17orf64	19	.	NM_181707	exon5	c.G492T	p.L164L	CAGTCTGCCCAAG	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65249052	65249052	+	Missense_Mutation	SNP	C	C	G	rs17245552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	84	163	0	0.444444	0	C|0.925;G|0.075	0.075	strong	.	SPTB	378	.	NM_001024858	exon19	c.G4222C	p.G1408R	CCTTGCCCGGGTC	.	PASS	Atlas-SNP
PRLR	5618	hgsc.bcm.edu	37	5	35072712	35072712	+	Missense_Mutation	SNP	T	T	G	rs72478580	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	142	289	0	0.520147	0	T|0.981;G|0.019	0.019	strong	.	PRLR	90	.	NM_000949	exon6	c.A508C	p.I170L	ATCGAATTTCATA	.	PASS	Atlas-SNP
ENTPD4	9583	hgsc.bcm.edu	37	8	23299225	23299225	+	Missense_Mutation	SNP	C	C	T	rs34849865	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	39	55	0	0.661017	0	C|0.993;T|0.007	0.007	strong	.	ENTPD4	56	.	NM_004901	exon8	c.G739A	p.V247I	CCACAACGGCCTC	.	PASS	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61587053	61587053	+	Missense_Mutation	SNP	G	G	A	rs17072146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	19	72	0	0.339286	0	G|0.856;A|0.144	0.144	strong	.	SERPINB10	53	.	NM_005024	exon4	c.G404A	p.G135D	ATTTTGGTGCAGA	.	PASS	Atlas-SNP
IPO13	9670	hgsc.bcm.edu	37	1	44424525	44424525	+	Silent	SNP	G	G	A	rs74073335	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	96	165	0	0.578313	0	G|0.991;A|0.009	0.009	strong	.	IPO13	86	.	NM_014652	exon11	c.G1992A	p.E664E	CCCTGAGCTTCGG	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	7023678	7023678	+	Missense_Mutation	SNP	G	G	A	rs1131197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	121	277	0	0.461832	0	0|0.023;T|0.097	.	strong	.	HDHD1	21	.	NM_001135565	exon3	c.C332T	p.T111M	GCAGCCGTGGGGA	.	PASS	Atlas-SNP
PF4V1	5197	hgsc.bcm.edu	37	4	74719624	74719624	+	Silent	SNP	C	C	G	rs34446485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	40	172	0	0.266667	0	C|0.981;G|0.019	0.019	strong	PF4V1,NS,carcinoma,0,1	PF4V1	8	1	NM_002620	exon2	c.C225G	p.L75L	CCAACTCATGTGA	.	scavenged	Atlas-SNP
BAALC	79870	hgsc.bcm.edu	37	8	104240275	104240275	+	Missense_Mutation	SNP	G	G	C	rs34542607	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	47	72	0	0.580247	0	G|0.971;C|0.029	0.029	strong	.	BAALC	15	.	NM_024812	exon3	c.G386C	p.S129T	CAGATAGCATCCA	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108029091	108029091	+	Silent	SNP	G	G	A	rs3734753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	65	121	0	0.439189	0	G|0.941;A|0.059	0.059	strong	.	SCML4	65	.	NM_198081	exon7	c.C1098T	p.H366H	CTCCACGTGAGGC	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30492237	30492237	+	Missense_Mutation	SNP	C	C	T	rs2075820	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	56	0	0.45	0	T|0.303;G|0.002	0.303	strong	.	NOD1	79	.	NM_006092	exon6	c.G796A	p.E266K	CCTCCTCGGGGTC	.	PASS	Atlas-SNP
BHLHB9	80823	hgsc.bcm.edu	37	X	102004046	102004046	+	Silent	SNP	G	G	A	rs17003869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	412	145	322	0	0.351942	0	0|0.003;A|0.015	0.015	strong	.	BHLHB9	60	.	NM_001142530	exon2	c.G123A	p.R41R	GACCAGGGCCAAA	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25670873	25670873	+	Silent	SNP	A	A	G	rs77142265		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	9	147	1	0.0439024	0.00680272	A|0.500;G|0.500	0.500	weak	PABPC3,colon,carcinoma,+2,1	PABPC3	129	1	NM_030979	exon1	c.A537G	p.R179R	AGAACGAGAAGCT	.	scavenged	Atlas-SNP
ZBTB40	9923	hgsc.bcm.edu	37	1	22816687	22816687	+	Silent	SNP	A	A	G	rs115103344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	62	107	0	0.508197	0	A|0.993;G|0.007	0.007	strong	.	ZBTB40	87	.	NM_001083621	exon3	c.A246G	p.K82K	GGGCAAACTACCT	.	PASS	Atlas-SNP
RGCC	28984	hgsc.bcm.edu	37	13	42032572	42032572	+	Silent	SNP	T	T	C	rs7136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	17	41	0	0.435897	0	T|0.426;C|0.574	0.574	strong	.	.	.	.	NM_014059	exon2	c.T201C	p.S67S	CGCCAGTGTCAGC	.	PASS	Atlas-SNP
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	17	37	1	0.425	0.027027	A|0.422;C|0.000;G|0.578	0.422	strong	SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	NM_152346	exon8	c.C927T	p.A309A	ACCTGCGGCATCC	.	scavenged	Atlas-SNP
FAM124A	220108	hgsc.bcm.edu	37	13	51855114	51855114	+	Missense_Mutation	SNP	G	G	T	rs74087446	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	51	113	0	0.459459	0	G|0.975;T|0.026	0.026	strong	.	FAM124A	61	.	NM_145019	exon5	c.G1471T	p.A491S	CACTGGGCAGCTC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179560847	179560847	+	Missense_Mutation	SNP	C	C	T	rs73038324	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	119	242	0	0.508547	0	C|0.968;T|0.032	0.032	strong	.	TTN	18412	.	NM_001267550	exon114	c.G30952A	p.E10318K	GTTCTTCGAAAGA	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	37	15	70968850	70968850	+	Silent	SNP	A	A	G	rs61741196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	30	50	0	0.576923	0	A|0.989;G|0.011	0.011	strong	.	UACA	235	.	NM_018003	exon13	c.T1113C	p.N371N	AAATCTATTTTTC	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169342926	169342926	+	Silent	SNP	G	G	A	rs73863330	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	62	110	0	0.584906	0	G|0.994;A|0.006	0.006	strong	DDX60L,NS,carcinoma,-1,1	DDX60L	116	1	NM_001012967	exon17	c.C2379T	p.Y793Y	TGCAACGTACACA	.	PASS	Atlas-SNP
CCDC105	126402	hgsc.bcm.edu	37	19	15133787	15133787	+	Silent	SNP	C	C	A	rs10424547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	70	189	0	0.419162	0	C|0.749;A|0.251	0.251	strong	.	CCDC105	53	.	NM_173482	exon7	c.C1356A	p.I452I	GAACATCGGGCAT	.	PASS	Atlas-SNP
SNX31	169166	hgsc.bcm.edu	37	8	101608919	101608919	+	Missense_Mutation	SNP	T	T	C	rs2248609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	61	143	0	0.516949	0	T|0.613;C|0.387	0.387	strong	.	SNX31	66	.	NM_152628	exon10	c.A926G	p.Q309R	ATGTCCTGGGTCT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92590448	92590448	+	Missense_Mutation	SNP	A	A	G	rs4753069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	121	139	1	0.991803	0.00719424	A|0.184;G|0.816	0.816	strong	.	FAT3	1822	.	NM_001008781	exon19	c.A11434G	p.S3812G	TGTGTCAGTTATG	.	PASS	Atlas-SNP
HIVEP1	3096	hgsc.bcm.edu	37	6	12124587	12124587	+	Missense_Mutation	SNP	C	C	G	rs2228212	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	44	85	0	0.571429	0	C|0.714;G|0.286	0.286	strong	.	HIVEP1	242	.	NM_002114	exon4	c.C4559G	p.A1520G	TCCATGCACCGCC	.	PASS	Atlas-SNP
DAW1	164781	hgsc.bcm.edu	37	2	228750106	228750106	+	Missense_Mutation	SNP	C	C	T	rs11894733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	28	70	0	0.41791	0	C|0.939;T|0.061	0.061	strong	.	.	.	.	NM_178821	exon2	c.C80T	p.T27I	TAAAGACTAAGTC	.	PASS	Atlas-SNP
MEI1	150365	hgsc.bcm.edu	37	22	42191540	42191540	+	Silent	SNP	C	C	T	rs6002488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	88	0	0.521277	0	C|0.830;T|0.170	0.170	strong	.	MEI1	87	.	NM_152513	exon29	c.C3660T	p.F1220F	CTTCTTCCAGCAG	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124862514	124862514	+	Silent	SNP	A	A	G	rs6590113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	19	49	0	0.475	0	A|0.728;G|0.272	0.272	strong	.	CCDC15	134	.	NM_025004	exon10	c.A2070G	p.E690E	GAGAGAAGAATTG	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133900495	133900495	+	Missense_Mutation	SNP	G	G	A	rs16904774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	60	116	0	0.434783	0	G|0.957;A|0.043	0.043	strong	.	TG	416	.	NM_003235	exon10	c.G2443A	p.G815R	GCTTCCGGAAACT	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215960167	215960167	+	Missense_Mutation	SNP	T	T	G	rs10864198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	154	0	1	0	T|0.409;G|0.591	0.591	strong	.	USH2A	1168	.	NM_206933	exon52	c.A10232C	p.E3411A	CAATGTTCTGTGG	.	PASS	Atlas-SNP
ZBTB11	27107	hgsc.bcm.edu	37	3	101370091	101370091	+	Silent	SNP	C	C	T	rs34525894	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	95	209	0	0.429864	0	C|0.948;T|0.052	0.052	strong	.	ZBTB11	77	.	NM_014415	exon11	c.G3081A	p.Q1027Q	TCCTTGCTGTTGT	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113729414	113729414	+	Missense_Mutation	SNP	C	C	T	rs74926660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	41	81	0	0.493976	0	C|0.990;T|0.010	0.010	strong	.	MCF2L	182	.	NM_001112732	exon11	c.C1219T	p.R407W	GAGCTCCGGCACC	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53298675	53298675	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	4	104	0	0.0310078	0	.	.	none	KRT8,NS,carcinoma,0,5	KRT8	41	5	NM_001256282	exon2	c.T175G	p.S59A	TGCGGGAACCGGG	.	scavenged	Atlas-SNP
SPHK2	56848	hgsc.bcm.edu	37	19	49132646	49132646	+	Silent	SNP	G	G	A	rs75629654	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	29	0	1	0	G|0.940;A|0.060	0.060	strong	.	SPHK2	62	.	NM_020126	exon7	c.G1581A	p.L527L	CCCGCTGCCCCCA	.	PASS	Atlas-SNP
GHR	2690	hgsc.bcm.edu	37	5	42719239	42719239	+	Missense_Mutation	SNP	A	A	C	rs6180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	109	243	0	0.422481	0	A|0.548;C|0.448	0.448	strong	.	GHR	94	.	NM_001242399	exon10	c.A1651C	p.I551L	AAGTGCATCCCTG	.	PASS	Atlas-SNP
GRIK5	2901	hgsc.bcm.edu	37	19	42560893	42560893	+	Missense_Mutation	SNP	G	G	A	rs139340543	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	54	126	0	0.442623	0	G|0.999;A|0.001	0.001	strong	.	GRIK5	220	.	NM_002088	exon7	c.C824T	p.P275L	TAGAAGGGGTGGG	.	PASS	Atlas-SNP
BAG6	7917	hgsc.bcm.edu	37	6	31611746	31611746	+	Silent	SNP	G	G	A	rs7770976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	72	0	0.478873	0	G|0.940;A|0.060	0.060	strong	.	BAG6	73	.	NM_004639	exon13	c.C1587T	p.A529A	CAGACCGGCGCCC	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14397238	14397238	+	Silent	SNP	T	T	C	rs30774	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	144	133	0	0.993103	0	T|0.590;C|0.410	0.410	strong	TRIO,NS,carcinoma,0,1	TRIO	305	1	NM_007118	exon29	c.T4398C	p.D1466D	CAATGATGCCATG	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43188940	43188940	+	Silent	SNP	C	C	T	rs6917902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	69	155	0	0.485915	0	C|0.767;T|0.233	0.233	strong	.	CUL9	248	.	NM_015089	exon34	c.C6633T	p.D2211D	GGTCGACGACGGT	.	PASS	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55307501	55307501	+	Silent	SNP	A	A	G	rs41297871	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	87	0	0.423077	0	A|0.737;G|0.263	0.263	strong	.	C1orf177	36	.	NM_001110533	exon10	c.A1212G	p.G404G	TAAGGGAAAGTGC	.	PASS	Atlas-SNP
C20orf196	149840	hgsc.bcm.edu	37	20	5843812	5843812	+	Silent	SNP	T	T	C	rs1699233	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	103	112	0	0.980952	0	T|0.525;C|0.475	0.475	strong	.	C20orf196	17	.	NM_152504	exon3	c.T321C	p.G107G	GTTTGGTCATCCA	.	PASS	Atlas-SNP
OR1E1	8387	hgsc.bcm.edu	37	17	3301293	3301293	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	5	176	0	0.0214592	0	.	.	none	OR1E1,caecum,carcinoma,+1,1	OR1E1	37	1	NM_003553	exon1	c.C412T	p.P138S	GCATGGGGCTCAT	.	scavenged	Atlas-SNP
C10orf25	220979	hgsc.bcm.edu	37	10	45496126	45496126	+	Missense_Mutation	SNP	G	G	A	rs41301609	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	95	0	0.486486	0	G|0.948;A|0.052	0.052	strong	.	C10orf25	11	.	NM_001039380	exon1	c.C182T	p.P61L	ATTTGTGGAAAGT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17087509	17087509	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	896	71	713	0	0.0792411	0	.	.	none	.	.	.	.	NM_001271733	exon2	c.G156A	p.Q52Q	ATCCTCCTGCCAA	.	PASS	Atlas-SNP
NACA	4666	hgsc.bcm.edu	37	12	57114869	57114869	+	Missense_Mutation	SNP	T	T	C	rs17118953	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	48	99	0	0.475248	0	T|0.920;C|0.080	0.080	strong	.	NACA	131	.	NM_001113203	exon3	c.A445G	p.K149E	AACTCTTCTGAAC	.	PASS	Atlas-SNP
F2RL3	9002	hgsc.bcm.edu	37	19	17001240	17001240	+	Silent	SNP	C	C	T	rs2227347	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	101	0	0.484127	0	C|0.971;A|0.000	.	strong	.	F2RL3	20	.	NM_003950	exon2	c.C966T	p.Y322Y	TGCCTACGTGCCC	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10639222	10639222	+	Silent	SNP	G	G	A	rs1801138	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	76	131	0	0.510067	0	G|0.841;A|0.159	0.159	strong	.	JAG1	213	.	NM_000214	exon4	c.C588T	p.C196C	CTTATTGCAGCCA	.	PASS	Atlas-SNP
TAF1	6872	hgsc.bcm.edu	37	X	70627477	70627477	+	Silent	SNP	G	G	A	rs7050748	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	316	136	316	0	0.43038	0	0|0.003;A|0.098	0.098	strong	.	TAF1	439	.	NM_004606	exon27	c.G4221A	p.S1407S	GCTGTCGTCCATC	.	PASS	Atlas-SNP
NCLN	56926	hgsc.bcm.edu	37	19	3207646	3207646	+	Missense_Mutation	SNP	A	A	G	rs2288949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	76	138	0	0.469136	0	A|0.876;G|0.124	0.124	strong	.	NCLN	27	.	NM_020170	exon15	c.A1652G	p.K551R	TCTACAAGACCGT	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60776307	60776307	+	Silent	SNP	G	G	C	rs79848107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	76	0	0.489583	0	G|0.870;C|0.130	0.130	strong	CD6_ENST00000313421,NS,carcinoma,0,2	CD6	122	2	NM_006725	exon4	c.G771C	p.A257A	GGGCGCGGTGTGC	.	PASS	Atlas-SNP
TTC23L	153657	hgsc.bcm.edu	37	5	34840841	34840841	+	Missense_Mutation	SNP	A	A	G	rs6451173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	84	134	0	0.47191	0	A|0.457;G|0.543	0.543	strong	.	TTC23L	47	.	NM_144725	exon2	c.A65G	p.H22R	GCTTCCATATGTA	.	PASS	Atlas-SNP
KIT	3815	hgsc.bcm.edu	37	4	55602765	55602765	+	Silent	SNP	G	G	C	rs3733542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	31	106	0	0.326316	0	G|0.828;C|0.172	0.172	strong	KIT,colon,carcinoma,0,10	KIT	7396	10	NM_000222	exon18	c.G2586C	p.L862L	GGAGCTGTTCTCT	.	PASS	Atlas-SNP
RAC2	5880	hgsc.bcm.edu	37	22	37622815	37622815	+	Silent	SNP	A	A	G	rs1064498	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	78	0	0.431373	0	T|0.000;G|0.229;A|0.771	0.229	strong	.	RAC2	22	.	NM_002872	exon6	c.T477C	p.A159A	GGTGAGAGCTGAG	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1119019	1119019	+	Silent	SNP	C	C	T	rs2074920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	25	0	1	0	C|0.519;T|0.481	0.481	strong	.	SBNO2	112	.	NM_014963	exon14	c.G1518A	p.A506A	CAGGGCCGCGCGG	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	334890	334890	+	Missense_Mutation	SNP	G	G	A	rs419949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	41	81	0	0.525641	0	G|0.849;A|0.151	0.151	strong	.	PDIA2	51	.	NM_006849	exon4	c.G553A	p.E185K	CAGGACGAGGACG	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7673922	7673922	+	Silent	SNP	A	A	T	rs9910089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	67	145	0	0.540323	0	A|0.949;T|0.051	0.051	strong	.	DNAH2	498	.	NM_020877	exon25	c.A4146T	p.I1382I	CGACATAGTACCC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489707	32489707	+	Silent	SNP	A	A	C	rs41559714	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	20	23	0	0.571429	0	.	.	weak	.	HLA-DRB5	31	.	NM_002125	exon2	c.T345G	p.G115G	GCTCTCACCAACC	.	PASS	Atlas-SNP
ZNF74	7625	hgsc.bcm.edu	37	22	20760106	20760106	+	Silent	SNP	C	C	T	rs2229316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	39	0	1	0	C|0.982;T|0.018	0.018	strong	.	ZNF74	54	.	NM_003426	exon5	c.C783T	p.S261S	GAGCTCCTCCCTC	.	PASS	Atlas-SNP
PLEKHA5	54477	hgsc.bcm.edu	37	12	19440471	19440471	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	83	175	0	0.51875	0	.	.	none	.	PLEKHA5	198	.	NM_001256470	exon13	c.A1844G	p.Q615R	GTCCCCAGAGCCT	.	PASS	Atlas-SNP
C3orf43	255798	hgsc.bcm.edu	37	3	196234777	196234777	+	Missense_Mutation	SNP	A	A	G	rs187809363	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	97	187	0	0.466346	0	A|0.999;G|0.001	0.001	strong	C3orf43,NS,malignant_melanoma,+1,1	C3orf43	25	1	NM_001077657	exon3	c.T626C	p.I209T	GATGGTATCAACT	.	PASS	Atlas-SNP
SRPK3	26576	hgsc.bcm.edu	37	X	153049535	153049535	+	Silent	SNP	A	A	G	rs4898444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	57	110	0	0.542857	0	A|0.477;G|0.523	0.523	strong	.	SRPK3	63	.	NM_014370	exon10	c.A1014G	p.P338P	CGCCCCAGGGGGC	.	PASS	Atlas-SNP
SDR42E1	93517	hgsc.bcm.edu	37	16	82033612	82033612	+	Missense_Mutation	SNP	T	T	C	rs16956174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	148	0	0.992754	0	T|0.823;C|0.177	0.177	strong	.	SDR42E1	26	.	NM_145168	exon3	c.A286G	p.K96E	CTTCTTTGATCAG	.	PASS	Atlas-SNP
RABEPK	10244	hgsc.bcm.edu	37	9	127975654	127975654	+	Missense_Mutation	SNP	C	C	T	rs1128362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	21	66	0	0.272727	0	C|0.880;T|0.120	0.120	strong	.	RABEPK	46	.	NM_005833	exon4	c.C217T	p.H73Y	GGAAAACACCAGT	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70218890	70218890	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	5	91	0	0.0485437	0	.	.	none	DNA2L,NS,carcinoma,-1,4	DNA2	76	4	NM_001080449	exon5	c.G690A	p.S230S	GTCAGTCGAAGTG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37173977	37173977	+	Silent	SNP	A	A	G	rs61746147	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	43	85	0	0.477778	0	A|0.974;G|0.026	0.026	strong	.	C5orf42	422	.	NM_023073	exon32	c.T6051C	p.A2017A	TTGTGAAGCAACA	.	PASS	Atlas-SNP
GSN	2934	hgsc.bcm.edu	37	9	124091256	124091256	+	Missense_Mutation	SNP	G	G	T	rs9696578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	25	38	0	0.510204	0	G|0.993;T|0.007	0.007	strong	.	GSN	81	.	NM_000177	exon14	c.G2003T	p.R668L	CTCCTCGCCTCTT	.	PASS	Atlas-SNP
POLR2A	5430	hgsc.bcm.edu	37	17	7400815	7400815	+	Silent	SNP	T	T	C	rs2228128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	57	154	0	0.416058	0	T|0.818;C|0.182	0.182	strong	.	POLR2A	157	.	NM_000937	exon6	c.T960C	p.N320N	GGACAATGAGCTG	.	PASS	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53005004	53005004	+	Missense_Mutation	SNP	T	T	C	rs607426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	97	218	0	0.459716	0	T|0.980;C|0.020	0.020	strong	.	KRT73	101	.	NM_175068	exon6	c.A1094G	p.E365G	ACACTCTCAATCT	.	PASS	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2380323	2380323	+	Silent	SNP	G	G	A	rs6114033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	157	239	2	0.518152	0.0083682	G|0.857;A|0.143	0.143	strong	TGM6,NS,carcinoma,0,1	TGM6	126	1	NM_198994	exon6	c.G789A	p.K263K	GCTCAAGGGCAGG	.	scavenged	Atlas-SNP
TM7SF3	51768	hgsc.bcm.edu	37	12	27148324	27148324	+	Missense_Mutation	SNP	G	G	C	rs34735713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	61	80	0	0.512605	0	G|0.971;C|0.029	0.029	strong	.	TM7SF3	41	.	NM_016551	exon5	c.C536G	p.P179R	TCACATGGTGGGG	.	PASS	Atlas-SNP
SPATC1L	84221	hgsc.bcm.edu	37	21	47581508	47581508	+	Missense_Mutation	SNP	C	C	A	rs74518516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	57	67	0	0.575758	0	C|0.971;A|0.029	0.029	strong	.	.	.	.	NM_001142854	exon5	c.G808T	p.V270L	GGTGCACGTCGCG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278020	27278020	+	Missense_Mutation	SNP	C	C	A	rs16897515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	54	77	0	0.556701	0	C|0.850;A|0.150	0.150	strong	.	POM121L2	61	.	NM_033482	exon1	c.G1930T	p.G644C	CTACACCAAAATC	.	PASS	Atlas-SNP
GKN1	56287	hgsc.bcm.edu	37	2	69204629	69204629	+	Silent	SNP	T	T	C	rs35624281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	97	177	0	0.530055	0	T|0.933;C|0.067	0.067	strong	.	GKN1	24	.	NM_019617	exon2	c.T57C	p.I19I	TCAGATTGTCTTT	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25670868	25670868	+	Missense_Mutation	SNP	G	G	A	rs200859889	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	9	149	0	0.044335	0	.	.	weak	PABPC3,NS,carcinoma,0,1	PABPC3	129	1	NM_030979	exon1	c.G532A	p.E178K	CGTAAAGAACGAG	.	scavenged	Atlas-SNP
SSBP3	23648	hgsc.bcm.edu	37	1	54747176	54747176	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	35	80	0	0.333333	0	.	.	none	.	SSBP3	65	.	NM_145716	exon5	c.G301A	p.V101M	CAAGCACGGGGCT	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117129921	117129921	+	Missense_Mutation	SNP	G	G	C	rs62640865	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	32	72	0	0.421053	0	G|0.957;C|0.043	0.043	strong	.	AKNA	119	.	NM_030767	exon6	c.C1630G	p.L544V	ACCCCAGGGTGGG	.	PASS	Atlas-SNP
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232169	50232169	+	Missense_Mutation	SNP	A	A	T	rs11169172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	5	9	0	0.333333	0	A|0.811;T|0.189	0.189	strong	BCDIN3D,NS,carcinoma,0,1	BCDIN3D	20	1	NM_181708	exon2	c.T864A	p.S288R	CTGGAAACTTAAT	.	scavenged	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	118	237	1	0.47012	0.00421941	C|0.753;T|0.247	0.247	strong	.	INPP4A	205	.	NM_001134224	exon25	c.C2691T	p.S897S	CAAGAGCGCTAAG	.	PASS	Atlas-SNP
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	25	72	0	0.373134	0	G|0.691;T|0.309	0.309	strong	.	DNAJC25	20	.	NM_001015882	exon3	c.G702T	p.G234G	AAAGGGGGGCTAT	.	PASS	Atlas-SNP
TSSK1B	83942	hgsc.bcm.edu	37	5	112770054	112770054	+	Silent	SNP	G	G	A	rs111560230	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	81	0	0.45	0	G|0.500;A|0.500	0.500	strong	.	TSSK1B	89	.	NM_032028	exon1	c.C483T	p.C161C	CCGCAGGCAGCGC	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657713	49657713	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	3	72	0	0.0340909	0	.	.	none	HRC,NS,carcinoma,0,1	HRC	85	1	NM_002152	exon1	c.A782T	p.D261V	GAGACATCATCAT	.	scavenged	Atlas-SNP
FBXW10	10517	hgsc.bcm.edu	37	17	18681913	18681913	+	Missense_Mutation	SNP	G	G	A	rs77288131	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	157	244	1	0.50974	0.00409836	G|0.912;A|0.088	0.088	strong	.	FBXW10	82	.	NM_001267585	exon14	c.G2461A	p.A821T	GTTAGCGCCCTGC	.	PASS	Atlas-SNP
SMPD2	6610	hgsc.bcm.edu	37	6	109762332	109762332	+	Missense_Mutation	SNP	C	C	T	rs1048197	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	34	94	0	0.343434	0	C|0.925;T|0.075	0.075	strong	.	SMPD2	25	.	NM_003080	exon1	c.C8T	p.P3L	TGAAGCCCAACTT	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45244930	45244930	+	Silent	SNP	C	C	T	rs2269543	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	39	87	0	0.464286	0	C|0.642;N|0.001	.	strong	.	PRR5-ARHGAP8	53	.	NM_181334	exon13	c.C1233T	p.L411L	GATTCTCGGGATC	.	PASS	Atlas-SNP
KCNK13	56659	hgsc.bcm.edu	37	14	90528797	90528797	+	Missense_Mutation	SNP	G	G	A	rs7157583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	41	48	0	0.532468	0	G|0.915;A|0.085	0.085	strong	.	KCNK13	76	.	NM_022054	exon1	c.G248A	p.R83Q	CCACTCGGGCCGG	.	PASS	Atlas-SNP
MBOAT4	619373	hgsc.bcm.edu	37	8	29990075	29990075	+	Missense_Mutation	SNP	C	C	T	rs16876563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	64	125	0	0.470588	0	C|0.952;T|0.048	0.048	strong	MBOAT4_ENST00000320542,NS,carcinoma,+1,1	MBOAT4	31	1	NM_001100916	exon3	c.G692A	p.G231E	GTCAGTCCCGCTC	.	PASS	Atlas-SNP
MACC1	346389	hgsc.bcm.edu	37	7	20199835	20199835	+	Missense_Mutation	SNP	G	G	A	rs17142503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	36	56	0	0.521739	0	G|0.982;A|0.018	0.018	strong	MACC1,colon,carcinoma,-1,1	MACC1	99	1	NM_182762	exon5	c.C149T	p.P50L	GCATCCGGCCAAT	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73477930	73477930	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	4	285	1	0.0147059	0.00350877	.	.	none	TRPM3_ENST00000423814,right_upper_lobe,carcinoma,0,2	TRPM3	700	2	NM_001007471	exon3	c.A356G	p.D119G	TGGATGTCATTTC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281228	152281228	+	Missense_Mutation	SNP	C	C	G	rs7546186	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	537	270	288	0	0.502793	0	C|0.969;G|0.031	0.031	strong	.	FLG	900	.	NM_002016	exon3	c.G6134C	p.S2045T	CTGTCACTGGCCT	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51096992	51096992	+	Missense_Mutation	SNP	G	G	A	rs61737866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	112	207	0	0.449799	0	G|0.974;A|0.026	0.026	strong	.	COBL	167	.	NM_015198	exon10	c.C1801T	p.H601Y	CGGGGTGCAGGGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9075737	9075737	+	Silent	SNP	T	T	C	rs2547071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	105	159	0	0.519802	0	T|0.560;C|0.440	0.440	strong	.	MUC16	4315	.	NM_024690	exon3	c.A11709G	p.V3903V	CCTTAATACACTG	.	PASS	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55272743	55272743	+	Missense_Mutation	SNP	A	A	G	rs115158797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	78	157	0	0.490566	0	A|0.989;G|0.011	0.011	strong	.	C1orf177	36	.	NM_001110533	exon2	c.A179G	p.Y60C	CGCGTTATTCTAC	.	PASS	Atlas-SNP
TTLL10	254173	hgsc.bcm.edu	37	1	1118275	1118275	+	Silent	SNP	C	C	T	rs61733845	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	78	127	0	0.509804	0	C|0.845;T|0.155	0.155	strong	.	TTLL10	66	.	NM_001130045	exon11	c.C936T	p.C312C	GATCTGCAAGCCC	.	PASS	Atlas-SNP
TBC1D17	79735	hgsc.bcm.edu	37	19	50386253	50386253	+	Silent	SNP	C	C	T	rs61741174	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	62	99	0	0.548673	0	C|0.989;T|0.011	0.011	strong	.	TBC1D17	39	.	NM_024682	exon9	c.C951T	p.R317R	GCGGCGCGAGGCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280782	152280782	+	Missense_Mutation	SNP	A	A	G	rs2184953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	767	767	423	0	1	0	A|0.483;G|0.517	0.517	strong	.	FLG	900	.	NM_002016	exon3	c.T6580C	p.Y2194H	TGTCATATGTTTT	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38781866	38781866	+	Silent	SNP	C	C	G	rs1678690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	88	162	0	0.533333	0	C|0.558;G|0.442	0.442	strong	DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	NM_001206927	exon25	c.C3294G	p.S1098S	TATTTCCTTTATA	.	PASS	Atlas-SNP
SRRT	51593	hgsc.bcm.edu	37	7	100482026	100482026	+	Silent	SNP	T	T	C	rs15624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	73	65	0	0.986486	0	T|0.462;C|0.538	0.538	strong	.	SRRT	108	.	NM_001128853	exon7	c.T795C	p.L265L	TGATCTTCGCATC	.	PASS	Atlas-SNP
ROBO4	54538	hgsc.bcm.edu	37	11	124767067	124767067	+	Missense_Mutation	SNP	T	T	C	rs59648931	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	59	170	0	0.412587	0	T|0.646;C|0.354	0.354	strong	.	ROBO4	130	.	NM_019055	exon2	c.A161G	p.Q54R	GAGGCTTGGCAGC	.	PASS	Atlas-SNP
WNK4	65266	hgsc.bcm.edu	37	17	40939460	40939460	+	Silent	SNP	C	C	T	rs9916754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	29	55	0	0.491525	0	C|0.919;T|0.081	0.081	strong	.	WNK4	182	.	NM_032387	exon7	c.C1641T	p.A547A	CATGGCCCCCGGT	.	PASS	Atlas-SNP
ITPR1	3708	hgsc.bcm.edu	37	3	4716811	4716811	+	Silent	SNP	A	A	C	rs2306877	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	66	175	0	0.4125	0	A|0.703;C|0.297	0.297	strong	.	ITPR1	659	.	NM_001099952	exon23	c.A2658C	p.L886L	CCTTCTACGATTA	.	PASS	Atlas-SNP
TUBB2A	7280	hgsc.bcm.edu	37	6	3154882	3154882	+	Missense_Mutation	SNP	C	C	T	rs76334433	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	499	69	302	1	0.138277	0.00331126	C|0.998;T|0.002	0.002	strong	TUBB2A,NS,carcinoma,0,1	TUBB2A	23	1	NM_001069	exon4	c.G553A	p.A185T	GGGTGGCGTTGTA	.	scavenged	Atlas-SNP
CDK6	1021	hgsc.bcm.edu	37	7	92462572	92462572	+	Silent	SNP	G	G	A	rs189208543	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	45	67	0	0.478723	0	G|0.998;A|0.002	0.002	strong	.	CDK6	30	.	NM_001259	exon2	c.C66T	p.G22G	ATAGGCGCCCTCC	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	70	112	0	0.503597	0	G|0.622;A|0.378	0.378	strong	.	SLC2A2	71	.	NM_000340	exon11	c.C1437T	p.F479F	AAATGTGAACAGG	.	PASS	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55873401	55873401	+	Missense_Mutation	SNP	A	A	G	rs115405120	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	61	121	0	0.54955	0	A|0.991;G|0.009	0.009	strong	.	OR8H2	117	.	NM_001005200	exon1	c.A883G	p.K295E	AGAAACAAAGAGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412561	105412561	+	Missense_Mutation	SNP	C	C	T	rs3000771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	120	271	0	0.97561	0	C|0.635;T|0.365	0.365	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G9227A	p.R3076H	CCCTTGCGATCTA	.	PASS	Atlas-SNP
TMEM253	643382	hgsc.bcm.edu	37	14	21570614	21570614	+	Silent	SNP	A	A	C	rs4982408	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	271	250	0	1	0	A|0.198;C|0.802	0.802	strong	.	.	.	.	NM_001146683	exon6	c.A327C	p.I109I	TTTCATAGTGGTG	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	43	80	0	0.52439	0	T|0.571;A|0.429	0.429	strong	.	NUP88	47	.	NM_002532	exon10	c.A1389T	p.P463P	TGGAGCTGGCTGC	.	PASS	Atlas-SNP
C8orf48	157773	hgsc.bcm.edu	37	8	13424767	13424767	+	Missense_Mutation	SNP	C	C	G	rs10096353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	36	95	0	0.433735	0	C|0.990;G|0.010	0.010	strong	.	C8orf48	18	.	NM_001007090	exon1	c.C267G	p.N89K	GATCAACTACCTC	.	PASS	Atlas-SNP
ROBO4	54538	hgsc.bcm.edu	37	11	124756406	124756406	+	Silent	SNP	G	G	A	rs7104934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	71	140	0	0.586777	0	G|0.783;A|0.217	0.217	strong	.	ROBO4	130	.	NM_019055	exon16	c.C2748T	p.S916S	ACCAAAGCTATCC	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139581461	139581461	+	Silent	SNP	C	C	T	rs6904970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	57	129	0	0.5	0	C|0.915;T|0.085	0.085	strong	.	TXLNB	96	.	NM_153235	exon6	c.G996A	p.K332K	ATATTCCTTTTCT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037560	33037560	+	Silent	SNP	G	G	A	rs1042176	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	133	163	0	0.985185	0	G|0.802;A|0.198	0.198	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.C204T	p.D68D	CTTCTTGTCCAGA	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487172	32487172	+	Silent	SNP	C	C	T	rs72508430	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	64	51	0	0.853333	0	C|0.764;T|0.235	0.235	strong	HLA-DRB5,NS,carcinoma,-2,1	HLA-DRB5	31	1	NM_002125	exon3	c.G627A	p.V209V	GCTCGTCACGCTT	.	scavenged	Atlas-SNP
GLYCTK	132158	hgsc.bcm.edu	37	3	52325039	52325039	+	Silent	SNP	G	G	A	rs35976326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	97	0	0.483051	0	G|0.845;A|0.155	0.155	strong	.	GLYCTK	30	.	NM_001144951	exon3	c.G441A	p.P147P	CCTCCCGGACCGC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414252	105414252	+	Silent	SNP	C	C	T	rs60106058	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	271	297	0	0.992674	0	C|0.601;T|0.399	0.399	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.G7536A	p.K2512K	CTCCACCTTCGGC	.	PASS	Atlas-SNP
CTRB1	1504	hgsc.bcm.edu	37	16	75258617	75258617	+	Silent	SNP	C	C	T	rs2287990	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	58	72	0	0.597938	0	C|0.884;T|0.116	0.116	strong	.	CTRB1	8	.	NM_001906	exon7	c.C645T	p.G215G	TGGCGGCCCCCTG	.	PASS	Atlas-SNP
RGS14	10636	hgsc.bcm.edu	37	5	176798996	176798996	+	Missense_Mutation	SNP	G	G	A	rs149981884	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	44	66	0	0.55	0	G|0.995;A|0.005	0.005	strong	.	RGS14	34	.	NM_006480	exon15	c.G1621A	p.E541K	AGCTCCGAGGAGA	.	PASS	Atlas-SNP
MCM2	4171	hgsc.bcm.edu	37	3	127323592	127323592	+	Silent	SNP	G	G	A	rs2257836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	17	35	0	0.404762	0	G|0.902;A|0.098	0.098	strong	.	MCM2	79	.	NM_004526	exon3	c.G378A	p.R126R	TGGCCGGGGCCTG	.	PASS	Atlas-SNP
RRP1	8568	hgsc.bcm.edu	37	21	45219524	45219524	+	Silent	SNP	T	T	C	rs4566449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	82	131	0	0.539474	0	T|0.688;C|0.312	0.312	strong	.	RRP1	23	.	NM_003683	exon9	c.T885C	p.V295V	CCCCGTTCTCCAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677974	100677974	+	Missense_Mutation	SNP	A	A	G	rs113876641	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	398	57	159	0	0.143216	0	A|0.998;G|0.002	0.002	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3277G	p.T1093A	ATGCCAACCTCAA	.	PASS	Atlas-SNP
SDCCAG8	10806	hgsc.bcm.edu	37	1	243493907	243493907	+	Missense_Mutation	SNP	A	A	T	rs2275155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	102	202	0	0.478873	0	A|0.746;T|0.254	0.254	strong	SDCCAG8,NS,carcinoma,+2,1	SDCCAG8	73	1	NM_006642	exon10	c.A1134T	p.E378D	AAAAGAACTTGCA	.	PASS	Atlas-SNP
POTEG	404785	hgsc.bcm.edu	37	14	19553494	19553494	+	Missense_Mutation	SNP	G	G	C	rs200256710	byfrequency;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	2158	285	1363	1	0.132067	0.000733676	G|0.996;A|0.004	.	alt	POTEG,NS,carcinoma,0,1	POTEG	118	1	NM_001005356	exon1	c.G78C	p.K26N	GGGCAAGTGGTGC	.	scavenged	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	37	19	50098423	50098423	+	Silent	SNP	G	G	A	rs12462756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	91	56	0	0.978495	0	G|0.749;A|0.251	0.251	strong	.	PRR12	157	.	NM_020719	exon4	c.G831A	p.P277P	ACCGCCGCCTGAG	.	PASS	Atlas-SNP
C1orf158	93190	hgsc.bcm.edu	37	1	12820870	12820870	+	Missense_Mutation	SNP	T	T	C	rs1132185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	135	0	1	0	T|0.173;C|0.827	0.827	strong	.	C1orf158	28	.	NM_152290	exon4	c.T571C	p.F191L	CATCCTTTCCCAC	.	PASS	Atlas-SNP
GABRP	2568	hgsc.bcm.edu	37	5	170239112	170239112	+	Missense_Mutation	SNP	C	C	A	rs1063310	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	107	0	1	0	C|0.739;A|0.261	0.261	strong	.	GABRP	65	.	NM_014211	exon10	c.C1173A	p.F391L	CAAGTTCAAGTTT	.	PASS	Atlas-SNP
NUP85	79902	hgsc.bcm.edu	37	17	73230796	73230796	+	Silent	SNP	T	T	C	rs35857535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	29	69	0	0.349398	0	T|0.935;C|0.065	0.065	strong	.	NUP85	44	.	NM_024844	exon17	c.T1680C	p.L560L	TCTCCTTCTGTCC	.	PASS	Atlas-SNP
CLU	1191	hgsc.bcm.edu	37	8	27457507	27457507	+	Silent	SNP	G	G	C	rs9331937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	38	84	0	0.44186	0	G|0.973;C|0.027	0.027	strong	.	CLU	54	.	NM_001831	exon7	c.C954G	p.P318P	CTGGGAGGGGTTG	.	PASS	Atlas-SNP
BRPF1	7862	hgsc.bcm.edu	37	3	9780737	9780737	+	Silent	SNP	C	C	T	rs17050537	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	97	177	0	0.570588	0	C|0.989;T|0.011	0.011	strong	.	BRPF1	104	.	NM_001003694	exon3	c.C654T	p.D218D	CATGGACGAGGAG	.	PASS	Atlas-SNP
ZBTB42	100128927	hgsc.bcm.edu	37	14	105268701	105268701	+	Silent	SNP	G	G	A	rs61734768	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	50	89	0	0.515464	0	G|0.959;A|0.041	0.041	strong	.	ZBTB42	10	.	NM_001137601	exon2	c.G1167A	p.P389P	GAAGCCGCATGCC	.	PASS	Atlas-SNP
ZNF689	115509	hgsc.bcm.edu	37	16	30616488	30616488	+	Silent	SNP	G	G	A	rs9937653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	51	125	0	0.425	0	G|0.972;A|0.028	0.028	strong	.	ZNF689	48	.	NM_138447	exon3	c.C600T	p.S200S	CTCGCCGGAGTGT	.	PASS	Atlas-SNP
KRT71	112802	hgsc.bcm.edu	37	12	52946543	52946543	+	Missense_Mutation	SNP	C	C	T	rs665522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	93	175	0	0.54386	0	C|0.784;T|0.216	0.216	strong	.	KRT71	70	.	NM_033448	exon1	c.G319A	p.V107I	CATTGACGGTAAC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88800913	88800913	+	Silent	SNP	C	C	T	rs34908386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	55	81	0	0.578947	0	C|0.891;T|0.109	0.109	strong	.	PIEZO1	79	.	NM_001142864	exon16	c.G2031A	p.V677V	CTCGGACACGCTG	.	PASS	Atlas-SNP
EXOC8	149371	hgsc.bcm.edu	37	1	231472916	231472916	+	Silent	SNP	G	G	A	rs73116365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	53	95	0	0.490741	0	G|0.983;A|0.017	0.017	strong	.	EXOC8	42	.	NM_175876	exon1	c.C576T	p.Y192Y	CGCATCGTATTCC	.	PASS	Atlas-SNP
MMP13	4322	hgsc.bcm.edu	37	11	102818662	102818662	+	Missense_Mutation	SNP	T	T	C	rs17860568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	32	85	0	0.359551	0	T|0.991;C|0.009	0.009	strong	.	MMP13	75	.	NM_002427	exon8	c.A1169G	p.D390G	CCTGTATCCTCAA	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56386358	56386358	+	Silent	SNP	T	T	A	rs2526360	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	38	64	0	0.487179	0	T|0.704;A|0.296	0.296	strong	BZRAP1_ENST00000355701,NS,carcinoma,0,2	BZRAP1	287	2	NM_004758	exon22	c.A4275T	p.R1425R	GTGTTCTCGGGGA	.	PASS	Atlas-SNP
LRIT2	340745	hgsc.bcm.edu	37	10	85982075	85982075	+	Silent	SNP	A	A	G	rs7901410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	41	56	0	0.525641	0	A|0.945;G|0.055	0.055	strong	.	LRIT2	81	.	NM_001017924	exon3	c.T1254C	p.Y418Y	CACAGCATAAGTA	.	PASS	Atlas-SNP
C4orf45	152940	hgsc.bcm.edu	37	4	159894277	159894277	+	Missense_Mutation	SNP	T	T	C	rs17037858	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	59	80	0	0.475806	0	T|0.903;C|0.097	0.097	strong	.	C4orf45	8	.	NM_152543	exon2	c.A251G	p.Y84C	AAATTATACTGTG	.	PASS	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84097021	84097021	+	Missense_Mutation	SNP	C	C	G	rs35417190	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	53	123	0	0.441667	0	C|0.997;G|0.003	0.003	strong	.	MBTPS1	85	.	NM_003791	exon19	c.G2461C	p.V821L	CAACAACTGCTGT	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592535	167592535	+	Missense_Mutation	SNP	G	G	C	rs145355467	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	93	0	0.542169	0	G|0.979;C|0.021	0.021	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G694C	p.G232R	AACTCCGGTGGCA	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16754991	16754991	+	Silent	SNP	C	C	T	rs61736777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	71	0	0.423077	0	C|0.973;T|0.027	0.027	strong	.	MYO10	198	.	NM_012334	exon19	c.G1875A	p.T625T	GCTTAGCGTTGCC	.	PASS	Atlas-SNP
CCKBR	887	hgsc.bcm.edu	37	11	6291120	6291120	+	Missense_Mutation	SNP	G	G	A	rs1805002	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	87	0	0.473684	0	G|0.949;A|0.051	0.051	strong	.	CCKBR	232	.	NM_176875	exon2	c.G373A	p.V125I	GGCACCGTCATCT	.	PASS	Atlas-SNP
DPYSL2	1808	hgsc.bcm.edu	37	8	26441477	26441477	+	Silent	SNP	G	G	A	rs11786691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	46	115	0	0.489362	0	G|0.903;A|0.097	0.097	strong	.	DPYSL2	49	.	NM_001197293	exon3	c.G606A	p.L202L	GGCCCTGGCTGGG	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802824	57802824	+	Silent	SNP	G	G	A	rs2041110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	48	98	0	0.489796	0	G|0.806;A|0.194	0.194	strong	.	ZNF460	59	.	NM_006635	exon3	c.G915A	p.K305K	TGAGAAGAAACCC	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72358407	72358407	+	Missense_Mutation	SNP	C	C	T	rs140787739	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	74	0	0.514706	0	C|0.999;T|0.001	0.001	strong	PRF1,caecum,carcinoma,-1,1	PRF1	64	1	NM_001083116	exon3	c.G1070A	p.R357Q	GCCTCCCGCCGCG	.	PASS	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	549949	549949	+	Missense_Mutation	SNP	G	G	A	rs371135949		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	27	79	0	0.36	0	.	.	weak	.	LRRC56	23	.	NM_198075	exon7	c.G374A	p.R125H	TGGCTCGCTGTGG	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44061123	44061123	+	Missense_Mutation	SNP	C	C	T	rs73314997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	65	131	0	0.481481	0	C|0.655;A|0.015	.	strong	MAPT,NS,carcinoma,-1,1	MAPT	135	1	NM_001123066	exon6	c.C953T	p.S318L	CGCACTCGGAGGA	.	PASS	Atlas-SNP
MAGI3	260425	hgsc.bcm.edu	37	1	113933814	113933814	+	Silent	SNP	C	C	T	rs182574963	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	26	26	0	0.742857	0	C|0.994;T|0.006	0.006	strong	.	MAGI3	181	.	NM_152900	exon1	c.C159T	p.G53G	GCCCGGCGGGGGC	.	PASS	Atlas-SNP
DIO1	1733	hgsc.bcm.edu	37	1	54359922	54359922	+	Silent	SNP	C	C	T	rs2294510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	117	218	0	0.485477	0	C|0.898;T|0.102	0.102	strong	.	DIO1	66	.	NM_001039715	exon1	c.C39T	p.L13L	GAGGCTCTGGGTG	.	PASS	Atlas-SNP
POTEF	728378	hgsc.bcm.edu	37	2	130872871	130872871	+	Silent	SNP	C	C	T	rs199770435	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	720	25	724	1	0.0347222	0.00138122	C|0.998;T|0.002	0.002	weak	POTEF,NS,carcinoma,0,5	POTEF	140	5	NM_001099771	exon4	c.G552A	p.G184G	TGAATTCCCATTG	.	scavenged	Atlas-SNP
OR8H3	390152	hgsc.bcm.edu	37	11	55889987	55889987	+	Missense_Mutation	SNP	C	C	A	rs7107077	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	98	301	0	0.280802	0	C|0.950;A|0.050	0.050	strong	OR8H3,caecum,carcinoma,0,1	OR8H3	92	1	NM_001005201	exon1	c.C139A	p.L47I	GGGATGCTATTGA	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225539363	225539363	+	Missense_Mutation	SNP	G	G	A	rs12408617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	59	167	0	0.427536	0	G|0.910;A|0.090	0.090	strong	.	DNAH14	300	.	NM_001373	exon70	c.G11032A	p.G3678S	GAAATAGGTGAAA	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449168	89449168	+	Silent	SNP	T	T	A	rs59048247	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	150	394	0	0.443787	0	T|0.940;A|0.060	0.060	strong	.	.	.	.	NM_001162536	exon3	c.A342T	p.G114G	ACTTCCTCCTCTT	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69996928	69996928	+	Missense_Mutation	SNP	G	G	A	rs616457	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	489	21	502	0	0.0429448	0	G|0.500;A|0.500	0.500	weak	CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	NM_001271197	exon12	c.G1261A	p.D421N	TGGAACGACCAGC	.	scavenged	Atlas-SNP
IFNA4	3441	hgsc.bcm.edu	37	9	21187146	21187146	+	Missense_Mutation	SNP	C	C	T	rs201186279		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	736	68	513	2	0.0923913	0.00389864	.	.	weak	IFNA4,NS,carcinoma,0,1	IFNA4	34	1	NM_021068	exon1	c.G385A	p.V129M	CTTCCACCCCAAC	.	scavenged	Atlas-SNP
ESR2	2100	hgsc.bcm.edu	37	14	64724051	64724051	+	Silent	SNP	C	C	T	rs1256049	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	74	117	0	0.486842	0	C|0.909;T|0.091	0.091	strong	ESR2,NS,carcinoma,0,1	ESR2	82	1	NM_001214902	exon5	c.G984A	p.V328V	GAGCCGCACTTGG	.	PASS	Atlas-SNP
NSUN4	387338	hgsc.bcm.edu	37	1	46810530	46810530	+	Missense_Mutation	SNP	A	A	G	rs3737744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	107	215	1	0.471366	0.00465116	G|0.311;N|0.000	0.311	strong	.	NSUN4	26	.	NM_199044	exon2	c.A151G	p.T51A	GACATGACTTACA	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112871458	112871458	+	Silent	SNP	C	C	G	rs77052070	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	41	96	0	0.376147	0	C|0.984;G|0.016	0.016	strong	.	YTHDC2	118	.	NM_022828	exon7	c.C1065G	p.L355L	AAATCTCTTTATA	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95076833	95076833	+	Missense_Mutation	SNP	C	C	G	rs373764183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	65	76	0	0.670103	0	.	.	weak	.	NOL8	118	.	NM_017948	exon7	c.G2074C	p.G692R	CAAAGCCTATGTT	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31709045	31709045	+	Missense_Mutation	SNP	C	C	T	rs28381349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	54	114	0	0.45	0	C|0.957;T|0.043	0.043	strong	.	MSH5	108	.	NM_172165	exon3	c.C253T	p.L85F	GAGAGCCTCAAGC	.	PASS	Atlas-SNP
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412125	39412125	+	Missense_Mutation	SNP	G	G	C	rs144403228	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	129	262	1	0.490494	0.00381679	G|0.987;C|0.013	0.013	strong	.	KRTAP9-9	24	.	NM_030975	exon1	c.G488C	p.C163S	CCAGCTGCTGCCA	.	PASS	Atlas-SNP
RIMKLA	284716	hgsc.bcm.edu	37	1	42880516	42880516	+	Silent	SNP	T	T	C	rs1055055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	77	86	3	1	0.0348837	T|0.444;C|0.556	0.556	strong	RIMKLA,NS,carcinoma,0,1	RIMKLA	32	1	NM_173642	exon5	c.T1047C	p.S349S	CTCTAGTGAAAGT	.	scavenged	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	50	93	0	0.568182	0	G|0.725;A|0.275	0.275	strong	.	NEU4	39	.	NM_001167599	exon4	c.G940A	p.G314R	GGCCCCGGGAGTC	.	PASS	Atlas-SNP
EXOSC8	11340	hgsc.bcm.edu	37	13	37580139	37580139	+	Silent	SNP	G	G	A	rs1127446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	75	153	0	0.503356	0	G|0.659;A|0.341	0.341	strong	.	EXOSC8	16	.	NM_181503	exon6	c.G321A	p.Q107Q	TAGCCAGTTCATT	.	PASS	Atlas-SNP
PSMB10	5699	hgsc.bcm.edu	37	16	67969930	67969930	+	Silent	SNP	A	A	G	rs20549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	57	0	0.46988	0	T|0.000;G|0.310;A|0.690	0.310	strong	.	PSMB10	19	.	NM_002801	exon4	c.T319C	p.L107L	TAGATAACGCGTG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107308	55107308	+	Missense_Mutation	SNP	G	G	C	rs35534776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	200	313	0	0.952381	0	G|0.851;C|0.149	0.149	strong	LILRA1,NS,carcinoma,0,1	LILRA1	105	1	NM_006863	exon6	c.G866C	p.R289P	TGAGCCGCTCCTA	.	PASS	Atlas-SNP
MEI1	150365	hgsc.bcm.edu	37	22	42177816	42177816	+	Silent	SNP	C	C	A	rs6002481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	85	184	0	0.47486	0	C|0.832;A|0.168	0.168	strong	.	MEI1	87	.	NM_152513	exon24	c.C3054A	p.S1018S	TGCCTCCTTCTCT	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124955032	124955032	+	Silent	SNP	T	T	C	rs948268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	129	129	0	1	0	T|0.312;C|0.688	0.688	strong	.	SLC37A2	105	.	NM_001145290	exon14	c.T1245C	p.D415D	TGCTGATCTGGTG	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206666601	206666601	+	Silent	SNP	C	C	A	rs144382861	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	93	0	0.494737	0	C|0.999;A|0.001	0.001	strong	.	IKBKE	77	.	NM_014002	exon20	c.C1935A	p.L645L	GCAGCTCCTGGAA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	40	166	0	0.285714	0	C|0.827;T|0.173	0.173	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon28	c.G13018A	p.E4340K	AGTCTTCGATGAC	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367433	128367433	+	Missense_Mutation	SNP	G	G	A	rs61741454	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	105	207	1	0.517241	0.00483092	G|0.993;A|0.007	0.007	strong	.	MYO7B	359	.	NM_001080527	exon24	c.G3034A	p.V1012I	GCCCTGGTCATAT	.	PASS	Atlas-SNP
GIF	2694	hgsc.bcm.edu	37	11	59612859	59612859	+	Missense_Mutation	SNP	T	T	C	rs35211634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	83	0	0.47561	0	T|0.902;C|0.098	0.098	strong	.	GIF	43	.	NM_005142	exon1	c.A68G	p.Q23R	GAACTCTGGGTCT	.	PASS	Atlas-SNP
ZNHIT2	741	hgsc.bcm.edu	37	11	64884599	64884599	+	Missense_Mutation	SNP	G	G	A	rs35983251	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	5	11	0	0.555556	0	G|0.980;A|0.020	0.020	strong	.	ZNHIT2	12	.	NM_014205	exon1	c.C527T	p.A176V	TCGGCGGCCGCGG	.	PASS	Atlas-SNP
C2orf49	79074	hgsc.bcm.edu	37	2	105959592	105959592	+	Missense_Mutation	SNP	G	G	A	rs28930676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	82	0	0.493506	0	G|0.949;A|0.051	0.051	strong	.	C2orf49	19	.	NM_024093	exon3	c.G554A	p.G185D	CTTCAGGCCCTGT	.	PASS	Atlas-SNP
EMP2	2013	hgsc.bcm.edu	37	16	10631912	10631912	+	Silent	SNP	C	C	T	rs2279868	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	41	74	0	0.5	0	C|0.762;T|0.238	0.238	strong	.	EMP2	21	.	NM_001424	exon4	c.G189A	p.A63A	CTGGACCGCCTGC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224587	248224587	+	Missense_Mutation	SNP	A	A	G	rs61525219	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	25	514	1	0.0739645	0.00194553	.	.	weak	OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	NM_001004687	exon1	c.A604G	p.T202A	TTGAGCACCACCA	.	scavenged	Atlas-SNP
CLU	1191	hgsc.bcm.edu	37	8	27468005	27468005	+	Silent	SNP	G	G	A	rs9331892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	53	116	0	0.384058	0	G|0.944;A|0.056	0.056	strong	.	CLU	54	.	NM_001831	exon2	c.C84T	p.D28D	CTCATTGTCTGAG	.	PASS	Atlas-SNP
INF2	64423	hgsc.bcm.edu	37	14	105180977	105180977	+	Missense_Mutation	SNP	G	G	A	rs9672065	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	26	44	0	0.666667	0	G|0.978;A|0.022	0.022	strong	.	INF2	148	.	NM_022489	exon21	c.G3478A	p.G1160S	AGCCGTGGTGCCA	.	PASS	Atlas-SNP
SPATA31C1	441452	hgsc.bcm.edu	37	9	90534206	90534206	+	Missense_Mutation	SNP	T	T	C	rs2481989	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	658	157	861	2	0.238602	0.00232288	.	.	weak	.	.	.	.	NM_001145124	exon2	c.T226C	p.C76R	TCCCAGTGTCCAA	.	PASS	Atlas-SNP
BBS4	585	hgsc.bcm.edu	37	15	73027478	73027478	+	Missense_Mutation	SNP	T	T	C	rs2277598	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	113	0	0.46	0	T|0.511;C|0.489	0.489	strong	.	BBS4	34	.	NM_033028	exon13	c.T1061C	p.I354T	AAGATATAGAAAA	.	PASS	Atlas-SNP
TTC4	7268	hgsc.bcm.edu	37	1	55197320	55197320	+	Silent	SNP	G	G	A	rs1062700	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	29	83	0	0.381579	0	G|0.946;A|0.054	0.054	strong	.	TTC4	21	.	NM_004623	exon7	c.G843A	p.L281L	CTTTCTGTACCCA	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27689137	27689137	+	Missense_Mutation	SNP	G	G	T	rs147094899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	54	89	0	0.435484	0	G|0.993;T|0.007	0.007	strong	.	KIAA0556	348	.	NM_015202	exon7	c.G628T	p.D210Y	GAGGAAGACATAC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276871	152276871	+	Silent	SNP	A	A	G	rs3126066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	421	421	421	0	1	0	A|0.703;G|0.297	0.297	strong	.	FLG	900	.	NM_002016	exon3	c.T10491C	p.D3497D	GGAGCCATCTCCT	.	PASS	Atlas-SNP
KIT	3815	hgsc.bcm.edu	37	4	55561862	55561862	+	Silent	SNP	G	G	T	rs56411694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	112	0	0.469388	0	G|0.981;T|0.019	0.019	strong	.	KIT	7396	.	NM_000222	exon2	c.G252T	p.T84T	GATCACGGAAAAG	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181019202	181019202	+	Silent	SNP	C	C	T	rs61731104	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	138	268	0	0.511111	0	C|0.967;T|0.033	0.033	strong	.	MR1	46	.	NM_001195035	exon4	c.C384T	p.T128T	AAGCACCACAGGA	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112298582	112298582	+	Silent	SNP	A	A	G	rs197392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	180	189	0	0.989011	0	A|0.755;G|0.245	0.245	strong	DDX20,NS,carcinoma,0,1	DDX20	50	1	NM_007204	exon1	c.A36G	p.A12A	CTTAGCAGCAGTG	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149720	11149720	+	Missense_Mutation	SNP	A	A	G	rs10845280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	72	161	0	0.418605	0	A|0.670;G|0.329	0.329	strong	.	TAS2R20	17	.	NM_176889	exon1	c.T755C	p.F252S	ATCTTAAAATTCC	.	PASS	Atlas-SNP
SAMD11	148398	hgsc.bcm.edu	37	1	865694	865694	+	Missense_Mutation	SNP	C	C	T	rs9988179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	112	240	0	0.46281	0	C|0.974;T|0.026	0.026	strong	.	SAMD11	34	.	NM_152486	exon3	c.C232T	p.H78Y	GGTCCGCACATCC	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30041009	30041009	+	Missense_Mutation	SNP	A	A	G	rs2074479	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	63	140	0	0.4375	0	A|0.808;G|0.192	0.192	strong	RNF39_ENST00000244360,NS,carcinoma,+1,1	RNF39	27	1	NM_025236	exon3	c.T607C	p.S203P	ACTTGGATGTTGG	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94337220	94337220	+	Silent	SNP	C	C	T	rs593690	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	23	87	0	0.333333	0	C|0.455;T|0.545	0.545	strong	.	PIWIL4	70	.	NM_152431	exon13	c.C1636T	p.L546L	GTTCAGCTGGTAA	.	PASS	Atlas-SNP
SSH3	54961	hgsc.bcm.edu	37	11	67075131	67075131	+	Silent	SNP	C	C	T	rs57238619	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	89	147	0	0.470899	0	C|0.916;T|0.084	0.084	strong	.	SSH3	54	.	NM_017857	exon7	c.C714T	p.S238S	GAACTCCGAACAG	.	PASS	Atlas-SNP
RAPGEF1	2889	hgsc.bcm.edu	37	9	134473655	134473655	+	Silent	SNP	C	C	T	rs11243446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	48	70	0	0.6	0	C|0.912;T|0.088	0.088	strong	.	RAPGEF1	126	.	NM_198679	exon13	c.G2040A	p.E680E	TTCCTCCTCCGAC	.	PASS	Atlas-SNP
ZBED5	58486	hgsc.bcm.edu	37	11	10875200	10875200	+	Silent	SNP	C	C	T	rs2232925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	28	98	0	0.358974	0	C|0.888;T|0.112	0.112	strong	.	ZBED5	50	.	NM_021211	exon3	c.G1293A	p.E431E	CCTCACCTCTGTA	.	PASS	Atlas-SNP
PSMD2	5708	hgsc.bcm.edu	37	3	184023918	184023918	+	Silent	SNP	A	A	G	rs34477849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	189	284	1	0.522099	0.00352113	A|0.976;G|0.024	0.024	strong	.	PSMD2	56	.	NM_002808	exon14	c.A1779G	p.T593T	CAACACACTGGTG	.	PASS	Atlas-SNP
SLC19A2	10560	hgsc.bcm.edu	37	1	169446639	169446639	+	Silent	SNP	C	C	A	rs150548640	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	50	76	0	0.609756	0	C|0.996;A|0.004	0.004	strong	.	SLC19A2	35	.	NM_006996	exon2	c.G561T	p.L187L	GCTGAACAGCGAC	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33927880	33927880	+	Missense_Mutation	SNP	C	C	G	rs16935295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	88	140	0	0.619718	0	C|0.965;G|0.035	0.035	strong	.	UBAP2	82	.	NM_018449	exon20	c.G2286C	p.M762I	GGTGTTCATGCTA	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170036466	170036466	+	Splice_Site	SNP	C	C	A	rs111656694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	119	106	0	1	0	C|0.980;A|0.020	0.020	strong	.	WDR27	129	.	NM_182552	exon20	c.2003+1G>T	.	TGCCTACCTCTTA	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	15	50	5	0.348837	0.1	G|0.870;A|0.130	0.130	strong	UBXN11,NS,carcinoma,0,2	UBXN11	54	2	NM_183008	exon16	c.C1476T	p.G492G	ACTGGGGCCGGGA	.	scavenged	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51738465	51738465	+	Missense_Mutation	SNP	G	G	A	rs58981829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	121	212	0	0.540179	0	G|0.955;A|0.045	0.045	strong	CD33,NS,carcinoma,0,1	CD33	55	1	NM_001772	exon5	c.G799A	p.V267I	GCTGGTGTTACAG	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	37	19	10407169	10407169	+	Silent	SNP	G	G	C	rs710845	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	15	6	0	1	0	G|0.499;C|0.501	0.501	strong	.	ICAM5	53	.	NM_003259	exon11	c.G2652C	p.L884L	GTGTCTGAACGGA	.	PASS	Atlas-SNP
DLK1	8788	hgsc.bcm.edu	37	14	101200780	101200780	+	Silent	SNP	T	T	C	rs2295660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	15	39	0	0.326087	0	T|0.981;C|0.019	0.019	strong	.	DLK1	57	.	NM_003836	exon5	c.T699C	p.C233C	CGAGTGTCTGTGC	.	PASS	Atlas-SNP
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	81	100	1	1	0.01	A|0.843;G|0.157	0.157	strong	BAIAP2_ENST00000321300,colon,carcinoma,0,1	BAIAP2	74	1	NM_001144888	exon14	c.A1556G	p.Q519R	ACGTCCAGCTGAA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017483	1017483	+	Missense_Mutation	SNP	T	T	G	rs79986665	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1213	220	901	170	0.181369	0.188679	T|0.500;G|0.500	0.500	weak	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.A5318C	p.H1773P	CTGGTGTGGTTGG	.	scavenged	Atlas-SNP
KIAA0196	9897	hgsc.bcm.edu	37	8	126079867	126079867	+	Silent	SNP	T	T	C	rs10429323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	72	132	0	0.48	0	T|0.971;C|0.029	0.029	strong	.	KIAA0196	90	.	NM_014846	exon10	c.A1245G	p.L415L	AGTATCTAACAGC	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	32716110	32716110	+	Silent	SNP	C	C	T	rs1800265	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	77	121	0	0.513333	0	C|0.852;T|0.148	0.148	strong	.	DMD	2127	.	NM_004006	exon9	c.G837A	p.T279T	ACTGACCGTGATC	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047354	46047354	+	Missense_Mutation	SNP	A	A	G	rs62220927	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	68	153	0	0.395349	0	A|0.896;G|0.104	0.104	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.A266G	p.Y89C	CGGCTTACTGCAC	.	PASS	Atlas-SNP
AJAP1	55966	hgsc.bcm.edu	37	1	4772053	4772053	+	Silent	SNP	T	T	C	rs1061968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	43	86	0	0.5375	0	T|0.549;C|0.451	0.451	strong	AJAP1,NS,carcinoma,0,1	AJAP1	68	1	NM_018836	exon2	c.T123C	p.C41C	CGCCTGTGAGGCC	.	PASS	Atlas-SNP
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	23	62	0	0.560976	0	A|0.607;T|0.393	0.393	strong	.	SLC30A5	54	.	NM_022902	exon14	c.A1800T	p.T600T	AGATACACTTGGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179479245	179479245	+	Silent	SNP	C	C	T	rs72677244	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	66	135	0	0.468085	0	C|0.941;T|0.059	0.059	strong	.	TTN	18412	.	NM_001267550	exon261	c.G48996A	p.E16332E	CACAGCCTCAATG	.	PASS	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	37	X	102962343	102962343	+	Missense_Mutation	SNP	T	T	C	rs61744012	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	84	116	0	0.617647	0	T|0.990;C|0.010	0.010	strong	.	GLRA4	86	.	NM_001024452	exon9	c.A1183G	p.I395V	TATAAATGCCAGA	.	PASS	Atlas-SNP
CXorf38	159013	hgsc.bcm.edu	37	X	40496354	40496354	+	Missense_Mutation	SNP	T	T	C	rs17145855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	155	319	0	0.479876	0	0|0.003;C|0.018	0.018	strong	.	CXorf38	29	.	NM_144970	exon4	c.A526G	p.T176A	GCCACGTAGAAGA	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385987	58385987	+	Missense_Mutation	SNP	C	C	G	rs111291730	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	126	234	1	0.490272	0.0042735	C|0.998;G|0.002	0.002	strong	.	ZNF814	93	.	NM_001144989	exon3	c.G771C	p.L257F	ATTACTCAAGCTA	.	PASS	Atlas-SNP
CNGA4	1262	hgsc.bcm.edu	37	11	6262715	6262715	+	Silent	SNP	G	G	A	rs7129498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	68	109	0	0.485714	0	G|0.774;A|0.226	0.226	strong	.	CNGA4	96	.	NM_001037329	exon5	c.G972A	p.Q324Q	CTTACAGCACTTG	.	PASS	Atlas-SNP
PRCP	5547	hgsc.bcm.edu	37	11	82550387	82550387	+	Silent	SNP	A	A	G	rs4843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	37	55	0	0.672727	0	A|0.900;G|0.100	0.100	strong	.	PRCP	69	.	NM_199418	exon8	c.T1065C	p.Y355Y	ATTGTAATATACA	.	PASS	Atlas-SNP
GAS6	2621	hgsc.bcm.edu	37	13	114526504	114526504	+	Silent	SNP	G	G	A	rs74118435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	54	86	0	0.568421	0	G|0.971;A|0.029	0.029	strong	.	GAS6	75	.	NM_000820	exon13	c.C1497T	p.V499V	AGTCCCGACGTCC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132514288	132514288	+	Silent	SNP	C	C	G	rs58319354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	26	81	0	0.351351	0	C|0.882;G|0.118	0.118	strong	.	EP400	370	.	NM_015409	exon28	c.C5424G	p.S1808S	CCCGTCCCTACGG	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38524226	38524226	+	Silent	SNP	A	A	G	rs2835632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	105	193	0	0.546875	0	A|0.931;G|0.069	0.069	strong	.	TTC3	182	.	NM_001001894	exon26	c.A2310G	p.K770K	CAAAAAATTGAAG	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48250026	48250026	+	Missense_Mutation	SNP	G	G	T	rs11863236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	52	30	0	0.981132	0	G|0.864;T|0.136	0.136	strong	.	ABCC11	177	.	NM_033151	exon6	c.C950A	p.A317E	ATTACCGCCAGTG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186057347	186057347	+	Silent	SNP	A	A	T	rs61745374	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	50	71	0	0.684932	0	A|0.953;T|0.047	0.047	strong	.	HMCN1	797	.	NM_031935	exon62	c.A9516T	p.T3172T	ATTAACATGTGAT	.	PASS	Atlas-SNP
CDH9	1007	hgsc.bcm.edu	37	5	26988328	26988328	+	Missense_Mutation	SNP	G	G	A	rs2288466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	81	198	0	0.452514	0	G|0.501;A|0.499	0.499	strong	CDH9,NS,carcinoma,+1,1	CDH9	305	1	NM_016279	exon2	c.C113T	p.A38V	AGACCCGCTATCT	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27679981	27679981	+	Missense_Mutation	SNP	T	T	C	rs3779620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	26	76	0	0.38806	0	T|0.817;C|0.183	0.183	strong	PBK_ENST00000301905,NS,carcinoma,0,1	PBK	29	1	NM_018492	exon5	c.A320G	p.N107S	CCATCATTGGCTT	.	PASS	Atlas-SNP
ALKBH5	54890	hgsc.bcm.edu	37	17	18088094	18088094	+	Silent	SNP	C	C	T	rs11078411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	83	0	0.490196	0	C|0.787;T|0.213	0.213	strong	.	ALKBH5	24	.	NM_017758	exon1	c.C537T	p.H179H	GGAGCACCGCGTC	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165649851	165649851	+	Missense_Mutation	SNP	C	C	G	rs1065756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	81	219	0	0.380282	0	C|0.978;G|0.022	0.022	strong	.	ALDH9A1	75	.	NM_000696	exon5	c.G662C	p.S221T	GCCTCACTGTAGA	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125316350	125316350	+	Missense_Mutation	SNP	C	C	T	rs1411272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	50	114	0	0.344828	0	C|0.431;N|0.000	.	strong	OR1N2,NS,carcinoma,0,1	OR1N2	51	1	NM_001004457	exon1	c.C902T	p.T301M	TTCCCACGCTAAA	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640785	3640785	+	Missense_Mutation	SNP	C	C	T	rs59939128	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	79	134	0	0.519737	0	C|0.927;T|0.073	0.073	strong	SLX4,NS,carcinoma,+2,1	SLX4	173	1	NM_032444	exon12	c.G2854A	p.A952T	CAAGCGCCTCCTC	.	PASS	Atlas-SNP
DPP8	54878	hgsc.bcm.edu	37	15	65739303	65739303	+	Silent	SNP	C	C	A	rs11009	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	32	90	0	0.372093	0	C|0.936;A|0.064	0.064	strong	.	DPP8	78	.	NM_197960	exon21	c.G2616T	p.S872S	TTCTCCCGATTCA	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43579679	43579679	+	Missense_Mutation	SNP	T	T	A	rs1058086	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	359	186	361	0	0.518106	0	T|0.897;A|0.103	0.103	strong	.	PSG2	84	.	NM_031246	exon3	c.A536T	p.Q179L	CACCACTGGTAGC	.	PASS	Atlas-SNP
ALKBH8	91801	hgsc.bcm.edu	37	11	107427616	107427616	+	Silent	SNP	C	C	G	rs17107135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	152	158	1	1	0.00632911	C|0.896;G|0.104	0.104	strong	.	ALKBH8	88	.	NM_138775	exon3	c.G243C	p.P81P	TGAGTACGGCTTG	.	PASS	Atlas-SNP
RUFY4	285180	hgsc.bcm.edu	37	2	218953991	218953991	+	Missense_Mutation	SNP	T	T	G	rs201137688	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	74	141	0	0.404372	0	T|0.999;G|0.001	0.001	weak	.	RUFY4	59	.	NM_198483	exon12	c.T1519G	p.W507G	CGCCTGTGGCAGA	.	PASS	Atlas-SNP
TBL3	10607	hgsc.bcm.edu	37	16	2025411	2025411	+	Silent	SNP	G	G	C	rs12925447	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	34	99	0	0.354167	0	G|0.918;C|0.082	0.082	strong	.	TBL3	54	.	NM_006453	exon9	c.G777C	p.G259G	CCCAGGGCTGTAC	.	PASS	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34811137	34811137	+	Silent	SNP	T	T	G	rs2271522	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	75	118	0	0.524476	0	T|0.715;G|0.285	0.285	strong	.	RAI14	100	.	NM_001145525	exon10	c.T480G	p.L160L	GCTGCTTCTTGCT	.	PASS	Atlas-SNP
OR1L3	26735	hgsc.bcm.edu	37	9	125437769	125437769	+	Missense_Mutation	SNP	A	A	G	rs16912099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	188	147	0	1	0	A|0.868;G|0.132	0.132	strong	.	OR1L3	51	.	NM_001005234	exon1	c.A361G	p.N121D	GCCATCAACCGCT	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261518	24261518	+	Silent	SNP	G	G	A	rs61731545	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	61	113	0	0.504132	0	G|0.979;A|0.021	0.021	strong	.	ADAMDEC1	69	.	NM_014479	exon13	c.G1323A	p.E441E	GAAGGAGTGTACC	.	PASS	Atlas-SNP
CARD9	64170	hgsc.bcm.edu	37	9	139264827	139264827	+	Silent	SNP	C	C	T	rs115057256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	71	87	0	0.78022	0	C|0.989;T|0.011	0.011	strong	CARD9,NS,NS,-1,1	CARD9	47	1	NM_052813	exon6	c.G870A	p.A290A	CCGCAGCGCCTGC	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39918323	39918323	+	Missense_Mutation	SNP	C	C	G	rs1803323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	329	178	303	0	0.541033	0	C|0.987;G|0.013	0.013	strong	.	ATF4	27	.	NM_001675	exon2	c.C772G	p.P258A	GCCCGTCCCAAAC	.	PASS	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62996038	62996038	+	Splice_Site	SNP	T	T	C	rs1783657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	80	0	0.505882	0	T|0.940;C|0.060	0.060	strong	.	SLC22A25	87	.	NM_199352	exon3	c.403-2A>G	.	TCCCACTGGAAGA	.	PASS	Atlas-SNP
DISP2	85455	hgsc.bcm.edu	37	15	40656141	40656141	+	Silent	SNP	T	T	C	rs12443160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	14	34	0	0.636364	0	T|0.861;C|0.139	0.139	strong	.	DISP2	86	.	NM_033510	exon2	c.T435C	p.H145H	GCACCATGTGGTC	.	PASS	Atlas-SNP
SPEM1	374768	hgsc.bcm.edu	37	17	7324340	7324340	+	Missense_Mutation	SNP	G	G	A	rs61741352	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	74	134	0	0.448485	0	G|0.962;A|0.038	0.038	strong	.	SPEM1	41	.	NM_199339	exon3	c.G346A	p.G116S	CGTCGAGGCTCTC	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61525488	61525488	+	Silent	SNP	A	A	G	rs112062101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	39	82	0	0.493671	0	A|0.994;G|0.006	0.006	strong	DIDO1,NS,carcinoma,-1,1	DIDO1	321	1	NM_080797	exon12	c.T2631C	p.S877S	CTTAACAGAAGCT	.	PASS	Atlas-SNP
GPRIN3	285513	hgsc.bcm.edu	37	4	90169025	90169025	+	Missense_Mutation	SNP	C	C	T	rs17015286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	92	169	0	0.522727	0	C|0.933;T|0.067	0.067	strong	.	GPRIN3	90	.	NM_198281	exon2	c.G2237A	p.R746K	CTTCCTCTGAGCT	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721812	101721812	+	Missense_Mutation	SNP	G	G	A	rs200409148	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	358	131	179	0	0.365922	0	.	.	weak	.	PABPC1	76	.	NM_002568	exon8	c.C1120T	p.R374C	CCTGGCGCTCTTC	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48265777	48265777	+	Missense_Mutation	SNP	C	C	T	rs16945988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	141	242	0	0.534091	0	C|0.880;T|0.120	0.120	strong	ABCC11,NS,carcinoma,-1,1	ABCC11	177	1	NM_033151	exon1	c.G56A	p.R19H	ATGCCACGATTCA	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130762732	130762732	+	Missense_Mutation	SNP	T	T	C	rs76700535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	47	101	0	0.401709	0	T|0.985;C|0.015	0.015	strong	.	GSDMC	71	.	NM_031415	exon11	c.A1028G	p.Y343C	ATACTGTAGAACA	.	PASS	Atlas-SNP
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381957	39381957	+	Silent	SNP	C	C	T	rs150187552	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	112	306	0	0.346749	0	C|0.998;T|0.002	0.002	strong	.	APOBEC3B	32	.	NM_004900	exon3	c.C315T	p.A105A	GCTGGCCGAATTC	.	PASS	Atlas-SNP
UGDH	7358	hgsc.bcm.edu	37	4	39510264	39510264	+	Silent	SNP	A	A	G	rs1129052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	24	50	0	0.631579	0	A|0.746;G|0.254	0.254	strong	.	UGDH	52	.	NM_003359	exon7	c.T828C	p.C276C	TTGGAAACAGCTC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901393	129901393	+	Missense_Mutation	SNP	T	T	C	rs11016071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	115	234	1	0.442308	0.0042735	T|0.781;C|0.219	0.219	strong	.	MKI67	363	.	NM_002417	exon13	c.A8711G	p.Q2904R	CTTGGCTGTCTCC	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139564101	139564101	+	Silent	SNP	C	C	T	rs12529180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	50	103	0	0.431034	0	C|0.908;T|0.092	0.092	strong	.	TXLNB	96	.	NM_153235	exon10	c.G1617A	p.K539K	TGGCTCCTTGAGA	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795913	29795913	+	Missense_Mutation	SNP	A	A	T	rs41551813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	53	81	0	0.602273	0	A|0.948;T|0.052	0.052	strong	.	HLA-G	90	.	NM_002127	exon3	c.A163T	p.T55S	GACGACACGCAGT	.	PASS	Atlas-SNP
METTL18	92342	hgsc.bcm.edu	37	1	169762807	169762807	+	Missense_Mutation	SNP	T	T	G	rs10489177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	73	155	0	0.5	0	T|0.802;G|0.198	0.198	strong	.	METTL18	23	.	NM_033418	exon2	c.A30C	p.E10D	ATGGTCTTCTATA	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170374	58170374	+	Missense_Mutation	SNP	T	T	C	rs12280114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	94	0	0.479167	0	T|0.668;C|0.332	0.332	strong	OR5B3,NS,carcinoma,0,1	OR5B3	65	1	NM_001005469	exon1	c.A509G	p.N170S	ACTTCATTGGACT	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	38	70	0	0.457831	0	T|0.693;C|0.307	0.307	strong	USHBP1,NS,carcinoma,0,2	USHBP1	85	2	NM_031941	exon9	c.A1315G	p.M439V	TCTTCATTAGAGA	.	PASS	Atlas-SNP
TTC14	151613	hgsc.bcm.edu	37	3	180325487	180325487	+	Silent	SNP	T	T	C	rs9858483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	36	73	0	0.409091	0	T|0.915;C|0.085	0.085	strong	.	TTC14	112	.	NM_001042601	exon10	c.T1224C	p.A408A	GAAAGCTTTGGCT	.	PASS	Atlas-SNP
CILP	8483	hgsc.bcm.edu	37	15	65496624	65496624	+	Missense_Mutation	SNP	C	C	G	rs140625947	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	75	137	0	0.457317	0	C|0.999;G|0.001	0.001	strong	.	CILP	124	.	NM_003613	exon6	c.G901C	p.A301P	ACTCTGCCTTGAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1265872	1265872	+	Missense_Mutation	SNP	G	G	A	rs200110372		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	460	58	432	0	0.126087	0	.	.	weak	MUC5B,NS,carcinoma,0,6	MUC5B	473	6	NM_002458	exon31	c.G7762A	p.G2588R	ACAACCGGGGCCA	.	scavenged	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854608	144854608	+	Missense_Mutation	SNP	T	T	G	rs2798855	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	394	61	337	0	0.154822	0	T|0.980;G|0.020	0.020	strong	.	PDE4DIP	817	.	NM_014644	exon42	c.A6862C	p.K2288Q	CCTGTTTGGATAC	.	PASS	Atlas-SNP
ELOVL5	60481	hgsc.bcm.edu	37	6	53159233	53159233	+	Silent	SNP	G	G	A	rs9474477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	76	124	0	0.546763	0	G|0.973;A|0.027	0.027	strong	.	ELOVL5	25	.	NM_001242831	exon3	c.C115T	p.L39L	GCTGTAGCCATCC	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56387421	56387421	+	Silent	SNP	T	T	C	rs34255389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	82	137	0	0.476744	0	T|0.996;C|0.004	0.004	strong	.	RFX7	170	.	NM_022841	exon9	c.A2505G	p.L835L	GCTATGTAGCTGC	.	PASS	Atlas-SNP
WDR64	128025	hgsc.bcm.edu	37	1	241929542	241929542	+	Missense_Mutation	SNP	G	G	A	rs12095445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	55	116	0	0.395683	0	G|0.839;A|0.161	0.161	strong	WDR64_ENST00000366552,NS,carcinoma,+1,2	WDR64	234	2	NM_144625	exon15	c.G1940A	p.R647Q	TATTACGAGTGAA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113149612	113149612	+	Missense_Mutation	SNP	T	T	C	rs114581956	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	80	247	0	0.33195	0	T|0.987;C|0.013	0.013	strong	.	SVEP1	326	.	NM_153366	exon42	c.A10013G	p.H3338R	GTGCAGTGTGCCT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037424	33037424	+	Missense_Mutation	SNP	T	T	C	rs1126542	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	137	169	0	1	0	T|0.680;G|0.000;C|0.319;A|0.000	0.319	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.A340G	p.T114A	CGTTGGTGGCCTG	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	81	141	0	0.47929	0	G|0.862;C|0.000;A|0.138	0.138	strong	NSUN2,colon,carcinoma,0,1	NSUN2	82	1	NM_017755	exon19	c.C2193T	p.D731D	AGTCACGTCATTG	.	PASS	Atlas-SNP
UBD	10537	hgsc.bcm.edu	37	6	29524003	29524003	+	Missense_Mutation	SNP	A	A	G	rs2076484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	71	149	0	0.493056	0	A|0.820;G|0.180	0.180	strong	.	UBD	13	.	NM_006398	exon2	c.T152C	p.L51S	CCCAGCAAAAGAA	.	PASS	Atlas-SNP
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679268	37679268	+	Missense_Mutation	SNP	G	G	T	rs9576175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	61	0	1	0	G|0.444;T|0.556	0.556	strong	CSNK1A1L,NS,carcinoma,0,1	CSNK1A1L	69	1	NM_145203	exon1	c.C126A	p.D42E	TGCTACGTCCTCG	.	PASS	Atlas-SNP
FPR1	2357	hgsc.bcm.edu	37	19	52249947	52249947	+	Missense_Mutation	SNP	C	C	G	rs2070745	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	81	143	0	0.50625	0	C|0.644;G|0.356	0.356	strong	FPR1,colon,carcinoma,0,2	FPR1	64	2	NM_001193306	exon3	c.G301C	p.V101L	TAAAGACGAATTT	.	PASS	Atlas-SNP
THAP4	51078	hgsc.bcm.edu	37	2	242572846	242572846	+	Silent	SNP	A	A	G	rs3208142	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	32	53	0	0.470588	0	A|0.650;G|0.350	0.350	strong	.	THAP4	27	.	NM_015963	exon2	c.T726C	p.S242S	GTGCTTAGAGGAG	.	PASS	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31417290	31417290	+	Missense_Mutation	SNP	T	T	C	rs76523220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	37	64	0	0.506849	0	T|0.964;C|0.036	0.036	strong	.	CAPN14	36	.	NM_001145122	exon9	c.A935G	p.N312S	CCGTCATTGTCTT	.	PASS	Atlas-SNP
PPP2R3B	28227	hgsc.bcm.edu	37	X	295132	295132	+	Silent	SNP	T	T	C	rs1133530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	13	16	0	1	0	T|0.485;C|0.515	0.515	strong	.	PPP2R3B	43	.	NM_013239	exon13	c.A1698G	p.A566A	CCCGCATGCGTAC	.	PASS	Atlas-SNP
FBLIM1	54751	hgsc.bcm.edu	37	1	16091700	16091700	+	Silent	SNP	G	G	A	rs61733331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	67	117	0	0.544715	0	G|0.988;A|0.012	0.012	strong	.	FBLIM1	46	.	NM_001024215	exon2	c.G222A	p.P74P	AGTGCCGGCTGCA	.	PASS	Atlas-SNP
SLC16A6	9120	hgsc.bcm.edu	37	17	66267734	66267734	+	Silent	SNP	T	T	C	rs61740584	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	54	134	0	0.453782	0	T|0.969;C|0.031	0.031	strong	.	SLC16A6	56	.	NM_001174166	exon6	c.A567G	p.L189L	TAACTGTAGTAGG	.	PASS	Atlas-SNP
CHD1L	9557	hgsc.bcm.edu	37	1	146763171	146763171	+	Missense_Mutation	SNP	T	T	A	rs61756300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	378	182	383	0	0.481481	0	T|0.984;A|0.016	0.016	strong	.	CHD1L	72	.	NM_004284	exon20	c.T2328A	p.S776R	CCTGAGTTTGGGA	.	PASS	Atlas-SNP
MIPEP	4285	hgsc.bcm.edu	37	13	24463414	24463414	+	Missense_Mutation	SNP	C	C	A	rs112735196	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	17	4	0	0.944444	0	C|0.994;A|0.006	0.006	strong	.	MIPEP	53	.	NM_005932	exon1	c.G46T	p.A16S	GCAGAGCTGCTGC	.	PASS	Atlas-SNP
FTSJ3	117246	hgsc.bcm.edu	37	17	61902011	61902011	+	Silent	SNP	C	C	T	rs9910549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	103	209	0	0.497585	0	C|0.976;T|0.024	0.024	strong	.	FTSJ3	63	.	NM_017647	exon10	c.G903A	p.G301G	CTTGCGCCCCAAC	.	PASS	Atlas-SNP
ZNF628	89887	hgsc.bcm.edu	37	19	55994975	55994975	+	Silent	SNP	G	G	T	rs114065657	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	50	72	0	0.537634	0	G|0.980;T|0.020	0.020	strong	.	ZNF628	75	.	NM_033113	exon3	c.G2415T	p.V805V	GAATGTGGGGGGT	.	PASS	Atlas-SNP
GPRASP1	9737	hgsc.bcm.edu	37	X	101912465	101912465	+	Silent	SNP	G	G	T	rs1124050	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	107	280	1	0.365188	0.00357143	0|0.003;A|0.000;G|0.981;T|0.016	0.016	strong	.	GPRASP1	140	.	NM_001099411	exon3	c.G3624T	p.P1208P	TTATCCGTCCTCC	.	PASS	Atlas-SNP
MFSD1	64747	hgsc.bcm.edu	37	3	158520011	158520011	+	Missense_Mutation	SNP	C	C	T	rs28364680	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	23	28	0	0.534884	0	C|0.842;T|0.158	0.158	strong	.	MFSD1	88	.	NM_022736	exon1	c.C217T	p.P73S	GGTGCCCCGGCCG	.	PASS	Atlas-SNP
SLC6A17	388662	hgsc.bcm.edu	37	1	110740931	110740931	+	Silent	SNP	G	G	A	rs6685009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	118	131	0	1	0	G|0.845;A|0.155	0.155	strong	.	SLC6A17	86	.	NM_001010898	exon12	c.G2049A	p.E683E	CAGTGAGGCACCT	.	PASS	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989243	60989243	+	Silent	SNP	T	T	C	rs34446012	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	33	61	0	0.507692	0	T|0.996;C|0.004	0.004	strong	.	.	.	.	NM_080833	exon10	c.A1164G	p.L388L	GACTGGTAGGGAG	.	PASS	Atlas-SNP
NT5E	4907	hgsc.bcm.edu	37	6	86195098	86195098	+	Silent	SNP	C	C	T	rs35478984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	109	0	0.431193	0	C|0.977;T|0.023	0.023	strong	.	NT5E	56	.	NM_001204813	exon4	c.C897T	p.N299N	AGGAAACGTCATC	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	42	111	0	0.336	0	C|0.665;T|0.335	0.335	strong	.	COL5A1	323	.	NM_000093	exon5	c.C738T	p.T246T	TGACACCGCAGTA	.	PASS	Atlas-SNP
GHITM	27069	hgsc.bcm.edu	37	10	85902479	85902479	+	Silent	SNP	A	A	T	rs146877821	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	46	61	0	0.474227	0	A|0.995;T|0.005	0.005	strong	.	GHITM	30	.	NM_014394	exon3	c.A198T	p.A66A	GGCAGCATTGGAA	.	PASS	Atlas-SNP
RHPN1	114822	hgsc.bcm.edu	37	8	144464073	144464073	+	Missense_Mutation	SNP	G	G	A	rs34746679	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	79	125	0	0.568345	0	G|0.989;A|0.011	0.011	strong	RHPN1_ENST00000289013,NS,carcinoma,-1,2	RHPN1	76	2	NM_052924	exon14	c.G1732A	p.A578T	AAGGCTGCGGGAG	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149323906	149323906	+	Silent	SNP	T	T	G	rs2277925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	62	99	0	0.529915	0	T|0.786;G|0.214	0.214	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon1	c.A331C	p.R111R	AAAGCCTGGTGGC	.	PASS	Atlas-SNP
BPI	671	hgsc.bcm.edu	37	20	36954790	36954790	+	Missense_Mutation	SNP	G	G	A	rs5743524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	52	143	0	0.422764	0	G|0.949;A|0.051	0.051	strong	.	BPI	67	.	NM_001725	exon10	c.G1129A	p.V377I	TTTGCCGTCCTCC	.	PASS	Atlas-SNP
KCNMB1	3779	hgsc.bcm.edu	37	5	169805956	169805956	+	Missense_Mutation	SNP	C	C	G	rs2301149	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	46	97	0	0.45098	0	C|0.898;G|0.102	0.102	strong	KCNMB1,NS,carcinoma,0,1	KCNMB1	38	1	NM_004137	exon4	c.G328C	p.E110Q	TGTCCACGCTGCC	.	PASS	Atlas-SNP
PTCH2	8643	hgsc.bcm.edu	37	1	45293518	45293518	+	Silent	SNP	A	A	G	rs7525308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	54	81	0	0.55102	0	A|0.574;G|0.426	0.426	strong	.	PTCH2	96	.	NM_001166292	exon14	c.T2055C	p.A685A	TACCTTAGCATGT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133953740	133953740	+	Missense_Mutation	SNP	A	A	C	rs61744749	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	147	292	1	0.472669	0.00342466	A|0.964;C|0.036	0.036	strong	TG,NS,carcinoma,+1,1	TG	416	1	NM_003235	exon26	c.A5186C	p.D1729A	CATGCGACCGTGA	.	PASS	Atlas-SNP
ZNF790	388536	hgsc.bcm.edu	37	19	37309790	37309790	+	Missense_Mutation	SNP	T	T	A	rs4369791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	19	48	0	0.463415	0	T|0.995;A|0.005	0.005	strong	.	ZNF790	89	.	NM_206894	exon5	c.A1456T	p.T486S	AAAAGGTCTTTCC	.	PASS	Atlas-SNP
SPRYD3	84926	hgsc.bcm.edu	37	12	53467230	53467230	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	53	0	0.407407	0	.	.	none	.	SPRYD3	29	.	NM_032840	exon6	c.C533A	p.S178Y	TCTGGGGACATGG	.	PASS	Atlas-SNP
BPHL	670	hgsc.bcm.edu	37	6	3152760	3152760	+	Missense_Mutation	SNP	T	T	C	rs2231370	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	84	146	0	0.5	0	T|0.949;C|0.051	0.051	strong	.	BPHL	32	.	NM_004332	exon7	c.T827C	p.L276S	TGCATTTGCGTTT	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149323772	149323772	+	Silent	SNP	G	G	A	rs2277926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	18	67	0	0.315789	0	G|0.807;A|0.193	0.193	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon1	c.C465T	p.N155N	CTCTGTGTTGGGG	.	PASS	Atlas-SNP
HOXD3	3232	hgsc.bcm.edu	37	2	177034130	177034130	+	Silent	SNP	G	G	A	rs77818566	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	56	141	0	0.482759	0	G|0.949;A|0.051	0.051	strong	.	HOXD3	65	.	NM_006898	exon2	c.G288A	p.G96G	CACTGGGAACAGC	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30039240	30039240	+	Missense_Mutation	SNP	G	G	T	rs2301753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	9	7	0	0.6	0	G|0.804;T|0.196	0.196	strong	.	RNF39	27	.	NM_025236	exon4	c.C911A	p.A304E	TCGTCCGCATCCT	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101816873	101816873	+	Missense_Mutation	SNP	A	A	G	rs35642150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	94	131	0	0.701493	0	A|0.988;G|0.012	0.012	strong	.	COL15A1	211	.	NM_001855	exon32	c.A2966G	p.K989R	GAGAGAAAGGATC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410775	105410775	+	Silent	SNP	A	A	G	rs2819424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	257	279	0	0.996124	0	A|0.444;G|0.556	0.556	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T11013C	p.D3671D	ACTCACATCGGCT	.	PASS	Atlas-SNP
TMEM30B	161291	hgsc.bcm.edu	37	14	61747644	61747644	+	Silent	SNP	A	A	G	rs3196765	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	0	0	1	.	A|0.214;G|0.786	0.786	strong	.	TMEM30B	13	.	NM_001017970	exon1	c.T222C	p.G74G	GCAGTTACCGGTG	.	PASS	Atlas-SNP
ZNF226	7769	hgsc.bcm.edu	37	19	44680489	44680489	+	Silent	SNP	G	G	A	rs2178342	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	98	131	0	0.989899	0	G|0.866;A|0.134	0.134	strong	.	.	.	.	NM_001032372	exon6	c.G1074A	p.T358T	CCACACGGCAGAG	.	PASS	Atlas-SNP
FTO	79068	hgsc.bcm.edu	37	16	53922838	53922838	+	Missense_Mutation	SNP	C	C	T	rs16952624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	156	299	0	0.478528	0	C|0.988;T|0.012	0.012	strong	FTO,NS,carcinoma,-1,1	FTO	51	1	NM_001080432	exon7	c.C1214T	p.A405V	TGGAAGCACTGTG	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127873186	127873186	+	Silent	SNP	C	C	T	rs55715053	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	26	9	0	0.962963	0	C|0.881;T|0.119	0.119	strong	.	FBN2	858	.	NM_001999	exon1	c.G111A	p.P37P	CCGGGGCGGCTTG	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88801457	88801457	+	Silent	SNP	G	G	A	rs115016757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	36	85	0	0.409091	0	G|0.966;A|0.034	0.034	strong	.	PIEZO1	79	.	NM_001142864	exon14	c.C1674T	p.P558P	CCGCGTGGGCTCT	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134048592	134048592	+	Missense_Mutation	SNP	G	G	T	rs34739733	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	66	106	0	0.478261	0	G|0.995;T|0.005	0.005	strong	.	NCAPD3	141	.	NM_015261	exon22	c.C2719A	p.P907T	GGGGGGGTGGCTG	.	PASS	Atlas-SNP
RGS13	6003	hgsc.bcm.edu	37	1	192628623	192628623	+	Missense_Mutation	SNP	G	G	C	rs16834603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	94	156	0	0.519337	0	G|0.955;C|0.045	0.045	strong	.	RGS13	31	.	NM_002927	exon7	c.G450C	p.L150F	ACTTTTGAAAACT	.	PASS	Atlas-SNP
OR1E2	8388	hgsc.bcm.edu	37	17	3336699	3336699	+	Missense_Mutation	SNP	C	C	G	rs78339092	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	96	225	0	0.421053	0	C|0.987;G|0.013	0.013	strong	OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	NM_003554	exon1	c.G437C	p.S146T	ATGGGGCTCATGA	.	PASS	Atlas-SNP
C6orf52	347744	hgsc.bcm.edu	37	6	10671764	10671764	+	Silent	SNP	G	G	A	rs3737278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	70	152	0	0.454545	0	G|0.907;A|0.093	0.093	strong	C6orf52,colon,carcinoma,0,1	C6orf52	9	1	NM_001145020	exon5	c.C384T	p.Y128Y	GGAGTCGTAGAGT	.	PASS	Atlas-SNP
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69098115	69098115	+	Silent	SNP	A	A	G	rs10018067	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	80	114	0	0.506329	0	A|0.973;G|0.027	0.027	strong	.	TMPRSS11B	66	.	NM_182502	exon6	c.T489C	p.S163S	CATTTCAGAAGCA	.	PASS	Atlas-SNP
DGKA	1606	hgsc.bcm.edu	37	12	56345408	56345408	+	Silent	SNP	T	T	G	rs11834873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	74	0	0.5	0	T|0.889;G|0.111	0.111	strong	.	DGKA	70	.	NM_201554	exon18	c.T1428G	p.G476G	CCTAGGTTATGAA	.	PASS	Atlas-SNP
SNAI1	6615	hgsc.bcm.edu	37	20	48600475	48600475	+	Missense_Mutation	SNP	C	C	T	rs34261470	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	19	43	0	0.38	0	C|0.979;T|0.021	0.021	strong	.	SNAI1	28	.	NM_005985	exon2	c.C197T	p.A66V	TCCTGGCGCCCCA	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156964944	156964944	+	Missense_Mutation	SNP	G	G	C	rs11134804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	91	0	0.483516	0	G|0.965;C|0.035	0.035	strong	.	ADAM19	216	.	NM_033274	exon4	c.C307G	p.Q103E	TGGTTTGAGGGTT	.	PASS	Atlas-SNP
LONRF2	164832	hgsc.bcm.edu	37	2	100915772	100915772	+	Missense_Mutation	SNP	A	A	G	rs4851287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	121	133	0	1	0	A|0.253;G|0.747	0.747	strong	.	LONRF2	62	.	NM_198461	exon6	c.T1277C	p.L426P	CTTTGAAGTGAGA	.	PASS	Atlas-SNP
OR6B2	389090	hgsc.bcm.edu	37	2	240969312	240969312	+	Missense_Mutation	SNP	A	A	G	rs61730690	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	481	186	443	0	0.386694	0	A|0.703;G|0.297	0.297	strong	.	OR6B2	30	.	NM_001005853	exon1	c.T535C	p.C179R	TGTCACAGAAGAA	.	PASS	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145281413	145281413	+	Missense_Mutation	SNP	G	G	A	rs76765512	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1480	388	1344	2	0.262162	0.0014881	G|0.980;A|0.020	0.020	strong	.	NOTCH2NL	100	.	NM_203458	exon4	c.G343A	p.A115T	CCCTGTGCAAATG	.	PASS	Atlas-SNP
ARSK	153642	hgsc.bcm.edu	37	5	94936744	94936744	+	Silent	SNP	G	G	A	rs61733083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	56	112	0	0.430769	0	G|0.990;A|0.010	0.010	strong	.	ARSK	29	.	NM_198150	exon7	c.G1290A	p.S430S	CTATTCGGATGGT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	112	265	0	0.449799	0	T|0.825;G|0.175	0.175	strong	.	CDRT1	83	.	NM_006382	exon11	c.A1930C	p.N644H	TCCCATTGAAGAA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179611851	179611851	+	Silent	SNP	C	C	T	rs72648910	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	146	283	3	0.530909	0.0106007	C|0.965;T|0.035	0.035	strong	TTN_ENST00000360870,NS,carcinoma,-2,1	TTN	18412	1	NM_133379	exon46	c.G15276A	p.L5092L	TCTCTCCAGAGTC	.	scavenged	Atlas-SNP
SDAD1	55153	hgsc.bcm.edu	37	4	76878716	76878716	+	Missense_Mutation	SNP	G	G	C	rs2242471	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	121	206	0	0.519313	0	G|0.688;C|0.312	0.312	strong	.	SDAD1	47	.	NM_018115	exon19	c.C1724G	p.S575C	TTCTGGGATTTCC	.	PASS	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	46999385	46999385	+	Missense_Mutation	SNP	C	C	T	rs113256776	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	15	37	0	0.214286	0	C|0.975;T|0.025	0.025	strong	.	GPRIN2	94	.	NM_014696	exon3	c.C505T	p.P169S	CAGGCCCCTGCAG	.	PASS	Atlas-SNP
STAG1	10274	hgsc.bcm.edu	37	3	136088038	136088038	+	Silent	SNP	G	G	A	rs9860801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	120	1	1	0.00833333	G|0.655;A|0.344	0.344	strong	.	STAG1	135	.	NM_005862	exon24	c.C2457T	p.F819F	TGGATTGAACACC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54120025	54120025	+	Missense_Mutation	SNP	A	A	T	rs805408	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	57	125	0	0.522936	0	A|0.713;T|0.287	0.287	strong	.	PSME4	247	.	NM_014614	exon36	c.T4111A	p.S1371T	CATGTGAATCTGC	.	PASS	Atlas-SNP
EMID1	129080	hgsc.bcm.edu	37	22	29621128	29621128	+	Missense_Mutation	SNP	C	C	G	rs743920	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	80	0	1	0	C|0.658;G|0.342	0.342	strong	.	EMID1	33	.	NM_133455	exon4	c.C326G	p.A109G	TTGCAGCTTCCTC	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	94	0	1	0	C|0.700;T|0.300	0.300	strong	ZNF30,colon,carcinoma,0,1	ZNF30	44	1	NM_001099438	exon3	c.C71T	p.S24F	CCTTCTCCCAGCA	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503155	140503155	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	444	13	370	2	0.0292793	0.00540541	.	.	none	PCDHB4,caecum,carcinoma,+1,1	PCDHB4	177	1	NM_018938	exon1	c.G1575T	p.A525A	GCAGGCGTTCGAG	.	scavenged	Atlas-SNP
CDH2	1000	hgsc.bcm.edu	37	18	25532304	25532304	+	Missense_Mutation	SNP	T	T	C	rs2289664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	51	103	0	0.481132	0	T|0.980;C|0.020	0.020	strong	.	CDH2	194	.	NM_001792	exon16	c.A2534G	p.N845S	GGGTCATTGTCAG	.	PASS	Atlas-SNP
GTPBP5	26164	hgsc.bcm.edu	37	20	60768615	60768615	+	Missense_Mutation	SNP	G	G	A	rs6062133	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	55	104	0	0.447154	0	A|0.128;C|0.000;G|0.872	0.128	strong	.	GTPBP5	43	.	NM_015666	exon2	c.G139A	p.G47S	TCGGTCGGCCGTG	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6538355	6538355	+	Silent	SNP	G	G	A	rs2301873	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	33	88	0	0.388235	0	G|0.637;A|0.363	0.363	strong	KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	NM_014804	exon2	c.C69T	p.S23S	GGGGTCGCTCCTC	.	PASS	Atlas-SNP
SLC2A8	29988	hgsc.bcm.edu	37	9	130162230	130162230	+	Silent	SNP	C	C	G	rs36057295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	32	155	0	0.296296	0	C|0.975;G|0.025	0.025	strong	.	SLC2A8	27	.	NM_014580	exon4	c.C471G	p.L157L	GTTGCTCGGCTCC	.	PASS	Atlas-SNP
NARS2	79731	hgsc.bcm.edu	37	11	78279744	78279744	+	Silent	SNP	T	T	C	rs60510975	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	97	185	0	0.502591	0	T|0.960;C|0.040	0.040	strong	NARS2,lower_third,carcinoma,-2,1	NARS2	62	1	NM_024678	exon3	c.A306G	p.P102P	TTTGGATGGACTT	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36004171	36004171	+	Missense_Mutation	SNP	C	C	A	rs12460932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	47	102	0	0.479592	0	C|0.751;A|0.249	0.249	strong	.	DMKN	116	.	NM_001190347	exon1	c.G207T	p.E69D	AAGGGCCTCACTG	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048539	33048539	+	Missense_Mutation	SNP	T	T	A	rs1042117	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	43	62	0	0.741379	0	T|0.803;A|0.197	0.197	strong	HLA-DPB1,rectum,carcinoma,-1,1	HLA-DPB1	28	1	NM_002121	exon2	c.T191A	p.F64Y	AGGAGTTCGCGCG	.	PASS	Atlas-SNP
GTDC1	79712	hgsc.bcm.edu	37	2	144899559	144899559	+	Missense_Mutation	SNP	C	C	A	rs3731958	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	55	183	0	0.458333	0	C|0.374;A|0.625	0.625	strong	.	GTDC1	61	.	NM_001006636	exon6	c.G411T	p.M137I	TTTTCCCATGGAA	.	PASS	Atlas-SNP
CHRNB4	1143	hgsc.bcm.edu	37	15	78922229	78922229	+	Missense_Mutation	SNP	T	T	C	rs56218866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	26	81	0	0.356164	0	T|0.982;C|0.018	0.018	strong	.	CHRNB4	59	.	NM_000750	exon5	c.A418G	p.S140G	GGACGCTGCCGTT	.	PASS	Atlas-SNP
PPP1R17	10842	hgsc.bcm.edu	37	7	31732089	31732089	+	Missense_Mutation	SNP	C	C	G	rs3735422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	44	98	0	0.376068	0	C|0.856;G|0.144	0.144	strong	C7orf16,NS,carcinoma,0,1	.	.	1	NM_006658	exon2	c.C34G	p.L12V	CTGGAACTCTCAG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3168816	3168816	+	Silent	SNP	G	G	A	rs2230167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	158	178	1	1	0.00561798	T|0.125;G|0.436;C|0.285;A|0.154	0.154	strong	.	MYOM1	192	.	NM_003803	exon9	c.C1338T	p.N446N	CTCACCGTTTCTG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90461235	90461235	+	Missense_Mutation	SNP	T	T	C	rs115558420	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	90	165	0	0.483871	0	T|0.997;C|0.003	0.003	strong	MDN1,NS,carcinoma,+2,1	MDN1	478	1	NM_014611	exon23	c.A3142G	p.K1048E	GCTCCTTGTCTCC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179594590	179594590	+	Silent	SNP	T	T	A	rs66523653	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	118	253	0	0.49789	0	T|0.984;A|0.016	0.016	strong	.	TTN	18412	.	NM_001267550	exon63	c.A18390T	p.T6130T	AGTGCCTGTTATT	.	PASS	Atlas-SNP
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	27	38	0	0.5625	0	C|0.902;T|0.098	0.098	strong	.	IHH	33	.	NM_002181	exon3	c.G600A	p.T200T	GCCGCCCGTCTTG	.	PASS	Atlas-SNP
RAET1G	353091	hgsc.bcm.edu	37	6	150240829	150240829	+	Missense_Mutation	SNP	G	G	C	rs9397449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	891	333	916	1	0.373737	0.0010917	G|0.807;C|0.193	0.193	strong	.	RAET1G	31	.	NM_001001788	exon2	c.C209G	p.T70R	GTGACTGTCTTGC	.	PASS	Atlas-SNP
ASPG	374569	hgsc.bcm.edu	37	14	104563932	104563932	+	Silent	SNP	G	G	T	rs1465163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	81	144	0	0.47093	0	G|0.778;T|0.222	0.222	strong	Q86U10_HUMAN,NS,carcinoma,0,2	ASPG	34	2	NM_001080464	exon5	c.G471T	p.L157L	GAACCTGCTGGGG	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71851080	71851080	+	Silent	SNP	C	C	T	rs12340440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	36	54	1	0.631579	0.0185185	C|0.983;T|0.017	0.017	strong	TJP2,colon,carcinoma,0,1	TJP2	120	1	NM_001170416	exon13	c.C2010T	p.D670D	GTATGACGGCAAG	.	scavenged	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	72	132	0	0.444444	0	T|0.784;C|0.216	0.216	strong	SCML4_ENST00000369020,colon,carcinoma,0,1	SCML4	65	1	NM_198081	exon7	c.A1080G	p.P360P	AGCCTGTGGGTCG	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2050151	2050151	+	Silent	SNP	A	A	G	rs114023844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	19	35	0	0.44186	0	A|0.978;G|0.022	0.022	strong	.	ZNF598	55	.	NM_178167	exon11	c.T1399C	p.L467L	GCGCCAACCCCAC	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71489695	71489695	+	Silent	SNP	C	C	T	rs2227915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	28	52	0	0.571429	0	C|0.968;T|0.032	0.032	strong	.	MAP1B	243	.	NM_005909	exon5	c.C513T	p.I171I	CCAGATCGGGGAG	.	PASS	Atlas-SNP
ARL11	115761	hgsc.bcm.edu	37	13	50205165	50205165	+	Missense_Mutation	SNP	G	G	C	rs35835937	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	91	167	0	0.56875	0	G|0.993;C|0.007	0.007	strong	.	ARL11	26	.	NM_138450	exon2	c.G582C	p.K194N	CAGCAAGAGATCT	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71061108	71061108	+	Silent	SNP	G	G	A	rs17662453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	61	105	0	0.580952	0	G|0.858;A|0.142	0.142	strong	.	CD207	47	.	NM_015717	exon3	c.C234T	p.V78V	CAACTGGACATTG	.	PASS	Atlas-SNP
IFNL1	282618	hgsc.bcm.edu	37	19	39789115	39789115	+	Missense_Mutation	SNP	A	A	G	rs30461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	183	0	1	0	A|0.733;G|0.267	0.267	strong	.	.	.	.	NM_172140	exon5	c.A562G	p.N188D	GATGGGAACCTGT	.	PASS	Atlas-SNP
KRT78	196374	hgsc.bcm.edu	37	12	53240025	53240025	+	Missense_Mutation	SNP	C	C	T	rs10876360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	95	0	0.986667	0	C|0.848;T|0.152	0.152	strong	.	KRT78	41	.	NM_173352	exon4	c.G712A	p.A238T	TCAGAGCCTCCAG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088825	56088825	+	Missense_Mutation	SNP	T	T	A	rs74445297	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	84	176	0	0.28866	0	T|0.752;A|0.248	0.248	strong	.	PSPH	23	.	NM_004577	exon4	c.A81T	p.R27S	TTCTTCTCTGATG	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289875	74289875	+	Silent	SNP	C	C	T	rs6501882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	65	143	0	0.477941	0	C|0.558;T|0.442	0.442	strong	.	QRICH2	143	.	NM_032134	exon4	c.G435A	p.G145G	CTGTCTCCCAGTA	.	PASS	Atlas-SNP
ZPBP2	124626	hgsc.bcm.edu	37	17	38028635	38028635	+	Silent	SNP	T	T	C	rs61737283	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	48	76	0	0.539326	0	T|0.868;C|0.132	0.132	strong	.	ZPBP2	33	.	NM_199321	exon5	c.T519C	p.S173S	GGATAGTCTAATT	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84924783	84924783	+	Missense_Mutation	SNP	G	G	C	rs73943384	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	77	0	0.493333	0	G|0.989;C|0.011	0.011	strong	.	DNAH6	194	.	NM_001370	exon47	c.G7609C	p.E2537Q	GAACTGGAGCAGG	.	PASS	Atlas-SNP
GABRB1	2560	hgsc.bcm.edu	37	4	47408850	47408850	+	Silent	SNP	C	C	T	rs115114447	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	235	222	0	1	0	C|0.982;T|0.018	0.018	strong	GABRB1,colon,carcinoma,+1,1	GABRB1	107	1	NM_000812	exon8	c.C987T	p.Y329Y	AAATTACATCTTC	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242066314	242066314	+	Silent	SNP	T	T	C	rs2240542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	45	111	0	0.351562	0	T|0.595;C|0.405	0.405	strong	.	PASK	230	.	NM_015148	exon10	c.A2016G	p.A672A	GGCTCCTGCAAGG	.	PASS	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75937971	75937971	+	Missense_Mutation	SNP	C	C	T	rs3822109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	83	165	0	0.50303	0	C|0.691;T|0.309	0.309	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.C380T	p.S127L	ACAGCTCGGGCAC	.	PASS	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52446200	52446200	+	Silent	SNP	G	G	A	rs6493537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	31	49	0	0.469697	0	G|0.873;A|0.127	0.127	strong	.	GNB5	28	.	NM_016194	exon4	c.C312T	p.H104H	GTTCCCGTGGCCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124417989	124417989	+	Missense_Mutation	SNP	C	C	T	rs61746561	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	43	76	0	0.409524	0	C|0.991;T|0.009	0.009	strong	.	DNAH10	888	.	NM_207437	exon76	c.C13054T	p.R4352C	CTGGACCGCTCCA	.	PASS	Atlas-SNP
CCDC54	84692	hgsc.bcm.edu	37	3	107096547	107096547	+	Missense_Mutation	SNP	G	G	A	rs709564	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	90	179	0	0.552147	0	G|0.632;A|0.368	0.368	strong	.	CCDC54	56	.	NM_032600	exon1	c.G113A	p.R38Q	AGATTCGGCACCA	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	120	204	0	0.43956	0	G|0.928;A|0.072	0.072	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.G301A	p.V101M	TGCTGTGTGCCCG	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	59	180	0	0.380645	0	C|0.709;T|0.291	0.291	strong	DYNC2H1_ENST00000398093,colon,carcinoma,-1,1	DYNC2H1	246	1	NM_001080463	exon76	c.C11060T	p.A3687V	TACAGGCGCTAAG	.	PASS	Atlas-SNP
PRDM14	63978	hgsc.bcm.edu	37	8	70967607	70967607	+	Silent	SNP	T	T	C	rs3750225	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	98	113	0	1	0	T|0.294;C|0.706	0.706	strong	.	PRDM14	102	.	NM_024504	exon7	c.A1416G	p.Q472Q	GGAAGATTGAGAG	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	73039594	73039594	+	Silent	SNP	C	C	T	rs80333477	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	97	147	0	0.548023	0	C|0.987;T|0.013	0.013	strong	.	UNC5B	123	.	NM_001244889	exon2	c.C96T	p.S32S	TGGCAGCGAGGTG	.	PASS	Atlas-SNP
RPH3AL	9501	hgsc.bcm.edu	37	17	171137	171137	+	Silent	SNP	C	C	A	rs78269977	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	22	76	0	0.366667	0	C|0.917;A|0.083	0.083	strong	.	RPH3AL	18	.	NM_001190413	exon3	c.G147T	p.P49P	CTCCGCCGGGCTG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37245935	37245935	+	Missense_Mutation	SNP	C	C	T	rs73750959	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	87	0	0.486486	0	C|0.980;T|0.020	0.020	strong	.	C5orf42	422	.	NM_023073	exon3	c.G94A	p.V32I	GAAAAACGGCTTC	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40122377	40122377	+	Missense_Mutation	SNP	G	G	A	rs78767806	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	104	250	0	0.433333	0	G|0.975;A|0.025	0.025	strong	.	N4BP2	166	.	NM_018177	exon9	c.G2646A	p.M882I	CATTATGGGTGAC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26699126	26699126	+	Silent	SNP	C	C	G	rs4335905	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	80	96	0	0.987654	0	C|0.421;G|0.579	0.579	strong	OTOF_ENST00000361394,NS,lymphoid_neoplasm,0,2	OTOF	524	2	NM_194248	exon23	c.G2736C	p.L912L	CAGGTACAGCTCC	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89857880	89857880	+	Silent	SNP	C	C	T	rs1800332	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	37	86	0	0.385417	0	C|0.967;T|0.033	0.033	strong	FANCA,NS,lymphoid_neoplasm,-1,1	FANCA	99	1	NM_000135	exon14	c.G1290A	p.A430A	CAGGAACGCAGTG	.	PASS	Atlas-SNP
LMNA	4000	hgsc.bcm.edu	37	1	156105028	156105028	+	Silent	SNP	T	T	C	rs538089	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	201	192	0	0.990148	0	T|0.808;C|0.192	0.192	strong	.	LMNA	31	.	NM_170707	exon5	c.T861C	p.A287A	GGGGGCTGCCCAC	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7571420	7571420	+	Silent	SNP	T	T	C	rs17168526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	131	283	0	0.41195	0	T|0.969;C|0.031	0.031	strong	.	COL28A1	113	.	NM_001037763	exon3	c.A240G	p.Q80Q	AGTCAATTGGAAA	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901887	52901887	+	Silent	SNP	A	A	G	rs75512966	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	47	0	0.5	0	A|0.981;G|0.019	0.019	strong	.	.	.	.	NM_019600	exon6	c.T1224C	p.L408L	CCGGAAAAGTTTT	.	PASS	Atlas-SNP
ZNF225	7768	hgsc.bcm.edu	37	19	44636802	44636802	+	Missense_Mutation	SNP	A	A	T	rs16978738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	98	171	0	0.547486	0	A|0.937;T|0.063	0.063	strong	ZNF225,NS,carcinoma,0,1	ZNF225	41	1	NM_013362	exon5	c.A2035T	p.T679S	GAGAAAACATCTA	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	6995417	6995417	+	Silent	SNP	C	C	T	rs2379207	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	97	157	0	0.518717	0	C|0.748;0|0.031	.	strong	.	HDHD1	21	.	NM_001135565	exon4	c.G423A	p.A141A	GAACGACGCGGAC	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56096686	56096686	+	Silent	SNP	A	A	C	rs74053638	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	84	168	0	0.575342	0	A|0.976;C|0.024	0.024	strong	.	KTN1	147	.	NM_004986	exon7	c.A1092C	p.T364T	GATGACAGAGAAA	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125592440	125592440	+	Silent	SNP	T	T	C	rs3733472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	147	307	0	0.480392	0	T|0.948;C|0.052	0.052	strong	.	ANKRD50	136	.	NM_020337	exon4	c.A1992G	p.L664L	ATGTTGTAGCAAA	.	PASS	Atlas-SNP
CYP39A1	51302	hgsc.bcm.edu	37	6	46563817	46563817	+	Missense_Mutation	SNP	A	A	T	rs7761731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	114	198	0	0.467213	0	A|0.592;T|0.408	0.408	strong	.	CYP39A1	41	.	NM_016593	exon8	c.T972A	p.N324K	AAGGAGATTCTCC	.	PASS	Atlas-SNP
FGGY	55277	hgsc.bcm.edu	37	1	59787350	59787350	+	Missense_Mutation	SNP	T	T	G	rs835409	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	97	143	0	0.451163	0	T|0.565;G|0.435	0.435	strong	FGGY_ENST00000303721,NS,carcinoma,0,1	FGGY	99	1	NM_001113411	exon2	c.T129G	p.N43K	TAAGAATTGGGAG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134622046	134622046	+	Missense_Mutation	SNP	C	C	T	rs73387072	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	72	94	0	0.585366	0	C|0.975;T|0.025	0.025	strong	.	TTC40	100	.	NM_001200049	exon58	c.G8027A	p.R2676H	CCCCGACGCAGAC	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	129989878	129989878	+	Silent	SNP	T	T	C	rs7808823	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	79	0	0.542857	0	C|0.512;N|0.000	0.512	strong	.	CPA5	61	.	NM_080385	exon5	c.T261C	p.S87S	TTTCTCTGAACTG	.	PASS	Atlas-SNP
DNAJC7	7266	hgsc.bcm.edu	37	17	40142302	40142302	+	Silent	SNP	T	T	C	rs1127182	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	50	114	0	0.510204	0	T|0.894;C|0.106	0.106	strong	.	DNAJC7	51	.	NM_003315	exon6	c.A579G	p.P193P	TGCTTCTGGATAA	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100087345	100087345	+	Silent	SNP	A	A	G	rs3747496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	66	78	0	0.733333	0	A|0.437;G|0.563	0.563	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon14	c.A1548G	p.S516S	GAGTTCACACCTC	.	PASS	Atlas-SNP
OR2K2	26248	hgsc.bcm.edu	37	9	114089883	114089883	+	Silent	SNP	G	G	A	rs61748722	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	123	167	0	0.719298	0	G|0.982;A|0.018	0.018	strong	.	OR2K2	77	.	NM_205859	exon1	c.C831T	p.Y277Y	CACTCCGTAAAGC	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	39	81	0	0.428571	0	T|0.448;C|0.552	0.552	strong	.	POLE	416	.	NM_006231	exon35	c.A4530G	p.A1510A	GACGGATGCCCTG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797696	29797696	+	Silent	SNP	A	A	G	rs1130363	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	208	202	1	1	0.00495049	A|0.442;G|0.558	0.558	strong	.	HLA-G	90	.	NM_002127	exon6	c.A999G	p.R333R	GTGGAGAAAGAAG	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33565755	33565755	+	Missense_Mutation	SNP	G	G	A	rs11906160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	14	45	0	0.35	0	G|0.858;A|0.142	0.142	strong	.	MYH7B	145	.	NM_020884	exon5	c.G73A	p.A25T	TGGGCCGCCTTGA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47925331	47925331	+	Missense_Mutation	SNP	C	C	G	rs10274334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	113	1	1	0.00884956	C|0.438;G|0.562	0.562	strong	.	PKD1L1	328	.	NM_138295	exon18	c.G3158C	p.R1053P	TCAGAGCGGCCAG	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25928508	25928508	+	Silent	SNP	C	C	T	rs142960034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	73	142	0	0.493243	0	C|0.996;T|0.004	0.004	strong	.	ATP10A	270	.	NM_024490	exon17	c.G3417A	p.G1139G	CAGCACCCCAGTC	.	PASS	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	37	5	140209429	140209429	+	Missense_Mutation	SNP	C	C	G	rs60309716	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	141	210	0	0.514599	0	C|0.940;G|0.060	0.060	strong	.	PCDHA6	442	.	NM_018909	exon1	c.C1753G	p.L585V	CGGTCACTGGGTG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20852029	20852029	+	Missense_Mutation	SNP	A	A	G	rs1760904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	8	0	1	0	A|0.367;G|0.633	0.633	strong	.	TEP1	224	.	NM_007110	exon25	c.T3583C	p.S1195P	CTAATGATGCCAC	.	PASS	Atlas-SNP
EIF4G3	8672	hgsc.bcm.edu	37	1	21177800	21177800	+	Missense_Mutation	SNP	A	A	T	rs2230572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	101	172	0	0.51269	0	A|0.995;T|0.005	0.005	strong	EIF4G3_ENST00000374937,NS,carcinoma,-2,2	EIF4G3	300	2	NM_001198801	exon26	c.T3663A	p.D1221E	CTCCACATCCACA	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45750725	45750725	+	Missense_Mutation	SNP	G	G	A	rs148023924	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	79	166	0	0.49375	0	G|0.997;A|0.003	0.003	strong	.	C21orf2	10	.	NM_004928	exon6	c.C623T	p.S208L	CTGCTCGAGGCAT	.	PASS	Atlas-SNP
SEC14L5	9717	hgsc.bcm.edu	37	16	5050678	5050678	+	Silent	SNP	C	C	T	rs61745575	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	50	125	0	0.480769	0	C|0.975;T|0.025	0.025	strong	SEC14L5,NS,carcinoma,+2,1	SEC14L5	79	1	NM_014692	exon9	c.C993T	p.L331L	CATCCTCCGCCTG	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931445	116931445	+	Missense_Mutation	SNP	T	T	C	rs2808770	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	60	83	0	0.594059	0	C|0.259;N|0.000	0.259	strong	.	COL27A1	200	.	NM_032888	exon3	c.T1610C	p.I537T	AGCCCATTGGATC	.	PASS	Atlas-SNP
TRIM67	440730	hgsc.bcm.edu	37	1	231298970	231298970	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	5	11	0	0.294118	0	.	.	none	.	TRIM67	160	.	NM_001004342	exon1	c.T255C	p.A85A	TGCAGCTGGCGGC	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370935	240370935	+	Silent	SNP	A	A	C	rs188083977	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	25	126	30	0.125628	0.238095	A|0.982;C|0.018	0.018	strong	FMN2,NS,carcinoma,+1,3	FMN2	451	3	NM_020066	exon5	c.A2823C	p.G941G	AGCGGGAATACCT	.	scavenged	Atlas-SNP
SGMS2	166929	hgsc.bcm.edu	37	4	108816880	108816880	+	Silent	SNP	G	G	A	rs150784082	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	101	0	0.530612	0	G|0.996;A|0.004	0.004	strong	.	SGMS2	39	.	NM_001136257	exon2	c.G171A	p.P57P	GTACCCGGACTAT	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24259600	24259600	+	Missense_Mutation	SNP	C	C	T	rs76707982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	39	53	0	0.639344	0	C|0.983;T|0.017	0.017	strong	ADAMDEC1_ENST00000256412,NS,malignant_melanoma,-1,1	ADAMDEC1	69	1	NM_014479	exon12	c.C1315T	p.P439S	GGCTCTCCTAAGG	.	PASS	Atlas-SNP
AMN	81693	hgsc.bcm.edu	37	14	103395212	103395212	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	54	45	0	0.580645	0	.	.	none	.	AMN	13	.	NM_030943	exon5	c.G413T	p.R138L	CCTGCCGCCACGA	.	PASS	Atlas-SNP
IL1RL2	8808	hgsc.bcm.edu	37	2	102808560	102808560	+	Missense_Mutation	SNP	G	G	A	rs138663033	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	95	226	0	0.39916	0	G|0.999;A|0.001	0.001	strong	.	IL1RL2	118	.	NM_003854	exon4	c.G469A	p.G157S	GTTTTGGGTCCAA	.	PASS	Atlas-SNP
ROGDI	79641	hgsc.bcm.edu	37	16	4849726	4849726	+	Missense_Mutation	SNP	G	G	C	rs143095485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	59	119	0	0.457364	0	G|0.980;C|0.020	0.020	strong	.	ROGDI	11	.	NM_024589	exon6	c.C393G	p.D131E	GCTCTGGTCCCGG	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39913634	39913634	+	Missense_Mutation	SNP	G	G	A	rs10407035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	65	89	0	0.53719	0	G|0.823;A|0.177	0.177	strong	.	PLEKHG2	329	.	NM_022835	exon18	c.G1940A	p.R647H	CCAGCCGCTGTGA	.	PASS	Atlas-SNP
HOXB8	3218	hgsc.bcm.edu	37	17	46690623	46690623	+	Missense_Mutation	SNP	G	G	C	rs112046402	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	65	143	0	0.460993	0	G|0.977;C|0.023	0.023	strong	.	HOXB8	26	.	NM_024016	exon2	c.C673G	p.L225V	GCTCCAGCTTCTG	.	PASS	Atlas-SNP
C19orf54	284325	hgsc.bcm.edu	37	19	41255603	41255603	+	Silent	SNP	G	G	A	rs2254338	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	89	126	0	0.559748	0	G|0.877;A|0.123	0.123	strong	.	C19orf54	13	.	NM_198476	exon1	c.C106T	p.L36L	AGTCCAGGGGACT	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27222266	27222266	+	Silent	SNP	A	A	G	rs35752220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	53	105	0	0.434426	0	A|0.970;G|0.030	0.030	strong	.	GABRG3	115	.	NM_001270873	exon2	c.A171G	p.E57E	AAGAGAATATGAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276699	152276699	+	Missense_Mutation	SNP	A	A	G	rs3126076	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	481	257	460	1	0.534304	0.00217391	A|0.167;G|0.833	0.833	weak	.	FLG	900	.	NM_002016	exon3	c.T10663C	p.W3555R	CAGACCACCTCTC	.	PASS	Atlas-SNP
KIAA1199	57214	hgsc.bcm.edu	37	15	81172064	81172064	+	Silent	SNP	G	G	A	rs35541581	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	62	112	0	0.496	0	G|0.928;A|0.072	0.072	strong	.	KIAA1199	118	.	NM_018689	exon4	c.G249A	p.L83L	CAAGCTGGTCATT	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123368013	123368013	+	Silent	SNP	A	A	G	rs1254392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	36	86	0	0.467532	0	A|0.731;G|0.269	0.269	strong	.	MYLK	224	.	NM_053025	exon25	c.T4317C	p.D1439D	ACCATCATCTGAC	.	PASS	Atlas-SNP
CYB561	1534	hgsc.bcm.edu	37	17	61513509	61513509	+	Silent	SNP	C	C	T	rs35447397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	85	0	0.460526	0	C|0.989;T|0.011	0.011	strong	.	CYB561	15	.	NM_001915	exon3	c.G207A	p.L69L	AACCAGCAGGGCT	.	PASS	Atlas-SNP
CCDC147	159686	hgsc.bcm.edu	37	10	106152111	106152111	+	Missense_Mutation	SNP	T	T	A	rs11192036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	35	53	0	0.538462	0	T|0.767;A|0.233	0.233	strong	.	CCDC147	137	.	NM_001008723	exon10	c.T1486A	p.S496T	GTGAGATCAGACA	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15290007	15290007	+	Missense_Mutation	SNP	C	C	T	rs10408676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	18	33	0	0.428571	0	C|0.924;T|0.076	0.076	strong	.	NOTCH3	340	.	NM_000435	exon22	c.G3547A	p.V1183M	GGTCCACGCAGGT	.	PASS	Atlas-SNP
PTDSS2	81490	hgsc.bcm.edu	37	11	490036	490036	+	Silent	SNP	G	G	A	rs75782220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	22	75	0	0.360656	0	G|0.960;A|0.040	0.040	strong	PTDSS2,caecum,carcinoma,0,3	PTDSS2	27	3	NM_030783	exon11	c.G1269A	p.A423A	CCTGGCGCTCACC	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113353285	113353285	+	Missense_Mutation	SNP	T	T	C	rs11726117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	133	0	1	0	C|0.679;N|0.000	0.679	strong	ALPK1,NS,carcinoma,-1,1	ALPK1	125	1	NM_001102406	exon11	c.T2582C	p.M861T	ACAGCATGGATGT	.	PASS	Atlas-SNP
HS3ST6	64711	hgsc.bcm.edu	37	16	1961866	1961866	+	Silent	SNP	G	G	A	rs61742747	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	97	93	0	0.989796	0	G|0.953;A|0.047	0.047	strong	.	HS3ST6	26	.	NM_001009606	exon2	c.C661T	p.L221L	TGACCAGACGCTC	.	PASS	Atlas-SNP
ATF6B	1388	hgsc.bcm.edu	37	6	32093922	32093922	+	Silent	SNP	G	G	A	rs204894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	70	120	0	0.530303	0	G|0.945;A|0.055	0.055	strong	.	ATF6B	40	.	NM_004381	exon5	c.C450T	p.N150N	GATAACGTTGATC	.	PASS	Atlas-SNP
LACC1	144811	hgsc.bcm.edu	37	13	44457925	44457925	+	Missense_Mutation	SNP	A	A	G	rs3764147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	61	110	0	0.442029	0	A|0.722;G|0.278	0.278	strong	.	.	.	.	NM_001128303	exon4	c.A760G	p.I254V	AATGACATCTGGA	.	PASS	Atlas-SNP
CDK12	51755	hgsc.bcm.edu	37	17	37682200	37682200	+	Missense_Mutation	SNP	A	A	G	rs61747430	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	106	202	0	0.443515	0	A|0.989;G|0.011	0.011	strong	.	CDK12	161	.	NM_016507	exon13	c.A3391G	p.I1131V	CTGAGCATCCCTC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	711905	711905	+	Silent	SNP	A	A	G	rs2301426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	32	79	0	0.390244	0	A|0.387;G|0.613	0.613	strong	WDR90,NS,carcinoma,0,1	WDR90	107	1	NM_145294	exon32	c.A3879G	p.P1293P	AGAGCCAGTCCCA	.	PASS	Atlas-SNP
NR1I2	8856	hgsc.bcm.edu	37	3	119530546	119530546	+	Silent	SNP	T	T	C	rs12721611	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	48	83	0	0.539326	0	T|0.981;C|0.019	0.019	strong	.	NR1I2	44	.	NM_022002	exon4	c.T609C	p.T203T	TGACACTACCTTC	.	PASS	Atlas-SNP
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	46	90	0	0.489362	0	C|0.786;T|0.214	0.214	strong	.	ZNF521	269	.	NM_015461	exon5	c.G3597A	p.K1199K	CTGACACTTGATG	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156067	39156067	+	Silent	SNP	A	A	G	rs9890989	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	64	177	0	0.335079	0	A|0.750;G|0.250	0.250	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.T39C	p.T13T	AGGCCCAGTGGGG	.	PASS	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942832	134942832	+	Silent	SNP	G	G	A	rs45586231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	61	22	0	0.983871	0	G|0.756;A|0.244	0.244	strong	.	GPR123	118	.	NM_001083909	exon7	c.G1500A	p.P500P	GCAGCCGGGCAGG	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55111364	55111364	+	Missense_Mutation	SNP	A	A	C	rs2296129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	69	146	0	0.530769	0	A|0.951;C|0.049	0.049	strong	.	.	.	.	NM_001013646	exon2	c.A386C	p.E129A	TGTCCGAAGTGCA	.	PASS	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475514	140475514	+	Missense_Mutation	SNP	C	C	A	rs73793576	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	72	135	0	0.521739	0	C|0.991;A|0.009	0.009	strong	.	PCDHB2	163	.	NM_018936	exon1	c.C1140A	p.N380K	AGACAACGGAAGG	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	38	54	0	0.463415	0	C|0.867;T|0.133	0.133	strong	.	KCNJ2	74	.	NM_000891	exon2	c.C1146T	p.L382L	TGCCCTCACAAGC	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149861927	149861927	+	Silent	SNP	G	G	A	rs184488465	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	44	69	0	0.666667	0	G|0.999;A|0.001	0.001	strong	.	KIF5C	166	.	NM_004522	exon22	c.G2394A	p.L798L	GACACTGCACAAC	.	PASS	Atlas-SNP
BRD7	29117	hgsc.bcm.edu	37	16	50368670	50368670	+	Missense_Mutation	SNP	C	C	A	rs113038433	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	59	136	0	0.307292	0	C|0.988;A|0.012	0.012	strong	.	BRD7	61	.	NM_013263	exon7	c.G839T	p.G280V	GCATCTCCAGAGT	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18354766	18354766	+	Silent	SNP	C	C	T	rs9617630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	46	87	0	0.484211	0	C|0.852;T|0.148	0.148	strong	.	MICAL3	53	.	NM_001136004	exon21	c.G2637A	p.P879P	GTTCTGCGGGAAC	.	PASS	Atlas-SNP
PPP1R12C	54776	hgsc.bcm.edu	37	19	55607447	55607447	+	Silent	SNP	G	G	A	rs35641913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	20	29	0	0.5	0	G|0.976;A|0.024	0.024	strong	PPP1R12C,NS,carcinoma,0,1	PPP1R12C	46	1	NM_017607	exon8	c.C1125T	p.D375D	ATCCTCGTCCTGG	.	PASS	Atlas-SNP
ANGPT4	51378	hgsc.bcm.edu	37	20	854973	854973	+	Silent	SNP	T	T	G	rs62641668	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	103	176	0	0.476852	0	T|0.983;G|0.017	0.017	strong	ANGPT4,bladder,carcinoma,-1,1	ANGPT4	77	1	NM_015985	exon8	c.A1305C	p.S435S	GTTGTCTGAGTCA	.	PASS	Atlas-SNP
SLC17A9	63910	hgsc.bcm.edu	37	20	61598731	61598731	+	Missense_Mutation	SNP	C	C	T	rs7271712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	126	209	0	0.529412	0	C|0.952;T|0.048	0.048	strong	.	SLC17A9	54	.	NM_022082	exon13	c.C1190T	p.T397M	AGACCACGGGCTC	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7495735	7495735	+	Missense_Mutation	SNP	T	T	C	rs55745506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	40	84	0	0.57971	0	T|0.729;C|0.271	0.271	strong	.	COL28A1	113	.	NM_001037763	exon16	c.A1311G	p.I437M	AGGTCCTATATCC	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1808343	1808343	+	Silent	SNP	C	C	T	rs147914724	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	41	67	0	0.431579	0	C|0.999;T|0.001	0.001	strong	ARHGEF10_ENST00000398564,colon,carcinoma,0,1	ARHGEF10	255	1	NM_014629	exon4	c.C474T	p.D158D	CCTGGACGAAGAA	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671536	238671536	+	Missense_Mutation	SNP	A	A	G	rs61744755	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	134	215	0	0.51938	0	A|0.948;G|0.052	0.052	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.A1180G	p.M394V	GAGGTCATGGGTG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16673975	16673975	+	Missense_Mutation	SNP	C	C	G	rs25901	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	91	99	0	0.98913	0	C|0.213;G|0.787	0.787	strong	.	MYO10	198	.	NM_012334	exon36	c.G4988C	p.S1663T	ATCTCGCTTCCTG	.	PASS	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108081217	108081217	+	Missense_Mutation	SNP	C	C	A	rs3792332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	25	79	0	0.462963	0	C|0.902;A|0.098	0.098	strong	.	HHLA2	95	.	NM_007072	exon7	c.C1032A	p.N344K	CCATAACAAAGGC	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74014628	74014628	+	Silent	SNP	G	G	A	rs2071193	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	95	196	0	0.437788	0	T|0.000;G|0.562;C|0.000;A|0.438	0.438	strong	.	EVPL	155	.	NM_001988	exon12	c.C1338T	p.H446H	CCAGGCGTGCGGG	.	PASS	Atlas-SNP
IL31RA	133396	hgsc.bcm.edu	37	5	55155402	55155402	+	Silent	SNP	C	C	T	rs1009639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	50	142	0	0.446429	0	C|0.334;T|0.666	0.666	strong	.	IL31RA	84	.	NM_001242637	exon2	c.C129T	p.P43P	GCTCCCCTCACTC	.	PASS	Atlas-SNP
C9orf66	157983	hgsc.bcm.edu	37	9	214908	214908	+	Silent	SNP	T	T	C	rs62533313	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	9	26	0	0.45	0	T|0.905;C|0.095	0.095	strong	.	C9orf66	16	.	NM_152569	exon1	c.A489G	p.R163R	GGCTACTCTGCGG	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657582	49657582	+	Missense_Mutation	SNP	T	T	C	rs114040533	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	65	182	1	0.283843	0.00549451	T|0.999;C|0.001	0.001	weak	HRC,NS,carcinoma,0,1	HRC	85	1	NM_002152	exon1	c.A913G	p.N305D	CATCATTGTCATC	.	scavenged	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	37	6	43496662	43496662	+	Silent	SNP	A	A	C	rs1106841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	56	0	1	0	A|0.635;C|0.365	0.365	strong	XPO5,colon,carcinoma,0,2	XPO5	79	2	NM_020750	exon24	c.T2679G	p.R893R	AAAGACACGTGCT	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76528790	76528790	+	Missense_Mutation	SNP	A	A	G	rs11651537	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	93	95	0	0.989362	0	A|0.513;G|0.487	0.487	strong	.	DNAH17	347	.	NM_173628	exon20	c.T2888C	p.I963T	ATCTCTATGAGGT	.	PASS	Atlas-SNP
CCNG2	901	hgsc.bcm.edu	37	4	78079768	78079768	+	Missense_Mutation	SNP	A	A	G	rs4150051	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	61	132	0	0.488	0	A|0.996;G|0.004	0.004	strong	.	CCNG2	27	.	NM_004354	exon2	c.A83G	p.E28G	AACAAGAAGAGAG	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43922535	43922535	+	Missense_Mutation	SNP	C	C	T	rs116482551	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	47	84	0	0.54023	0	C|0.995;T|0.005	0.005	strong	.	.	.	.	NM_175882	exon1	c.C263T	p.P88L	AGCGGCCCCTCCG	.	PASS	Atlas-SNP
ORC3	23595	hgsc.bcm.edu	37	6	88362943	88362943	+	Silent	SNP	C	C	T	rs2307393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	41	85	0	0.5	0	C|0.945;T|0.055	0.055	strong	.	ORC3	51	.	NM_181837	exon14	c.C1492T	p.L498L	GAGTTCCTGGCCC	.	PASS	Atlas-SNP
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190973	39190973	+	Missense_Mutation	SNP	C	C	G	rs62624960	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	51	193	0	0.223684	0	C|0.926;G|0.074	0.074	strong	.	KRTAP1-3	18	.	NM_030966	exon1	c.G101C	p.C34S	TGGCAGCAGCTGG	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	83	0	1	0	T|0.516;C|0.484	0.484	strong	IGDCC4,caecum,carcinoma,-1,1	IGDCC4	95	1	NM_020962	exon20	c.A3483G	p.P1161P	AGCCTCTGGAGGC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592265	1592265	+	Silent	SNP	A	A	G	rs45471597	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	65	136	0	0.315534	0	A|0.417;G|0.583	0.583	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.T171C	p.T57T	CAGGGAAGTCACA	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029474	136029474	+	Silent	SNP	C	C	T	rs35808997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	69	88	0	0.584746	0	C|0.934;T|0.066	0.066	strong	.	GBGT1	25	.	NM_021996	exon7	c.G534A	p.E178E	GGATGTCTCCTCC	.	PASS	Atlas-SNP
SYT8	90019	hgsc.bcm.edu	37	11	1858076	1858076	+	Missense_Mutation	SNP	C	C	T	rs115217397	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	21	55	0	0.368421	0	C|0.991;T|0.009	0.009	strong	.	SYT8	29	.	NM_138567	exon7	c.C817T	p.R273C	GGCCTGCGTCCAG	.	PASS	Atlas-SNP
WHAMM	123720	hgsc.bcm.edu	37	15	83499665	83499665	+	Silent	SNP	G	G	A	rs3814282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	25	48	0	0.378788	0	G|0.863;A|0.137	0.137	strong	.	WHAMM	63	.	NM_001080435	exon9	c.G1956A	p.P652P	GCCACCGCCGCCC	.	PASS	Atlas-SNP
SMARCA4	6597	hgsc.bcm.edu	37	19	11094903	11094903	+	Missense_Mutation	SNP	G	G	A	rs145867502	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	58	0	0.473684	0	G|0.999;A|0.001	0.001	strong	.	SMARCA4	502	.	NM_003072	exon2	c.G76A	p.A26T	CCTGGAGCCATGC	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	533001	533001	+	Missense_Mutation	SNP	T	T	C	rs1127410	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	113	222	0	0.502222	0	T|0.790;C|0.210	0.210	strong	.	PIGG	86	.	NM_001127178	exon13	c.T2795C	p.F932S	CAGTTTTCACGTA	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19118992	19118992	+	Missense_Mutation	SNP	A	A	G	rs3747052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	60	107	0	0.631579	0	A|0.959;G|0.041	0.041	strong	.	TSSK2	29	.	NM_053006	exon1	c.A80G	p.K27R	AAGTCAAATCTGC	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280234	39280234	+	Silent	SNP	C	C	T	rs611651	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	71	146	0	0.972603	0	C|0.333;T|0.667	0.667	weak	.	KRTAP4-12	32	.	NM_031854	exon1	c.G141A	p.R47R	CTGGGGCCTGCAG	.	PASS	Atlas-SNP
DHRS2	10202	hgsc.bcm.edu	37	14	24114490	24114490	+	Silent	SNP	G	G	A	rs7150155	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	39	61	1	0.549296	0.0163934	G|0.966;A|0.034	0.034	strong	DHRS2_ENST00000344777,NS,carcinoma,+1,1	DHRS2	78	1	NM_182908	exon9	c.G882A	p.V294V	AGCTGTGGTCCCA	.	scavenged	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	260	199	0	0.996169	0	G|0.641;A|0.359	0.359	strong	.	DNAH17	347	.	NM_173628	exon52	c.C8040T	p.L2680L	GCGGACGAGGTCC	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200971353	200971353	+	Silent	SNP	A	A	G	rs61740482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	81	155	0	0.54	0	A|0.959;G|0.041	0.041	strong	KIF21B,NS,carcinoma,0,1	KIF21B	208	1	NM_017596	exon9	c.T1338C	p.D446D	GATGGCATCGATG	.	PASS	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	91	241	0	0.450495	0	C|0.686;T|0.314	0.314	strong	.	DDX47	37	.	NM_201224	exon2	c.C150T	p.I50I	CAAGATCCAGATT	.	PASS	Atlas-SNP
GFM1	85476	hgsc.bcm.edu	37	3	158372389	158372389	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	62	110	0	0.488189	0	.	.	none	.	GFM1	83	.	NM_024996	exon8	c.A1052C	p.H351P	ATTCCCACCCATT	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53104078	53104078	+	Silent	SNP	G	G	A	rs72598686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	37	61	0	0.389474	0	G|0.706;A|0.294	0.294	strong	POM121L12,NS,carcinoma,0,1	POM121L12	146	1	NM_182595	exon1	c.G714A	p.P238P	GAAGCCGAGCCTC	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778261	84778261	+	Silent	SNP	G	G	A	rs77170713	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	77	119	0	0.531034	0	G|0.997;A|0.003	0.003	strong	.	USP10	51	.	NM_001272075	exon5	c.G186A	p.E62E	AATTGAGTTTGGT	.	PASS	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12089704	12089704	+	Missense_Mutation	SNP	G	G	A	rs79043756	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	63	122	0	0.533898	0	G|0.979;A|0.021	0.021	strong	.	ZNF763	31	.	NM_001012753	exon4	c.G974A	p.R325H	CATTCCGTAGTTA	.	PASS	Atlas-SNP
PPP2R3B	28227	hgsc.bcm.edu	37	X	299360	299360	+	Missense_Mutation	SNP	G	G	A	rs1133520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	68	124	0	0.468966	0	G|0.755;A|0.245	0.245	strong	.	PPP2R3B	43	.	NM_013239	exon12	c.C1556T	p.A519V	TCTCCCGCAGTCT	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5291126	5291126	+	Missense_Mutation	SNP	T	T	C	rs149760662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	61	86	0	0.512605	0	T|0.998;C|0.002	0.002	strong	.	NUP88	47	.	NM_002532	exon12	c.A1742G	p.D581G	GCCAAGTCCTGTT	.	PASS	Atlas-SNP
ATF7IP2	80063	hgsc.bcm.edu	37	16	10527404	10527404	+	Missense_Mutation	SNP	G	G	A	rs141089693	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	81	152	0	0.509434	0	G|0.999;A|0.001	0.001	strong	.	ATF7IP2	40	.	NM_024997	exon4	c.G858A	p.M286I	GAGGATGTTTTCA	.	PASS	Atlas-SNP
SLC22A3	6581	hgsc.bcm.edu	37	6	160769811	160769811	+	Silent	SNP	C	C	T	rs668871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	4	2	0	0.8	0	T|0.369;G|0.002;C|0.629	0.369	strong	.	SLC22A3	58	.	NM_021977	exon1	c.C360T	p.R120R	CAACCGCTCGGCT	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27356271	27356271	+	Silent	SNP	T	T	C	rs112497527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	50	127	0	0.45045	0	T|0.988;C|0.012	0.012	strong	.	IL4R	70	.	NM_000418	exon5	c.T291C	p.D97D	TGCGGATAACTAT	.	PASS	Atlas-SNP
NTSR1	4923	hgsc.bcm.edu	37	20	61386231	61386231	+	Silent	SNP	C	C	T	rs6010685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	19	35	0	0.655172	0	C|0.934;T|0.066	0.066	strong	NTSR1,NS,malignant_melanoma,+1,1	NTSR1	59	1	NM_002531	exon2	c.C909T	p.R303R	CGTGCGCGTCCTA	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	417691	417691	+	Missense_Mutation	SNP	C	C	G	rs114486517	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	69	119	0	0.514925	0	C|0.937;G|0.063	0.063	strong	.	MRPL28	15	.	NM_006428	exon6	c.G755C	p.R252T	CTGGCTCTCTTCT	.	PASS	Atlas-SNP
INSC	387755	hgsc.bcm.edu	37	11	15170686	15170686	+	Missense_Mutation	SNP	G	G	A	rs61877970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	47	0	1	0	G|0.946;A|0.054	0.054	strong	.	INSC	104	.	NM_001031853	exon2	c.G107A	p.R36H	ACGACCGCTGCAA	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	119	198	0	0.512931	0	A|0.526;G|0.474	0.474	strong	.	NUP88	47	.	NM_002532	exon17	c.T2172C	p.H724H	CCTTATATGTTCA	.	PASS	Atlas-SNP
KRT81	3887	hgsc.bcm.edu	37	12	52685213	52685213	+	Missense_Mutation	SNP	T	T	G	rs79897879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	21	43	1	0.617647	0.0232558	T|0.923;G|0.077	0.077	strong	KRT81,NS,carcinoma,0,2	KRT81	46	2	NM_002281	exon1	c.A37C	p.S13R	TGCAGCTGAAGGC	.	scavenged	Atlas-SNP
EIF3M	10480	hgsc.bcm.edu	37	11	32622233	32622233	+	Splice_Site	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	12	86	0	0.111111	0	.	.	none	.	EIF3M	37	.	NM_006360	exon9	c.800-2A>T	.	TTTTCTAGGCCTG	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	63	100	0	0.45	0	C|0.758;G|0.242	0.242	strong	.	ST8SIA2	41	.	NM_006011	exon5	c.C621G	p.P207P	GAACCCCTCGGTC	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109904249	109904249	+	Missense_Mutation	SNP	C	C	T	rs61734250	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	97	213	0	0.482587	0	C|0.977;T|0.023	0.023	strong	TMEM232_ENST00000455884,rectum,carcinoma,0,2	TMEM232	57	2	NM_001039763	exon11	c.G1354A	p.E452K	GTTCTTCGTCTCC	.	PASS	Atlas-SNP
LHFPL2	10184	hgsc.bcm.edu	37	5	77784810	77784810	+	Silent	SNP	A	A	C	rs35110604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	83	163	0	0.497006	0	A|0.982;C|0.018	0.018	strong	.	LHFPL2	9	.	NM_005779	exon5	c.T597G	p.A199A	GAAGACAGCACAG	.	PASS	Atlas-SNP
MBLAC2	153364	hgsc.bcm.edu	37	5	89769834	89769834	+	Silent	SNP	G	G	A	rs9293544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	49	60	0	0.590361	0	G|0.951;A|0.049	0.049	strong	.	MBLAC2	9	.	NM_203406	exon1	c.C276T	p.L92L	CTGGTAGAGGCCG	.	PASS	Atlas-SNP
FAM155B	27112	hgsc.bcm.edu	37	X	68725640	68725640	+	Missense_Mutation	SNP	T	T	C	rs1171942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	269	261	1	0.996296	0.00383142	T|0.456;C|0.544	0.544	strong	.	FAM155B	44	.	NM_015686	exon1	c.T515C	p.L172P	ACTCCCTTTCCCG	.	PASS	Atlas-SNP
ABL1	25	hgsc.bcm.edu	37	9	133761001	133761001	+	Silent	SNP	A	A	G	rs1056171	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	141	1	1	0.0070922	A|0.391;G|0.609	0.609	strong	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	NM_007313	exon11	c.A3381G	p.P1127P	TGGTCCAGCGGCC	.	PASS	Atlas-SNP
AKTIP	64400	hgsc.bcm.edu	37	16	53526366	53526366	+	Silent	SNP	T	T	C	rs16952272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	87	180	0	0.472826	0	T|0.990;C|0.010	0.010	strong	.	AKTIP	16	.	NM_022476	exon10	c.A837G	p.S279S	CTGTACTGAGCCA	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48063076	48063076	+	Silent	SNP	T	T	C	rs568215	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	40	88	0	0.39604	0	T|0.258;C|0.742	0.742	strong	.	SEMA6D	322	.	NM_153618	exon19	c.T2316C	p.P772P	TCTTCCTACTCCT	.	PASS	Atlas-SNP
EXOC3L1	283849	hgsc.bcm.edu	37	16	67219107	67219107	+	Missense_Mutation	SNP	G	G	C	rs9939768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	49	103	0	0.401639	0	G|0.838;C|0.162	0.162	strong	.	EXOC3L1	52	.	NM_178516	exon11	c.C1681G	p.Q561E	CACTTTGCAGGAG	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102463407	102463407	+	Silent	SNP	A	A	G	rs12893215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	110	153	0	0.564103	0	A|0.836;G|0.164	0.164	strong	DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	NM_001376	exon16	c.A3600G	p.Q1200Q	AAAGCAAAGGTTC	.	PASS	Atlas-SNP
SLC9A4	389015	hgsc.bcm.edu	37	2	103148868	103148868	+	Silent	SNP	G	G	A	rs59687519	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	59	80	0	0.578431	0	G|0.981;A|0.019	0.019	strong	.	SLC9A4	115	.	NM_001011552	exon12	c.G2118A	p.E706E	GCAAGAGGCACAA	.	PASS	Atlas-SNP
TRPS1	7227	hgsc.bcm.edu	37	8	116631902	116631902	+	Silent	SNP	C	C	A	rs7823278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	97	0	1	0	C|0.873;A|0.127	0.127	strong	TRPS1_ENST00000395715,NS,carcinoma,-1,2	TRPS1	516	2	NM_014112	exon3	c.G423T	p.P141P	TCTTTGCGGAGAC	.	PASS	Atlas-SNP
RNF208	727800	hgsc.bcm.edu	37	9	140115554	140115554	+	Silent	SNP	G	G	A	rs144152667	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	48	129	0	0.307692	0	G|0.964;A|0.036	0.036	strong	.	RNF208	11	.	NM_031297	exon1	c.C111T	p.H37H	TTCAGGGTGGACA	.	PASS	Atlas-SNP
PIDD	55367	hgsc.bcm.edu	37	11	800186	800186	+	Missense_Mutation	SNP	C	C	T	rs148849040	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	41	61	0	0.683333	0	C|1.000;T|0.000	0.000	weak	.	PIDD	76	.	NM_145886	exon14	c.G2219A	p.R740Q	CTCTGCCGGGCAG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39265558	39265558	+	Silent	SNP	T	T	A	rs41292757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	61	101	0	0.476562	0	T|0.972;A|0.028	0.028	strong	.	FREM2	385	.	NM_207361	exon1	c.T4077A	p.G1359G	TACTGGTGCCTTT	.	PASS	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	37	8	103311153	103311153	+	Silent	SNP	C	C	T	rs61752302	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	54	142	0	0.432	0	C|0.972;T|0.028	0.028	strong	.	UBR5	285	.	NM_015902	exon25	c.G3249A	p.A1083A	AGCATTCGCCTTT	.	PASS	Atlas-SNP
PMFBP1	83449	hgsc.bcm.edu	37	16	72156842	72156842	+	Missense_Mutation	SNP	T	T	G	rs16973716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	35	75	0	0.4375	0	T|0.542;G|0.458	0.458	strong	.	PMFBP1	101	.	NM_031293	exon19	c.A2739C	p.K913N	AATGTATTTCACC	.	PASS	Atlas-SNP
PRRG2	5639	hgsc.bcm.edu	37	19	50086806	50086806	+	Silent	SNP	C	C	T	rs3745474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	60	0	1	0	C|0.741;T|0.259	0.259	strong	PRRG2,NS,carcinoma,0,1	PRRG2	13	1	NM_000951	exon3	c.C93T	p.F31F	AGTCTTCCTGGGT	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912736	45912736	+	Missense_Mutation	SNP	C	C	A	rs3212986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	8	25	0	0.333333	0	C|0.723;A|0.277	0.277	strong	.	CD3EAP	27	.	NM_012099	exon3	c.C1510A	p.Q504K	CGGAAGCAGCAGC	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123894246	123894246	+	Missense_Mutation	SNP	A	A	G	rs79669172	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	500	267	415	0	0.534	0	A|0.952;G|0.048	0.048	strong	.	OR10G9	80	.	NM_001001953	exon1	c.A527G	p.Y176C	AGCACTATTTGTG	.	PASS	Atlas-SNP
C4orf22	255119	hgsc.bcm.edu	37	4	81866010	81866010	+	Missense_Mutation	SNP	A	A	C	rs201959026	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	148	282	1	0.451219	0.0035461	.	.	weak	.	C4orf22	35	.	NM_001206997	exon6	c.A574C	p.N192H	AGTCCCAACTATC	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	91	168	0	0.419355	0	C|0.789;T|0.211	0.211	strong	.	WBSCR28	24	.	NM_182504	exon2	c.C111T	p.L37L	CCTGCTCCTCAAG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	44	104	0	0.235294	0	C|0.996;T|0.004	0.004	strong	PSPH,rectum,carcinoma,0,1	PSPH	23	1	NM_004577	exon4	c.G4A	p.V2I	GGGAGACCATCGC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225152298	225152298	+	Missense_Mutation	SNP	A	A	T	rs79645812	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	47	134	0	0.484536	0	A|0.995;T|0.005	0.005	strong	.	DNAH14	300	.	NM_144989	exon5	c.A485T	p.K162M	TTCAGAAGATTAC	.	PASS	Atlas-SNP
CRYZ	1429	hgsc.bcm.edu	37	1	75175886	75175886	+	Missense_Mutation	SNP	T	T	C	rs3819946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	121	205	0	0.465385	0	C|0.339;N|0.000	0.339	strong	.	CRYZ	28	.	NM_001130043	exon6	c.A526G	p.I176V	CCAAAATCTTTAA	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30915262	30915262	+	Silent	SNP	C	C	T	rs10215354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	118	124	0	1	0	C|0.858;T|0.142	0.142	strong	.	FAM188B	62	.	NM_032222	exon15	c.C1962T	p.N654N	TTACAACATGTGC	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	68	92	0	0.612613	0	0|0.025;A|0.455	0.455	strong	.	GPR112	459	.	NM_153834	exon6	c.C1103A	p.P368H	AACCACCTACACC	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43236176	43236176	+	Silent	SNP	G	G	A	rs4075967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	88	136	0	0.502857	0	G|0.802;A|0.198	0.198	strong	.	PRDM15	110	.	NM_022115	exon26	c.C3375T	p.H1125H	CAGCGCGTGCTTG	.	PASS	Atlas-SNP
PEPD	5184	hgsc.bcm.edu	37	19	33968991	33968991	+	Missense_Mutation	SNP	T	T	A	rs61748998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	80	194	0	0.509554	0	T|0.978;A|0.022	0.022	strong	.	PEPD	48	.	NM_000285	exon7	c.A509T	p.E170V	TTGACTTCGAACC	.	PASS	Atlas-SNP
LRGUK	136332	hgsc.bcm.edu	37	7	133881794	133881794	+	Silent	SNP	T	T	C	rs35258804	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	54	135	0	0.55102	0	T|0.963;C|0.037	0.037	strong	.	LRGUK	113	.	NM_144648	exon13	c.T1482C	p.N494N	ATTAAATAGGGAC	.	PASS	Atlas-SNP
RPA1	6117	hgsc.bcm.edu	37	17	1795180	1795180	+	Silent	SNP	T	T	C	rs2230931	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	34	61	0	0.548387	0	T|0.751;C|0.249	0.249	strong	.	RPA1	48	.	NM_002945	exon15	c.T1605C	p.S535S	GGAGTCTGCTGAA	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42179424	42179424	+	Missense_Mutation	SNP	C	C	T	rs890499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	140	231	0	0.510949	0	C|0.929;T|0.071	0.071	strong	.	SPTBN5	171	.	NM_016642	exon6	c.G770A	p.R257K	AGTCTCCTCTGGA	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229783361	229783361	+	Silent	SNP	C	C	T	rs137900306	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	74	168	0	0.521127	0	C|0.999;T|0.001	0.001	strong	.	URB2	152	.	NM_014777	exon7	c.C4011T	p.I1337I	GGCCATCGGCAAC	.	PASS	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	37	11	71948536	71948536	+	Missense_Mutation	SNP	C	C	G	rs11548491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	78	149	0	0.493671	0	C|0.871;G|0.129	0.129	strong	.	INPPL1	120	.	NM_001567	exon26	c.C3248G	p.A1083G	GTGGGGCTGAGGC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32032689	32032689	+	Silent	SNP	C	C	T	rs35206129	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	64	128	0	0.481203	0	C|0.995;T|0.005	0.005	strong	.	TNXB	553	.	NM_019105	exon19	c.G6750A	p.S2250S	CAGGCCCGAGATG	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10610236	10610236	+	Silent	SNP	A	A	G	rs1048287	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	131	0	0.991304	0	A|0.885;G|0.115	0.115	strong	.	KEAP1	182	.	NM_012289	exon2	c.T474C	p.G158G	GACAGCACCGTTC	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	32	77	0	0.376471	0	C|0.865;T|0.135	0.135	strong	.	DHX9	114	.	NM_001357	exon16	c.C1746T	p.T582T	GATGACCCACTTT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152285137	152285137	+	Missense_Mutation	SNP	G	G	T	rs3120654	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	228	252	1	0.987013	0.00396825	G|0.892;T|0.108	0.108	strong	.	FLG	900	.	NM_002016	exon3	c.C2225A	p.S742Y	CCACTGGACCCTC	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21134282	21134282	+	Missense_Mutation	SNP	C	C	G	rs41277370	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	26	59	0	0.40625	0	C|0.937;G|0.063	0.063	strong	NEBL,NS,carcinoma,0,1	NEBL	199	1	NM_006393	exon12	c.G1132C	p.D378H	CAAAATCCTCTTT	.	PASS	Atlas-SNP
KIAA0319	9856	hgsc.bcm.edu	37	6	24551664	24551664	+	Missense_Mutation	SNP	T	T	C	rs807534	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	314	321	0	1	0	T|0.886;C|0.114	0.114	strong	.	KIAA0319	117	.	NM_001168375	exon20	c.A3038G	p.Y1013C	TTACCATATTTGG	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167689296	167689296	+	Silent	SNP	C	C	T	rs17632540	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	173	166	1	1	0.0060241	C|0.820;T|0.180	0.180	strong	.	.	.	.	NM_001122679	exon29	c.C7779T	p.N2593N	GAACAACGCCTAC	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	60	126	0	0.48	0	G|0.813;A|0.187	0.187	strong	TNN,right_upper_lobe,carcinoma,+1,1	TNN	297	1	NM_022093	exon15	c.G3312A	p.T1104T	GGAAACGGACGGA	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60776103	60776103	+	Silent	SNP	T	T	C	rs61899223	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	53	98	0	0.481818	0	T|0.838;C|0.162	0.162	strong	.	CD6	122	.	NM_006725	exon4	c.T567C	p.T189T	TGACACTTGGGAC	.	PASS	Atlas-SNP
RXRB	6257	hgsc.bcm.edu	37	6	33162507	33162507	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	42	60	0	0.466667	0	.	.	none	RXRB,colon,carcinoma,0,1	RXRB	34	1	NM_001270401	exon10	c.C1566T	p.I522I	GGTGTCGATGGGG	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170025	58170025	+	Silent	SNP	C	C	G	rs12271646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	105	206	1	0.483871	0.00485437	C|0.665;G|0.335	0.335	strong	OR5B3,NS,carcinoma,0,1	OR5B3	65	1	NM_001005469	exon1	c.G858C	p.L286L	ATAGACCAGAGGG	.	scavenged	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656246	46656246	+	Missense_Mutation	SNP	T	T	G	rs7291444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	73	151	0	0.493243	0	A|0.001;G|0.248;T|0.751	0.248	strong	.	PKDREJ	195	.	NM_006071	exon1	c.A2974C	p.T992P	GCACTGTGCTGTC	.	PASS	Atlas-SNP
NSFL1C	55968	hgsc.bcm.edu	37	20	1433171	1433171	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	34	99	0	0.354167	0	.	.	none	.	NSFL1C	38	.	NM_016143	exon7	c.A752G	p.K251R	AAGGCTTTGAAGG	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	C	G	rs67093638	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	2	129	1	0.0119048	0.00775194	C|0.986;G|0.014	0.014	strong	PAK2_ENST00000327134,NS,carcinoma,0,4	PAK2	113	4	NM_002577	exon2	c.C5G	p.S2C	TCATGTCTGATAA	.	scavenged	Atlas-SNP
OR4D11	219986	hgsc.bcm.edu	37	11	59271637	59271637	+	Missense_Mutation	SNP	T	T	C	rs7120079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	427	220	431	3	0.515222	0.00696056	T|0.696;C|0.304	0.304	strong	OR4D11,NS,carcinoma,0,1	OR4D11	62	1	NM_001004706	exon1	c.T589C	p.F197L	CTTGAGTTCTTGA	.	scavenged	Atlas-SNP
AP4E1	23431	hgsc.bcm.edu	37	15	51233881	51233881	+	Missense_Mutation	SNP	A	A	G	rs58909326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	62	114	0	0.484375	0	A|0.982;G|0.018	0.018	strong	.	AP4E1	78	.	NM_007347	exon10	c.A1085G	p.Y362C	TTACCTATGTTAT	.	PASS	Atlas-SNP
SLCO4A1	28231	hgsc.bcm.edu	37	20	61292475	61292475	+	Missense_Mutation	SNP	C	C	T	rs201057493	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	25	40	0	0.403226	0	C|1.000;T|0.000	0.000	strong	SLCO4A1,uveal_tract,malignant_melanoma,0,1	SLCO4A1	65	1	NM_016354	exon5	c.C1069T	p.R357C	AGCAGCCGTGGGG	.	PASS	Atlas-SNP
SYT8	90019	hgsc.bcm.edu	37	11	1857762	1857762	+	Silent	SNP	C	C	T	rs3741230	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	57	112	0	0.537736	0	C|0.910;T|0.090	0.090	strong	.	SYT8	29	.	NM_138567	exon6	c.C666T	p.T222T	GGGCACCGTGGAT	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127230864	127230864	+	Missense_Mutation	SNP	G	G	A	rs7854446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	119	174	1	0.983471	0.00574713	G|0.967;A|0.033	0.033	strong	.	GPR144	33	.	NM_001161808	exon14	c.G2221A	p.V741M	ATGCTGGTGGAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513540	195513540	+	Silent	SNP	A	A	G	rs201447574	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	599	13	663	11	0.0217028	0.0165913	A|0.990;G|0.010	0.010	strong	MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	NM_018406	exon2	c.T4911C	p.N1637N	GGAAGCATTGGTG	.	scavenged	Atlas-SNP
CASP4	837	hgsc.bcm.edu	37	11	104819333	104819333	+	Missense_Mutation	SNP	C	C	A	rs55901059	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	86	147	0	0.609929	0	C|0.979;A|0.021	0.021	strong	.	CASP4	57	.	NM_001225	exon6	c.G852T	p.E284D	TAGGTTCTCAGAT	.	PASS	Atlas-SNP
SMAD9	4093	hgsc.bcm.edu	37	13	37453576	37453576	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	2	66	0	0.0273973	0	.	.	none	SMAD9_ENST00000379826,NS,carcinoma,-1,2	SMAD9	91	2	NM_005905	exon2	c.G251A	p.R84H	CCCTTGCGGTGGG	.	scavenged	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92445179	92445179	+	Missense_Mutation	SNP	G	G	A	rs114276662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	92	195	0	0.446602	0	G|0.995;A|0.005	0.005	strong	.	BRDT	133	.	NM_001242806	exon8	c.G1164A	p.M388I	GAGTATGCCTTTA	.	PASS	Atlas-SNP
UBA5	79876	hgsc.bcm.edu	37	3	132384704	132384704	+	Missense_Mutation	SNP	G	G	A	rs61748106	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	44	102	0	0.444444	0	G|0.999;A|0.001	0.001	strong	UBA5,colon,carcinoma,0,1	UBA5	33	1	NM_024818	exon2	c.G199A	p.D67N	GTAAGCGACTATG	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321293	52321293	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	54	106	0	0.524272	0	.	.	none	.	PXDNL	414	.	NM_144651	exon17	c.A2891T	p.H964L	GCCAGATGCTCGT	.	PASS	Atlas-SNP
ZNF439	90594	hgsc.bcm.edu	37	19	11978898	11978898	+	Silent	SNP	T	T	C	rs113442649	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	71	87	0	0.657407	0	T|0.989;C|0.011	0.011	strong	.	ZNF439	67	.	NM_152262	exon3	c.T1014C	p.L338L	CTCTCTTACAAGT	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41547748	41547748	+	Silent	SNP	G	G	A	rs7816734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	90	90	0	0.989011	0	G|0.811;A|0.189	0.189	strong	.	ANK1	497	.	NM_001142446	exon34	c.C4224T	p.A1408A	CACCTTGGCGCAG	.	PASS	Atlas-SNP
ND4L	0	hgsc.bcm.edu	37	MT	10688	10688	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	11	0	1	0	.	.	none	.	.	.	.	ENST00000361335	exon1	c.G219A	p.V73V	AGCGGTGGGCCTA	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	883105	883105	+	Silent	SNP	C	C	T	rs113652875	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	52	77	0	0.619048	0	C|0.969;T|0.031	0.031	strong	.	SUN1	157	.	NM_001171945	exon7	c.C669T	p.P223P	GCACCCCGCGGCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105407208	105407208	+	Silent	SNP	T	T	C	rs11851053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	73	71	0	0.986486	0	T|0.457;C|0.543	0.543	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A14580G	p.V4860V	AAAAGATACCTGA	.	PASS	Atlas-SNP
SPSB4	92369	hgsc.bcm.edu	37	3	140785175	140785175	+	Silent	SNP	C	C	A	rs890529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	25	28	0	0.714286	0	C|0.613;A|0.387	0.387	strong	.	SPSB4	19	.	NM_080862	exon2	c.C229A	p.R77R	TTCCACCGGCACC	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18738281	18738281	+	Missense_Mutation	SNP	C	C	T	rs10766494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	159	0	1	0	C|0.232;T|0.768	0.768	strong	.	IGSF22	211	.	NM_173588	exon10	c.G1240A	p.V414I	GGTCAACAGTGAG	.	PASS	Atlas-SNP
PKMYT1	9088	hgsc.bcm.edu	37	16	3023185	3023185	+	Missense_Mutation	SNP	G	G	A	rs150931982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	65	0	0.444444	0	G|0.995;A|0.005	0.005	strong	.	PKMYT1	23	.	NM_004203	exon8	c.C1342T	p.R448W	CAGTCCGGGCCAG	.	PASS	Atlas-SNP
B3GNT7	93010	hgsc.bcm.edu	37	2	232263127	232263127	+	Missense_Mutation	SNP	G	G	A	rs2290130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	113	174	0	0.562189	0	G|0.763;A|0.237	0.237	strong	.	B3GNT7	38	.	NM_145236	exon2	c.G697A	p.V233I	CCCCACGTCCCCT	.	PASS	Atlas-SNP
OR5V1	81696	hgsc.bcm.edu	37	6	29323655	29323655	+	Silent	SNP	G	G	A	rs7761746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	56	90	0	0.533333	0	G|0.926;A|0.074	0.074	strong	.	OR5V1	63	.	NM_030876	exon1	c.C318T	p.F106F	TACAAAGAAAACA	.	PASS	Atlas-SNP
NTSR2	23620	hgsc.bcm.edu	37	2	11798675	11798675	+	Missense_Mutation	SNP	G	G	A	rs61753869	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	69	117	0	0.453947	0	G|0.911;A|0.089	0.089	strong	NTSR2,NS,carcinoma,-1,1	NTSR2	36	1	NM_012344	exon4	c.C1163T	p.P388L	GGCTTCGGGGGTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515079	195515079	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	396	15	174	4	0.0378788	0.0229885	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C3372T	p.T1124T	AGTGTCGGTGACA	.	scavenged	Atlas-SNP
RASGRF2	5924	hgsc.bcm.edu	37	5	80390736	80390736	+	Silent	SNP	C	C	T	rs34039392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	26	59	0	0.553191	0	C|0.946;T|0.054	0.054	strong	.	RASGRF2	165	.	NM_006909	exon12	c.C1680T	p.D560D	TCCTGACGCTGCC	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19339285	19339285	+	Silent	SNP	G	G	A	rs10406347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	77	0	0.453333	0	G|0.970;A|0.030	0.030	strong	.	NCAN	277	.	NM_004386	exon8	c.G2856A	p.P952P	GGTACCGTGGGAC	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160482929	160482929	+	Missense_Mutation	SNP	C	C	G	rs8191844	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	156	0	0.480263	0	C|0.991;G|0.009	0.009	strong	.	IGF2R	251	.	NM_000876	exon25	c.C3551G	p.T1184S	TCTCCACCAGGAT	.	PASS	Atlas-SNP
TAS2R50	259296	hgsc.bcm.edu	37	12	11138852	11138852	+	Missense_Mutation	SNP	C	C	T	rs1376251	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	61	138	0	0.438849	0	C|0.687;A|0.002	.	strong	.	TAS2R50	37	.	NM_176890	exon1	c.G608A	p.C203Y	TGTTTACACAGAG	.	PASS	Atlas-SNP
GIPC3	126326	hgsc.bcm.edu	37	19	3586543	3586543	+	Silent	SNP	G	G	A	rs8113232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	118	120	0	1	0	G|0.758;A|0.242	0.242	strong	.	GIPC3	27	.	NM_133261	exon2	c.G276A	p.L92L	GCTCCTGGGGGGT	.	PASS	Atlas-SNP
SKA1	220134	hgsc.bcm.edu	37	18	47911631	47911631	+	Silent	SNP	A	A	G	rs11538068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	25	66	0	0.304878	0	A|0.920;G|0.080	0.080	strong	.	SKA1	21	.	NM_001039535	exon5	c.A357G	p.E119E	AGTTGAAGAACCT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13841066	13841066	+	Silent	SNP	G	G	A	rs6880264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	63	127	0	0.446809	0	G|0.985;A|0.015	0.015	strong	.	DNAH5	868	.	NM_001369	exon34	c.C5658T	p.Y1886Y	AGTCTCGTATTTC	.	PASS	Atlas-SNP
GAL3ST4	79690	hgsc.bcm.edu	37	7	99758136	99758136	+	Silent	SNP	T	T	G	rs3800951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	47	84	0	0.447619	0	T|0.464;G|0.536	0.536	strong	.	GAL3ST4	59	.	NM_024637	exon4	c.A876C	p.A292A	CAGCCATGCCAGA	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	142	0	0.482517	0	G|0.656;T|0.344	0.344	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C351A	p.T117T	CATTAGGGTGTAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9063594	9063594	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	3	185	0	0.0152284	0	.	.	none	MUC16_ENST00000397910,bladder,carcinoma,-1,3	MUC16	4315	3	NM_024690	exon3	c.G23852A	p.R7951K	CCCCTCCTCATAA	.	scavenged	Atlas-SNP
LRRFIP2	9209	hgsc.bcm.edu	37	3	37154417	37154417	+	Missense_Mutation	SNP	T	T	C	rs34902788	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	16	43	0	0.347826	0	T|0.987;C|0.013	0.013	strong	.	LRRFIP2	71	.	NM_006309	exon9	c.A427G	p.K143E	GGTCTTTATGAGA	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3839685	3839685	+	Silent	SNP	G	G	A	rs1062683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	134	263	0	0.575107	0	T|0.000;G|0.815;C|0.000;A|0.184	0.184	strong	.	ATP2A3	148	.	NM_174956	exon16	c.C2400T	p.D800D	TAGGCCGTCTGTC	.	PASS	Atlas-SNP
PDIA6	10130	hgsc.bcm.edu	37	2	10933249	10933249	+	Silent	SNP	C	C	T	rs4799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	76	172	0	0.460606	0	C|0.592;T|0.408	0.408	strong	.	PDIA6	31	.	NM_005742	exon5	c.G426A	p.R142R	TCCGCTCCGTCCC	.	PASS	Atlas-SNP
C9orf135	138255	hgsc.bcm.edu	37	9	72472831	72472831	+	Silent	SNP	C	C	T	rs10780682	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	13	71	0	0.22807	0	C|0.722;T|0.278	0.278	strong	.	C9orf135	25	.	NM_001010940	exon4	c.C387T	p.T129T	GGTCACCGGATTG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919884	28919884	+	Missense_Mutation	SNP	A	A	C	rs16961689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	126	0	0.444444	0	A|0.885;C|0.115	0.115	strong	.	DSG1	176	.	NM_001942	exon11	c.A1583C	p.Y528S	AAGTATATTCTTC	.	PASS	Atlas-SNP
NR1D1	9572	hgsc.bcm.edu	37	17	38253469	38253469	+	Silent	SNP	G	G	A	rs9905506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	84	153	0	0.477273	0	G|0.979;A|0.021	0.021	strong	.	NR1D1	45	.	NM_021724	exon2	c.C219T	p.P73P	CAGGCTGGGTGGA	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196544948	196544948	+	Silent	SNP	T	T	C	rs56172538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	35	65	0	0.564516	0	T|0.896;C|0.104	0.104	strong	.	PAK2	113	.	NM_002577	exon12	c.T1074C	p.F358F	GGAGTTTTTACAT	.	PASS	Atlas-SNP
POLD1	5424	hgsc.bcm.edu	37	19	50905762	50905762	+	Silent	SNP	T	T	C	rs1143666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	67	159	0	0.465278	0	T|0.880;C|0.120	0.120	strong	.	POLD1	174	.	NM_002691	exon7	c.T810C	p.A270A	CCCAGCTGGGAAA	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	17	32	0	0.447368	0	C|0.736;G|0.264	0.264	strong	.	MEGF6	91	.	NM_001409	exon27	c.G3410C	p.G1137A	GCAGCGCCAGGCG	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132625884	132625884	+	Missense_Mutation	SNP	C	C	T	rs142395492	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	18	13	0	0.642857	0	C|0.992;T|0.008	0.008	strong	.	DDX51	33	.	NM_175066	exon8	c.G1186A	p.E396K	GGTCCTCGCTCTG	.	PASS	Atlas-SNP
DYNC1I1	1780	hgsc.bcm.edu	37	7	95499234	95499234	+	Silent	SNP	A	A	G	rs3757697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	68	122	0	0.489209	0	A|0.899;G|0.101	0.101	strong	.	DYNC1I1	111	.	NM_004411	exon6	c.A465G	p.Q155Q	CACCCAAGTGGAT	.	PASS	Atlas-SNP
NCAM2	4685	hgsc.bcm.edu	37	21	22790831	22790831	+	Silent	SNP	T	T	C	rs986371	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	139	237	0	0.47931	0	T|0.992;C|0.008	0.008	strong	.	NCAM2	220	.	NM_004540	exon11	c.T1422C	p.N474N	CTATAATTGCACA	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247021085	247021085	+	Silent	SNP	G	G	C	rs41308162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	118	283	0	0.457364	0	G|0.826;C|0.174	0.174	strong	AHCTF1,NS,carcinoma,0,1	AHCTF1	187	1	NM_015446	exon30	c.C4191G	p.L1397L	AACTAAGAGATCC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45029208	45029208	+	Missense_Mutation	SNP	G	G	A	rs10408247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	164	184	0	0.993939	0	G|0.725;A|0.275	0.275	strong	.	CEACAM20	31	.	NM_001102600	exon2	c.C122T	p.A41V	TGGGTGGCATCAA	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57180563	57180563	+	Missense_Mutation	SNP	G	G	C	rs59615456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	18	35	0	0.486486	0	G|0.738;C|0.262	0.262	strong	.	KIAA1211	178	.	NM_020722	exon8	c.G895C	p.G299R	GCGCCAGGTTGGG	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3674170	3674170	+	Silent	SNP	G	G	A	rs61734520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	69	130	0	0.579832	0	G|0.980;A|0.020	0.020	strong	.	SIGLEC1	210	.	NM_023068	exon13	c.C3432T	p.A1144A	GGAGGTGGCATCC	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	37	2	210818971	210818971	+	Silent	SNP	G	G	A	rs16843977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	103	0	0.526882	0	G|0.937;A|0.063	0.063	strong	.	UNC80	280	.	NM_032504	exon47	c.G7236A	p.L2412L	CCTTTTGTACAGT	.	PASS	Atlas-SNP
LIPF	8513	hgsc.bcm.edu	37	10	90438207	90438207	+	Silent	SNP	A	A	G	rs1228187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	72	140	0	0.503497	0	A|0.799;G|0.201	0.201	strong	.	LIPF	62	.	NM_001198829	exon11	c.A996G	p.Q332Q	GTCCCAACCTCCC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20070349	20070349	+	Silent	SNP	C	C	T	rs78806867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	76	141	0	0.490323	0	C|0.988;T|0.012	0.012	strong	.	NAV2	255	.	NM_001244963	exon16	c.C4047T	p.S1349S	CATCTCCAATCCT	.	PASS	Atlas-SNP
ANKRD16	54522	hgsc.bcm.edu	37	10	5920244	5920244	+	Missense_Mutation	SNP	T	T	C	rs61729846	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	30	33	0	0.638298	0	T|0.928;C|0.072	0.072	strong	.	ANKRD16	32	.	NM_001009941	exon7	c.A935G	p.H312R	GCCAGATGCAGGG	.	PASS	Atlas-SNP
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	70	228	0	0.404624	0	G|0.902;A|0.098	0.098	strong	.	FASTKD1	86	.	NM_024622	exon8	c.C1323T	p.A441A	TAAAACGGCTTCA	.	PASS	Atlas-SNP
MTMR3	8897	hgsc.bcm.edu	37	22	30403307	30403307	+	Silent	SNP	C	C	T	rs146523702	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	64	63	0	1	0	C|0.997;T|0.003	0.003	strong	MTMR3_ENST00000401950,NS,lymphoid_neoplasm,+2,1	MTMR3	106	1	NM_021090	exon10	c.C876T	p.F292F	GGAGTTCGGTAAG	.	PASS	Atlas-SNP
CYP4F11	57834	hgsc.bcm.edu	37	19	16024605	16024605	+	Silent	SNP	C	C	G	rs75284625	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	81	130	0	0.54	0	C|0.990;G|0.010	0.010	strong	.	CYP4F11	83	.	NM_001128932	exon13	c.G1512C	p.L504L	CAATATCAGCTCG	.	PASS	Atlas-SNP
TMEM203	94107	hgsc.bcm.edu	37	9	140099675	140099675	+	Silent	SNP	G	G	A	rs113235610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	56	77	0	0.7	0	G|0.992;A|0.008	0.008	strong	TMEM203,NS,carcinoma,0,1	TMEM203	8	1	NM_053045	exon1	c.C192T	p.T64T	GATGGTGGTGAAG	.	PASS	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	37	14	31619392	31619392	+	Silent	SNP	T	T	C	rs11620816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	79	234	0	0.429348	0	C|0.246;T|0.754	0.246	strong	.	HECTD1	159	.	NM_015382	exon13	c.A1968G	p.Q656Q	ACCTTGTTGCAAT	.	PASS	Atlas-SNP
CAAP1	79886	hgsc.bcm.edu	37	9	26842506	26842506	+	Silent	SNP	G	G	A	rs10967558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	140	289	0	0.474576	0	G|0.941;A|0.059	0.059	strong	.	.	.	.	NM_024828	exon6	c.C879T	p.D293D	CTCCAGGTCATCT	.	PASS	Atlas-SNP
BPTF	2186	hgsc.bcm.edu	37	17	65914911	65914911	+	Silent	SNP	T	T	C	rs80201495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	76	153	0	0.513514	0	T|0.981;C|0.019	0.019	strong	.	BPTF	415	.	NM_004459	exon14	c.T5763C	p.D1921D	GGATGATATGGCG	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133398638	133398638	+	Missense_Mutation	SNP	G	G	A	rs141852501	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	58	112	0	0.522523	0	G|0.997;A|0.003	0.003	strong	.	GOLGA3	234	.	NM_001172557	exon2	c.C77T	p.A26V	AGTGGGGCCTCGG	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3845927	3845927	+	Silent	SNP	A	A	G	rs17846889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	30	29	0	1	0	G|0.461;C|0.000;A|0.539	0.461	strong	.	ATP2A3	148	.	NM_174956	exon12	c.T1518C	p.T506T	CTGGCCAGTAGGG	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279921	39279921	+	Missense_Mutation	SNP	A	A	G	rs623410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	128	133	1	0.977099	0.0075188	A|0.835;G|0.165	0.165	strong	.	KRTAP4-12	32	.	NM_031854	exon1	c.T454C	p.C152R	AGGGGCAGCAGCT	.	PASS	Atlas-SNP
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802621	31802621	+	Missense_Mutation	SNP	T	T	A	rs73899382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	102	206	0	0.428571	0	T|0.992;A|0.008	0.008	strong	.	KRTAP13-4	46	.	NM_181600	exon1	c.T28A	p.F10I	AGAAACTTCTCCT	.	PASS	Atlas-SNP
ATPAF2	91647	hgsc.bcm.edu	37	17	17924447	17924447	+	Missense_Mutation	SNP	T	T	C	rs34607655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	81	0	0.523364	0	T|0.996;C|0.004	0.004	strong	.	ATPAF2	15	.	NM_145691	exon7	c.A722G	p.E241G	TACTCCTCCTCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679760	100679760	+	Missense_Mutation	SNP	G	G	A	rs73168394	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	21	123	0	0.172131	0	G|0.989;A|0.011	0.011	strong	MUC17,caecum,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.G5063A	p.G1688E	CTGAAGGAAGAAC	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235933535	235933535	+	Missense_Mutation	SNP	C	C	G	rs6665568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	74	172	0	0.480519	0	C|0.943;G|0.057	0.057	strong	.	LYST	370	.	NM_000081	exon20	c.G5847C	p.Q1949H	CATCTGCTGGTGG	.	PASS	Atlas-SNP
ABCA9	10350	hgsc.bcm.edu	37	17	67031882	67031882	+	Silent	SNP	A	A	G	rs16973534	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	430	196	435	0	0.455814	0	A|0.970;G|0.030	0.030	strong	.	ABCA9	192	.	NM_080283	exon7	c.T861C	p.L287L	TACAATAAGAGCC	.	PASS	Atlas-SNP
ASH1L	55870	hgsc.bcm.edu	37	1	155451343	155451343	+	Missense_Mutation	SNP	A	A	C	rs114218266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	77	137	0	0.430168	0	A|0.981;C|0.019	0.019	strong	.	ASH1L	279	.	NM_018489	exon3	c.T1318G	p.C440G	TACTACAAGAAGC	.	PASS	Atlas-SNP
PLCD4	84812	hgsc.bcm.edu	37	2	219483526	219483526	+	Missense_Mutation	SNP	G	G	C	rs200863393	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	48	88	0	0.475248	0	G|1.000;C|0.000	0.000	strong	.	PLCD4	51	.	NM_032726	exon4	c.G406C	p.D136H	CGCCTGGACCAGT	.	PASS	Atlas-SNP
TMC8	147138	hgsc.bcm.edu	37	17	76134237	76134237	+	Missense_Mutation	SNP	G	G	A	rs11651675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	66	143	0	0.488889	0	G|0.969;A|0.031	0.031	strong	.	TMC8	44	.	NM_152468	exon12	c.G1501A	p.V501I	AATAGCGTCTTCC	.	PASS	Atlas-SNP
SPAG9	9043	hgsc.bcm.edu	37	17	49043640	49043640	+	Missense_Mutation	SNP	T	T	C	rs9896965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	103	0	1	0	T|0.917;C|0.083	0.083	strong	.	SPAG9	151	.	NM_001130528	exon30	c.A3959G	p.N1320S	CACTCATTGCCAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283975	152283975	+	Silent	SNP	A	A	G	rs77811823		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	445	443	438	1	0.995506	0.0022831	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.T3387C	p.S1129S	ATGGGCAGACTCA	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183594275	183594275	+	Missense_Mutation	SNP	T	T	C	rs201144002	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	100	210	1	0.512821	0.0047619	.	.	weak	.	.	.	.	NM_001080477	exon6	c.T1229C	p.I410T	TCTTCATTGATCA	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068177	5068177	+	Missense_Mutation	SNP	A	A	T	rs2500018	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	163	247	0	0.545151	0	A|0.494;T|0.506	0.506	strong	OR52J3,NS,carcinoma,-1,1	OR52J3	77	1	NM_001001916	exon1	c.A422T	p.Q141L	CATCCCAAGTGTT	.	PASS	Atlas-SNP
CTXN3	613212	hgsc.bcm.edu	37	5	126993262	126993262	+	Missense_Mutation	SNP	G	G	A	rs61743797	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	49	68	0	0.590361	0	G|0.998;A|0.002	0.002	strong	.	CTXN3	19	.	NM_001048252	exon3	c.G49A	p.E17K	GGGAACGAATCAG	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138645228	138645228	+	Silent	SNP	G	G	A	rs3734301	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	57	0	0.443182	0	G|0.789;A|0.211	0.211	strong	KIAA1244,NS,carcinoma,+1,1	KIAA1244	236	1	NM_020340	exon31	c.G4938A	p.A1646A	AGTGGCGGCCCCG	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs1613929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	70	83	0	0.972222	0	A|0.686;C|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T549G	p.V183V	GAACCGAACCTAA	.	PASS	Atlas-SNP
LIPM	340654	hgsc.bcm.edu	37	10	90580023	90580023	+	Missense_Mutation	SNP	C	C	T	rs61735049	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	15	45	0	0.384615	0	C|0.994;T|0.006	0.006	strong	.	LIPM	17	.	NM_001128215	exon9	c.C1037T	p.T346M	ATATGACGGTCCC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46777896	46777896	+	Missense_Mutation	SNP	C	C	G	rs7287089	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	12	15	0	0.413793	0	C|0.985;G|0.015	0.015	strong	.	CELSR1	242	.	NM_014246	exon21	c.G6935C	p.R2312P	CCCGGGCGCGTGG	.	PASS	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95278683	95278683	+	Missense_Mutation	SNP	G	G	A	rs75139274	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	110	256	1	0.438247	0.00390625	G|0.931;A|0.069	0.069	strong	.	CEP55	35	.	NM_018131	exon7	c.G1043A	p.R348K	AAACAAGGGTAGC	.	PASS	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116122954	116122954	+	Silent	SNP	A	A	G	rs752757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	19	80	0	0.223529	0	G|0.353;C|0.000;N|0.000;A|0.647	0.353	strong	BSPRY,NS,carcinoma,0,2	BSPRY	21	2	NM_017688	exon3	c.A468G	p.K156K	GCAGAAACTTGAC	.	PASS	Atlas-SNP
ZBTB3	79842	hgsc.bcm.edu	37	11	62519565	62519565	+	Missense_Mutation	SNP	G	G	C	rs544641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	44	0	1	0	G|0.908;C|0.092	0.092	strong	.	ZBTB3	47	.	NM_024784	exon2	c.C1722G	p.I574M	CCCTTAGATGTTA	.	PASS	Atlas-SNP
DHX8	1659	hgsc.bcm.edu	37	17	41570819	41570819	+	Silent	SNP	G	G	A	rs146528228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	60	109	0	0.472441	0	G|0.998;A|0.002	0.002	strong	.	DHX8	98	.	NM_004941	exon7	c.G870A	p.R290R	GAAGCGGTGGGAA	.	PASS	Atlas-SNP
PPP1R16B	26051	hgsc.bcm.edu	37	20	37534665	37534665	+	Silent	SNP	C	C	T	rs4812332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	92	0	0.470588	0	C|0.671;T|0.329	0.329	strong	.	PPP1R16B	103	.	NM_015568	exon7	c.C750T	p.D250D	CCTGGACCATGGA	.	PASS	Atlas-SNP
CLEC12B	387837	hgsc.bcm.edu	37	12	10163381	10163381	+	Missense_Mutation	SNP	C	C	T	rs11833101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	28	67	0	0.363636	0	C|0.976;T|0.024	0.024	strong	.	CLEC12B	25	.	NM_001129998	exon1	c.C23T	p.A8V	CCTACGCGACACT	.	PASS	Atlas-SNP
CLEC1B	51266	hgsc.bcm.edu	37	12	10150961	10150961	+	Missense_Mutation	SNP	G	G	A	rs2273987	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	94	207	1	0.487047	0.00483092	G|0.909;A|0.091	0.091	strong	CLEC1B,NS,carcinoma,+1,2	CLEC1B	39	2	NM_016509	exon2	c.C83T	p.S28F	CACCAGGAGGAGG	.	PASS	Atlas-SNP
ZNF444	55311	hgsc.bcm.edu	37	19	56669889	56669889	+	Silent	SNP	G	G	A	rs61736530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	214	214	0	1	0	G|0.981;A|0.019	0.019	strong	.	ZNF444	15	.	NM_001253792	exon4	c.G324A	p.S108S	TGGGTCGTCAGCA	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595183	140595183	+	Silent	SNP	G	G	T	rs2910330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	145	279	1	0.486577	0.00358423	A|0.000;G|0.862;T|0.138	0.138	strong	.	PCDHB13	142	.	NM_018933	exon1	c.G1488T	p.P496P	GGACCCGCACCTG	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132192949	132192949	+	Silent	SNP	T	T	C	rs156962	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	71	125	0	0.546154	0	T|0.598;C|0.402	0.402	strong	PLXNA4_ENST00000359827,NS,carcinoma,0,2	PLXNA4	873	2	NM_001105543	exon2	c.A504G	p.S168S	AAAGACTGAGCCG	.	PASS	Atlas-SNP
ALLC	55821	hgsc.bcm.edu	37	2	3729254	3729254	+	Missense_Mutation	SNP	C	C	T	rs13426642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	38	80	0	0.469136	0	C|0.801;T|0.199	0.199	strong	.	ALLC	61	.	NM_018436	exon6	c.C329T	p.T110I	GAGGAACCAGGAC	.	PASS	Atlas-SNP
BLZF1	8548	hgsc.bcm.edu	37	1	169345883	169345883	+	Missense_Mutation	SNP	A	A	G	rs112226207	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	71	143	0	0.493056	0	A|0.997;G|0.003	0.003	strong	.	BLZF1	57	.	NM_003666	exon3	c.A134G	p.H45R	AGCATCATAGTCT	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7950394	7950394	+	Missense_Mutation	SNP	G	G	A	rs9895916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	25	64	0	0.531915	0	G|0.923;A|0.077	0.077	strong	ALOX15B,caecum,carcinoma,+1,2	ALOX15B	66	2	NM_001141	exon10	c.G1457A	p.R486H	TGGAACGGTGAGG	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6979179	6979179	+	Silent	SNP	A	A	G	rs364569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	125	1	1	0.008	A|0.544;G|0.456	0.456	strong	.	CLEC10A	40	.	NM_182906	exon7	c.T546C	p.P182P	GTTGACAGGGCAG	.	PASS	Atlas-SNP
TRIM7	81786	hgsc.bcm.edu	37	5	180626927	180626927	+	Missense_Mutation	SNP	A	A	G	rs416574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	109	0	1	0	A|0.532;G|0.468	0.468	strong	TRIM7,NS,carcinoma,0,1	TRIM7	56	1	NM_203293	exon3	c.T773C	p.V258A	ATCTCAACCCCGA	.	PASS	Atlas-SNP
CSF1	1435	hgsc.bcm.edu	37	1	110466776	110466776	+	Silent	SNP	C	C	T	rs3208449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	51	69	0	0.53125	0	C|0.996;T|0.004	0.004	strong	.	CSF1	40	.	NM_000757	exon6	c.C1533T	p.A511A	GCTGGCCGTCGGA	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43531325	43531325	+	Nonsense_Mutation	SNP	C	C	T	rs114358105	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	24	36	0	0.55814	0	C|0.985;T|0.015	0.015	strong	.	UMODL1	186	.	NM_173568	exon11	c.C1993T	p.Q665X	CTCAGACAGGAGA	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242065635	242065635	+	Missense_Mutation	SNP	A	A	G	rs77674262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	74	126	0	0.517483	0	A|0.979;G|0.021	0.021	strong	.	PASK	230	.	NM_015148	exon10	c.T2695C	p.Y899H	GATGGTAGCAGCT	.	PASS	Atlas-SNP
STAMBPL1	57559	hgsc.bcm.edu	37	10	90681048	90681048	+	Silent	SNP	C	C	T	rs34083181	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	58	0	0.482143	0	C|0.982;T|0.018	0.018	strong	.	STAMBPL1	63	.	NM_020799	exon9	c.C1050T	p.P350P	ACATCCCACTCAA	.	PASS	Atlas-SNP
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	34	76	0	0.377778	0	T|0.588;C|0.412	0.412	strong	C11orf67,NS,carcinoma,0,1	.	.	1	NM_024684	exon2	c.T96C	p.G32G	AGGGGGTAGTCGG	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500255	59500255	+	Silent	SNP	C	C	T	rs61740133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	33	96	0	0.417722	0	C|0.923;T|0.077	0.077	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.C1116T	p.L372L	AACACTCTGGGAA	.	PASS	Atlas-SNP
USP46	64854	hgsc.bcm.edu	37	4	53494283	53494283	+	Silent	SNP	G	G	A	rs115007179	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	101	102	0	0.990196	0	G|0.997;A|0.003	0.003	strong	.	USP46	38	.	NM_022832	exon3	c.C165T	p.F55F	ACGGCAGAAGTAC	.	PASS	Atlas-SNP
TTC17	55761	hgsc.bcm.edu	37	11	43413028	43413028	+	Missense_Mutation	SNP	A	A	C	rs12099204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	203	195	1	1	0.00512821	A|0.883;C|0.117	0.117	strong	.	TTC17	112	.	NM_018259	exon4	c.A433C	p.I145L	GATTATATAGACA	.	PASS	Atlas-SNP
RILP	83547	hgsc.bcm.edu	37	17	1553003	1553003	+	Silent	SNP	G	G	T	rs9896488	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	0	0	1	.	G|0.922;T|0.078	0.078	strong	.	RILP	24	.	NM_031430	exon1	c.C96A	p.A32A	GGCCCCGGCTAGA	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	76	192	0	0.429379	0	G|0.939;A|0.061	0.061	strong	DAAM1,colon,carcinoma,+1,1	DAAM1	95	1	NM_001270520	exon13	c.G1527A	p.A509A	GGTGGCGGACCTC	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18499629	18499629	+	Missense_Mutation	SNP	A	A	T	rs77656456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	73	119	0	0.489933	0	A|0.998;T|0.002	0.002	strong	.	PIK3C2G	315	.	NM_004570	exon11	c.A1484T	p.N495I	TAATCAATGTCTA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557486	32557486	+	Missense_Mutation	SNP	T	T	A	rs201540428	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	22	370	0	0.082397	0	T|0.848;A|0.152	0.152	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.A34T	p.M12L	CTGTCATGCAGGA	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860685	16860685	+	Missense_Mutation	SNP	C	C	T	rs61998161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	70	0	0.494118	0	C|0.979;T|0.021	0.021	strong	.	NWD1	303	.	NM_001007525	exon6	c.C1232T	p.T411I	CCCACACCAGGGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149499254	149499254	+	Missense_Mutation	SNP	G	G	A	rs59522380	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	21	26	0	0.477273	0	G|0.945;A|0.055	0.055	strong	.	.	.	.	NM_198455	exon51	c.G7622A	p.R2541Q	GTGACCGGTTCCG	.	PASS	Atlas-SNP
OR4A47	403253	hgsc.bcm.edu	37	11	48510654	48510654	+	Missense_Mutation	SNP	A	A	C	rs7103557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	98	193	0	0.535519	0	A|0.441;C|0.559	0.559	strong	.	OR4A47	72	.	NM_001005512	exon1	c.A310C	p.I104L	GAGCACATTTTCG	.	PASS	Atlas-SNP
PTPRA	5786	hgsc.bcm.edu	37	20	2969015	2969015	+	Silent	SNP	C	C	G	rs61742610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	80	133	0	0.551724	0	C|0.977;G|0.023	0.023	strong	.	PTPRA	75	.	NM_002836	exon13	c.C633G	p.S211S	CAGATCCCCAAGC	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19687517	19687517	+	Missense_Mutation	SNP	T	T	G	rs11088674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	75	0	0.469388	0	T|0.943;G|0.057	0.057	strong	.	TMPRSS15	189	.	NM_002772	exon17	c.A1978C	p.N660H	AGAGATTCACCAG	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24848345	24848345	+	Missense_Mutation	SNP	C	C	A	rs35254980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	62	142	0	0.484375	0	C|0.985;A|0.015	0.015	strong	.	FAM65B	134	.	NM_015864	exon12	c.G985T	p.A329S	TCCCAGCGCCTGA	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	961054	961054	+	Silent	SNP	C	C	T	rs2277892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	25	90	0	0.454545	0	C|0.774;T|0.226	0.226	strong	LMF1,NS,carcinoma,0,1	LMF1	42	1	NM_022773	exon4	c.G540A	p.T180T	GAACCCCGTCTCC	.	PASS	Atlas-SNP
NCF4	4689	hgsc.bcm.edu	37	22	37271802	37271802	+	Silent	SNP	C	C	T	rs2072712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	55	92	0	0.639535	0	C|0.886;T|0.114	0.114	strong	.	NCF4	66	.	NM_000631	exon8	c.C735T	p.Y245Y	CTACTACGAAGAC	.	PASS	Atlas-SNP
FGFRL1	53834	hgsc.bcm.edu	37	4	1018705	1018705	+	Missense_Mutation	SNP	C	C	A	rs4647930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	12	25	0	0.48	0	C|0.820;A|0.180	0.180	strong	.	FGFRL1	77	.	NM_001004356	exon7	c.C1085A	p.P362Q	AACCGCCAGGGCC	.	PASS	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60183401	60183401	+	Missense_Mutation	SNP	G	G	T	rs376669252		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	77	168	0	0.469512	0	.	.	weak	.	MS4A14	120	.	NM_001261828	exon6	c.G1059T	p.L353F	AGACTTGCCATCC	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36982785	36982785	+	Missense_Mutation	SNP	C	C	G	rs2232586	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	32	66	0	0.571429	0	C|0.994;G|0.006	0.006	strong	.	LBP	60	.	NM_004139	exon4	c.C470G	p.S157C	CTGCCTCCAGCTG	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7436151	7436151	+	Silent	SNP	T	T	C	rs61738663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	66	0	0.431373	0	T|0.963;C|0.037	0.037	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.A456G	p.P152P	GGAGAGTGGCCTC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78936358	78936358	+	Missense_Mutation	SNP	G	G	A	rs1110222	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	49	62	0	0.7	0	G|0.679;A|0.321	0.321	strong	.	PCSK5	329	.	NM_001190482	exon30	c.G3824A	p.G1275D	AAGACGGCATATG	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107041612	107041612	+	Missense_Mutation	SNP	A	A	C	rs3974037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1268	108	1034	0	0.0851735	0	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	NM_001144013	exon20	c.T2811G	p.S937R	CTTTTCACTTTTC	.	scavenged	Atlas-SNP
USP2	9099	hgsc.bcm.edu	37	11	119243912	119243912	+	Silent	SNP	C	C	T	rs79464246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	50	73	0	0.555556	0	C|0.991;T|0.009	0.009	strong	.	USP2	71	.	NM_004205	exon2	c.G279A	p.E93E	CTGGCTCTCTGCC	.	PASS	Atlas-SNP
GPRC5D	55507	hgsc.bcm.edu	37	12	13103196	13103196	+	Silent	SNP	G	G	A	rs150759739	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	48	74	0	0.685714	0	G|0.997;A|0.003	0.003	strong	.	GPRC5D	23	.	NM_018654	exon1	c.C123T	p.L41L	TGCTAAGAGTAGC	.	PASS	Atlas-SNP
DVL1	1855	hgsc.bcm.edu	37	1	1277183	1277183	+	Missense_Mutation	SNP	C	C	T	rs61735963	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	50	88	0	0.46729	0	C|0.931;T|0.069	0.069	strong	.	DVL1	36	.	NM_004421	exon5	c.G469A	p.A157T	TCCGGGCGGCTGT	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262103	39262103	+	Missense_Mutation	SNP	A	A	T	rs374629799		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	42	125	0	0.225806	0	.	.	weak	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	NM_001146041	exon1	c.A463T	p.S155C	AGCTGCAGCATCT	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43536047	43536047	+	Silent	SNP	C	C	T	rs141581454	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	116	212	0	0.497854	0	C|0.998;T|0.002	0.002	strong	.	UMODL1	186	.	NM_173568	exon13	c.C2811T	p.N937N	TCGCAACGCAAGC	.	PASS	Atlas-SNP
C4orf6	10141	hgsc.bcm.edu	37	4	5527102	5527102	+	Missense_Mutation	SNP	C	C	A	rs886532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	71	119	0	0.581967	0	C|0.932;A|0.068	0.068	strong	.	C4orf6	6	.	NM_005750	exon1	c.C45A	p.N15K	AAAGAACCAATTT	.	PASS	Atlas-SNP
NDNL2	56160	hgsc.bcm.edu	37	15	29561467	29561467	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	58	111	0	0.5	0	.	.	none	.	NDNL2	19	.	NM_138704	exon1	c.A443C	p.K148T	TTGCTCTTGGGTT	.	PASS	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	37	3	36898699	36898699	+	Silent	SNP	G	G	A	rs187740236	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	35	54	0	0.472973	0	G|0.998;A|0.002	0.002	strong	.	TRANK1	398	.	NM_014831	exon12	c.C2382T	p.C794C	TGAAGTGCACTCG	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	51	59	0	1	0	A|0.479;C|0.521	0.521	strong	.	PIGZ	34	.	NM_025163	exon3	c.T852G	p.A284A	GGATGTAGCGGGG	.	PASS	Atlas-SNP
HAVCR1	26762	hgsc.bcm.edu	37	5	156479583	156479583	+	Silent	SNP	C	C	G	rs192652646	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	457	5	421	0	0.0109409	0	C|0.981;G|0.019	0.019	strong	HAVCR1,colon,carcinoma,-1,2	HAVCR1	84	2	NM_001099414	exon4	c.G462C	p.T154T	AACAGTCGTTGTC	.	scavenged	Atlas-SNP
GRM5	2915	hgsc.bcm.edu	37	11	88338074	88338074	+	Silent	SNP	G	G	A	rs61745770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	40	65	0	0.56338	0	G|0.971;A|0.029	0.029	strong	.	GRM5	414	.	NM_000842	exon5	c.C1206T	p.N402N	GATGGCGTTGATC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48452147	48452147	+	Silent	SNP	G	G	A	rs369363967		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	85	121	0	0.559211	0	.	.	weak	.	ABCA13	1192	.	NM_152701	exon41	c.G12426A	p.T4142T	CCTGACGGGCTAT	.	PASS	Atlas-SNP
FMR1	2332	hgsc.bcm.edu	37	X	147010320	147010320	+	Silent	SNP	G	G	A	rs25707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	182	241	1	0.627586	0.00414938	0|0.002;A|0.101	0.101	strong	.	FMR1	93	.	NM_002024	exon5	c.G414A	p.R138R	CTTACGGCAAATG	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12187475	12187475	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	3	99	0	0.0361446	0	.	.	none	ZNF844,NS,carcinoma,0,6	ZNF844	69	6	NM_001136501	exon4	c.C1540G	p.H514D	CCTTCACATCTGC	.	scavenged	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15808861	15808861	+	Silent	SNP	G	G	A	rs149566621	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	129	0	0.508065	0	G|0.998;A|0.002	0.002	strong	.	MYH11	520	.	NM_001040114	exon41	c.C5712T	p.N1904N	GTTGGCGTTGATG	.	PASS	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95262980	95262980	+	Silent	SNP	C	C	T	rs62642530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	43	102	0	0.52439	0	C|0.996;T|0.004	0.004	strong	.	CEP55	35	.	NM_018131	exon3	c.C294T	p.T98T	TACTACCACATTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179528378	179528378	+	Missense_Mutation	SNP	C	C	T	rs2163008	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	136	0	1	0	C|0.832;T|0.168	0.168	strong	.	TTN	18412	.	NM_001267550	exon171	c.G36508A	p.E12170K	CAGGCTCTTTAGG	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40144467	40144467	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	3	125	0	0.0247934	0	.	.	none	N4BP2,NS,carcinoma,0,1	N4BP2	166	1	NM_018177	exon15	c.T4960C	p.F1654L	GCCACCTTTTATG	.	scavenged	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528207	20528207	+	Missense_Mutation	SNP	G	G	A	rs1958715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	41	103	0	0.455556	0	G|0.535;A|0.465	0.465	strong	.	OR4L1	98	.	NM_001004717	exon1	c.G4A	p.D2N	TAAATGGATCTTA	.	PASS	Atlas-SNP
PRDM12	59335	hgsc.bcm.edu	37	9	133553993	133553993	+	Silent	SNP	C	C	T	rs7021384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	112	0	1	0	C|0.650;T|0.350	0.350	strong	.	PRDM12	24	.	NM_021619	exon4	c.C648T	p.P216P	TGTGCCCGGGCTA	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115375528	115375528	+	Silent	SNP	C	C	A	rs11196397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	444	221	449	0	0.497748	0	C|0.772;A|0.228	0.228	strong	NRAP,NS,carcinoma,0,1	NRAP	208	1	NM_001261463	exon27	c.G3021T	p.P1007P	AGCAGTCGGTGTG	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10404766	10404766	+	Silent	SNP	C	C	T	rs61730793	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	86	144	0	0.5375	0	C|0.994;T|0.006	0.006	strong	.	MYH1	403	.	NM_005963	exon27	c.G3399A	p.R1133R	TTTGGCCCGGGAG	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919263	51919263	+	Missense_Mutation	SNP	G	G	T	rs7258951	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	31	148	0	0.172222	0	G|0.718;T|0.282	0.282	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.C913A	p.P305T	CCAGGGGTCTAGG	.	PASS	Atlas-SNP
POP5	51367	hgsc.bcm.edu	37	12	121019009	121019009	+	Silent	SNP	G	G	C	rs74750729	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	45	88	0	0.529412	0	G|0.998;C|0.002	0.002	strong	.	POP5	14	.	NM_198202	exon2	c.C72G	p.L24L	GTCATCGAGGCTT	.	PASS	Atlas-SNP
MATN3	4148	hgsc.bcm.edu	37	2	20205680	20205680	+	Silent	SNP	C	C	T	rs28401180	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	63	130	0	0.496063	0	C|0.513;T|0.487	0.487	strong	.	MATN3	28	.	NM_002381	exon2	c.G615A	p.E205E	CGCCACCTCATTC	.	PASS	Atlas-SNP
LILRA2	11027	hgsc.bcm.edu	37	19	55098742	55098742	+	Missense_Mutation	SNP	G	G	T	rs73939008	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	109	227	0	0.43083	0	G|0.991;T|0.009	0.009	strong	LILRA2,right_upper_lobe,carcinoma,0,1	LILRA2	99	1	NM_001130917	exon8	c.G1381T	p.V461L	GTCCTGGTGGTCC	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	32466654	32466654	+	Silent	SNP	G	G	A	rs143628111	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	127	269	0	0.492248	0	G|0.983;A|0.017	0.017	strong	.	DMD	2127	.	NM_004006	exon27	c.C3705T	p.A1235A	TTTTAAGGCCTCT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133953673	133953673	+	Missense_Mutation	SNP	C	C	T	rs61744678	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	135	233	0	0.492701	0	C|0.929;T|0.071	0.071	strong	TG,right_upper_lobe,carcinoma,-1,1	TG	416	1	NM_003235	exon26	c.C5119T	p.P1707S	TACAACCCCATTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	552	550	379	4	0.996377	0.0105541	C|0.682;T|0.318	0.318	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.G7633A	p.G2545R	AGTGTCCAGAGCT	.	scavenged	Atlas-SNP
HMMR	3161	hgsc.bcm.edu	37	5	162909716	162909716	+	Missense_Mutation	SNP	C	C	T	rs299295	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	369	177	317	0	0.479675	0	C|0.774;N|0.000	.	strong	.	HMMR	64	.	NM_001142556	exon13	c.C1454T	p.A485V	AAAAAGCGGCCAA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134144113	134144113	+	Silent	SNP	C	C	T	rs2294024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	88	165	0	0.53012	0	C|0.522;T|0.478	0.478	strong	TG,NS,carcinoma,0,1	TG	416	1	NM_003235	exon46	c.C7920T	p.Y2640Y	AGCCTACGAGGGG	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17191019	17191019	+	Silent	SNP	A	A	G	rs214936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	139	237	0	0.476027	0	A|0.601;G|0.399	0.399	strong	.	PIK3C2A	148	.	NM_002645	exon1	c.T270C	p.I90I	TACATCAATATCT	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	37	15	90167610	90167610	+	Missense_Mutation	SNP	G	G	T	rs115865608	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	34	63	0	0.566667	0	G|0.996;T|0.004	0.004	strong	.	.	.	.	NM_152259	exon20	c.G4069T	p.V1357F	TGCCCTGTTCCCT	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7166388	7166388	+	Silent	SNP	G	G	A	rs2229429	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	53	60	0	1	0	T|0.000;G|0.746;C|0.000;A|0.254	0.254	strong	.	INSR	265	.	NM_000208	exon8	c.C1638T	p.D546D	CTGCCCGTCGAAC	.	PASS	Atlas-SNP
C1orf112	55732	hgsc.bcm.edu	37	1	169796859	169796859	+	Silent	SNP	A	A	C	rs149832132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	26	67	0	0.342105	0	A|0.997;C|0.003	0.003	strong	.	C1orf112	74	.	NM_018186	exon12	c.A1005C	p.P335P	CCTGCCATGTGAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs61737593	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	392	193	342	1	0.492347	0.00292398	C|0.929;T|0.071	0.071	strong	MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	NM_002458	exon31	c.C9452T	p.T3151M	GCCCCACGGCCAC	.	PASS	Atlas-SNP
SEZ6	124925	hgsc.bcm.edu	37	17	27284443	27284443	+	Missense_Mutation	SNP	A	A	G	rs12941884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	77	115	0	0.546099	0	A|0.847;G|0.153	0.153	strong	.	SEZ6	61	.	NM_001098635	exon12	c.T2417C	p.M806T	CTGCCCATCAGCA	.	PASS	Atlas-SNP
C16orf82	162083	hgsc.bcm.edu	37	16	27078705	27078705	+	Missense_Mutation	SNP	T	T	C	rs115398674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	26	66	0	0.351351	0	T|0.980;C|0.020	0.020	strong	.	.	.	.	NM_001145545	exon1	c.T389C	p.I130T	GCTCCATAGACCC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476414	228476414	+	Silent	SNP	G	G	A	rs3795791	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	85	192	0	0.456989	0	G|0.910;A|0.090	0.090	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.G11451A	p.A3817A	CAAGGCGGCCCCC	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52493996	52493996	+	Missense_Mutation	SNP	C	C	T	rs28507587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	51	70	0	0.476636	0	C|0.979;T|0.021	0.021	strong	NID2,NS,carcinoma,-1,1	NID2	201	1	NM_007361	exon12	c.G2597A	p.R866Q	ACACACCGGGCCT	.	PASS	Atlas-SNP
GNA12	2768	hgsc.bcm.edu	37	7	2834577	2834577	+	Silent	SNP	T	T	C	rs2230878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	40	74	0	0.416667	0	T|0.980;C|0.020	0.020	strong	.	GNA12	35	.	NM_007353	exon2	c.A510G	p.R170R	CTCGCTTCTCCGG	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39586343	39586343	+	Silent	SNP	G	G	C	rs9576697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	83	140	0	0.488235	0	G|0.818;C|0.182	0.182	strong	.	.	.	.	NM_025138	exon12	c.C2589G	p.G863G	AGAACTGCCTGCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412542	105412542	+	Silent	SNP	A	A	G	rs12433815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	113	262	2	1	0.00763359	A|0.668;G|0.332	0.332	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T9246C	p.D3082D	CTTGACATCTATC	.	PASS	Atlas-SNP
HK2	3099	hgsc.bcm.edu	37	2	75116527	75116527	+	Missense_Mutation	SNP	G	G	A	rs2229629	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	205	199	1	1	0.00502513	G|0.805;A|0.195	0.195	strong	.	HK2	85	.	NM_000189	exon17	c.G2531A	p.R844K	TGGACAGGATACG	.	PASS	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169566326	169566326	+	Silent	SNP	G	G	A	rs6135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	81	204	0	0.433155	0	G|0.774;A|0.226	0.226	strong	.	SELP	132	.	NM_003005	exon11	c.C1794T	p.C598C	GAAATGGCAGGTG	.	PASS	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	37	16	28898793	28898793	+	Silent	SNP	T	T	C	rs6565259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	50	81	0	0.458716	0	T|0.631;C|0.369	0.369	strong	.	ATP2A1	116	.	NM_004320	exon8	c.T678C	p.T226T	CACCACTGGTGTG	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	37	19	12800597	12800597	+	Missense_Mutation	SNP	T	T	C	rs73921601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	29	85	0	0.345238	0	T|0.944;C|0.056	0.056	strong	FBXW9_ENST00000393261,caecum,carcinoma,+1,3	FBXW9	30	3	NM_032301	exon7	c.A1124G	p.N375S	CAGCCGTTGCGGT	.	PASS	Atlas-SNP
CDKAL1	54901	hgsc.bcm.edu	37	6	21201493	21201493	+	Silent	SNP	G	G	A	rs9465994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	58	0	1	0	G|0.451;A|0.549	0.549	strong	CDKAL1,NS,carcinoma,+1,1	CDKAL1	55	1	NM_017774	exon15	c.G1536A	p.S512S	AGTCTCGGGTTTG	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19451090	19451090	+	Missense_Mutation	SNP	T	T	C	rs183578825	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	79	164	0	0.473054	0	T|0.999;C|0.001	0.001	strong	UBR4,NS,carcinoma,0,1	UBR4	415	1	NM_020765	exon65	c.A9533G	p.N3178S	CGAGAATTGGTGT	.	PASS	Atlas-SNP
ZDHHC19	131540	hgsc.bcm.edu	37	3	195935346	195935346	+	Missense_Mutation	SNP	C	C	T	rs75505676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	116	242	0	0.47541	0	C|0.996;T|0.004	0.004	strong	.	ZDHHC19	25	.	NM_001039617	exon4	c.G494A	p.C165Y	TAGAGGCACAGGG	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713099	32713099	+	Silent	SNP	G	G	A	rs9469266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	145	1	1	0.00689655	G|0.926;A|0.074	0.074	strong	.	HLA-DQA2	27	.	NM_020056	exon2	c.G246A	p.P82P	TGACCCGCAGAGT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	2201	89	1941	41	0.0404362	0.0211231	.	.	none	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5952C	p.M1984I	TGCAGTCATAGGA	.	scavenged	Atlas-SNP
WDR4	10785	hgsc.bcm.edu	37	21	44273691	44273691	+	Silent	SNP	G	G	A	rs146863277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	43	61	0	0.623188	0	G|0.995;A|0.005	0.005	strong	.	WDR4	35	.	NM_018669	exon9	c.C963T	p.G321G	CTGGTCGCCCACA	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40590176	40590176	+	Silent	SNP	G	G	T	rs76171323	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	66	114	0	0.589286	0	G|0.984;T|0.016	0.016	strong	BRWD1_ENST00000333229,NS,lymphoid_neoplasm,0,2	BRWD1	325	2	NM_018963	exon31	c.C3561A	p.G1187G	AACAGGGCCTGCA	.	PASS	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33696897	33696897	+	Silent	SNP	C	C	T	rs11084712	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	62	0	0.530612	0	C|0.769;T|0.231	0.231	strong	LRP3,rectum,carcinoma,0,2	LRP3	46	2	NM_002333	exon5	c.C1221T	p.G407G	CAGCGGCCGAGAC	.	PASS	Atlas-SNP
ZNF780A	284323	hgsc.bcm.edu	37	19	40580426	40580426	+	Silent	SNP	A	A	G	rs399405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	268	247	0	1	0	A|0.899;G|0.101	0.101	strong	.	ZNF780A	156	.	NM_001142577	exon6	c.T1926C	p.S642S	CATTCAAGATGCC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144871829	144871829	+	Silent	SNP	C	C	T	rs111761861	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	26	107	0	0.192593	0	C|0.969;T|0.031	0.031	strong	.	PDE4DIP	817	.	NM_014644	exon32	c.G5133A	p.L1711L	TGAGGGCAATGGT	.	PASS	Atlas-SNP
SLC35C1	55343	hgsc.bcm.edu	37	11	45832509	45832509	+	Missense_Mutation	SNP	A	A	G	rs7130656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	59	0	1	0	A|0.866;G|0.134	0.134	strong	SLC35C1,NS,carcinoma,0,2	SLC35C1	23	2	NM_018389	exon2	c.A718G	p.I240V	GCCTGCATCCTCT	.	PASS	Atlas-SNP
TRIP11	9321	hgsc.bcm.edu	37	14	92441066	92441066	+	Missense_Mutation	SNP	C	C	T	rs1051340	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	97	199	0	0.518717	0	C|0.709;T|0.291	0.291	strong	.	TRIP11	184	.	NM_004239	exon19	c.G5479A	p.G1827S	TAACACCGCCCTG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249152	71249152	+	Silent	SNP	C	C	T	rs112809261	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	88	284	0	0.389381	0	C|0.896;T|0.104	0.104	strong	KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	NM_021046	exon1	c.C51T	p.C17C	GGGCTGCGGCTCT	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152285188	152285188	+	Missense_Mutation	SNP	G	G	A	rs80233522		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	272	243	1	0.992701	0.00411523	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.C2174T	p.T725I	TGCCCAGTGCCTG	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193210768	193210768	+	Silent	SNP	A	A	G	rs2130407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	38	79	0	0.395833	0	A|0.508;G|0.492	0.492	strong	.	ATP13A4	154	.	NM_032279	exon5	c.T471C	p.L157L	AGAACTAAGCCAG	.	PASS	Atlas-SNP
EFEMP1	2202	hgsc.bcm.edu	37	2	56145110	56145110	+	Silent	SNP	G	G	T	rs12292	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	122	248	0	0.532751	0	G|0.951;T|0.049	0.049	strong	.	EFEMP1	81	.	NM_001039349	exon4	c.C207A	p.L69L	AAGGCAGAGGTAT	.	PASS	Atlas-SNP
APPBP2	10513	hgsc.bcm.edu	37	17	58603185	58603185	+	Silent	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	73	134	0	0.544776	0	.	.	none	.	APPBP2	48	.	NM_006380	exon1	c.C108G	p.P36P	GTTCTCGGGCAAG	.	PASS	Atlas-SNP
NDUFA10	4705	hgsc.bcm.edu	37	2	240961728	240961728	+	Silent	SNP	T	T	C	rs2083411	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	215	177	0	1	0	T|0.299;C|0.701	0.701	strong	.	NDUFA10	40	.	NM_004544	exon2	c.A105G	p.K35K	GCGCAGTTTGCAC	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52344245	52344245	+	Silent	SNP	T	T	G	rs72901974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	50	111	0	0.45045	0	T|0.972;G|0.028	0.028	strong	.	NRD1	89	.	NM_001101662	exon1	c.A43C	p.R15R	ACTTCCTCCGGGT	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132238286	132238286	+	Silent	SNP	C	C	T	rs111626841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	61	207	0	0.406667	0	C|0.831;T|0.169	0.169	strong	.	TUBA3D	60	.	NM_080386	exon4	c.C1020T	p.T340T	GCGCACCATCCAG	.	PASS	Atlas-SNP
AEBP1	165	hgsc.bcm.edu	37	7	44146151	44146151	+	Missense_Mutation	SNP	C	C	T	rs75107445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	19	40	0	0.413043	0	C|0.999;T|0.001	0.001	strong	AEBP1,larynx,carcinoma,-1,1	AEBP1	102	1	NM_001129	exon2	c.C260T	p.P87L	TGCCTCCGGAAAA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677285	100677285	+	Missense_Mutation	SNP	G	G	A	rs74852422	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	53	132	0	0.25	0	G|0.988;A|0.013	0.013	strong	.	MUC17	804	.	NM_001040105	exon3	c.G2588A	p.G863E	GTGAAGGAAGAAC	.	PASS	Atlas-SNP
PKMYT1	9088	hgsc.bcm.edu	37	16	3026956	3026956	+	Silent	SNP	T	T	C	rs4149786	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	21	76	0	0.323077	0	T|0.993;C|0.007	0.007	strong	.	PKMYT1	23	.	NM_182687	exon3	c.A87G	p.P29P	GTAGGCTGGGACT	.	PASS	Atlas-SNP
TTC7A	57217	hgsc.bcm.edu	37	2	47301029	47301029	+	Silent	SNP	A	A	G	rs3739099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	104	264	0	0.466368	0	A|0.774;G|0.226	0.226	strong	TTC7A,NS,carcinoma,0,1	TTC7A	80	1	NM_020458	exon20	c.A2544G	p.V848V	CCCTGTACTGCCC	.	PASS	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	37	19	54803141	54803141	+	Missense_Mutation	SNP	C	C	T	rs147561158	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	167	315	2	0.482659	0.00634921	C|0.998;T|0.002	0.002	strong	LILRA3,right_upper_lobe,carcinoma,0,2	LILRA3	65	2	NM_006865	exon4	c.G536A	p.R179Q	ATGGCCCGGGATG	.	scavenged	Atlas-SNP
GLRA3	8001	hgsc.bcm.edu	37	4	175688141	175688141	+	Silent	SNP	G	G	A	rs12651268	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	55	106	0	0.561224	0	G|0.704;A|0.296	0.296	strong	.	GLRA3	76	.	NM_001042543	exon3	c.C240T	p.S80S	GCCAAAGCTGTTG	.	PASS	Atlas-SNP
HIP1	3092	hgsc.bcm.edu	37	7	75211414	75211414	+	Silent	SNP	A	A	G	rs237238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	73	0	0.520548	0	A|0.912;G|0.088	0.088	strong	HIP1,NS,carcinoma,-1,1	HIP1	91	1	NM_005338	exon6	c.T519C	p.A173A	TTCTCCAGCCTCG	.	PASS	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	37	1	103491461	103491461	+	Missense_Mutation	SNP	T	T	G	rs12731843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	35	47	0	0.636364	0	T|0.922;G|0.078	0.078	strong	.	COL11A1	972	.	NM_080629	exon6	c.A828C	p.K276N	CTTTGATTTAGTA	.	PASS	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	37	19	49368843	49368843	+	Missense_Mutation	SNP	T	T	C	rs506425	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	163	0	1	0	T|0.549;G|0.003	.	strong	.	PLEKHA4	70	.	NM_001161354	exon3	c.A109G	p.I37V	CGTGGATCTTGTT	.	PASS	Atlas-SNP
DUS3L	56931	hgsc.bcm.edu	37	19	5789565	5789565	+	Missense_Mutation	SNP	T	T	C	rs2436487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	6	13	0	0.428571	0	T|0.554;C|0.446	0.446	strong	DUS3L,NS,carcinoma,0,1	DUS3L	42	1	NM_020175	exon3	c.A553G	p.R185G	CGGGCCTCAGGTG	.	PASS	Atlas-SNP
OTC	5009	hgsc.bcm.edu	37	X	38260570	38260570	+	Silent	SNP	T	T	C	rs145777402	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	74	229	0	0.413408	0	T|0.994;C|0.006	0.006	strong	.	OTC	60	.	NM_000531	exon5	c.T429C	p.Y143Y	AGTGTATAAACAA	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5863113	5863113	+	Silent	SNP	G	G	A	rs10742810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	67	146	1	0.489051	0.00684932	G|0.605;A|0.395	0.395	strong	OR52E6,NS,carcinoma,0,1	OR52E6	70	1	NM_001005167	exon1	c.C15T	p.N5N	GGTGTCGTTAGCT	.	scavenged	Atlas-SNP
ODF1	4956	hgsc.bcm.edu	37	8	103573024	103573024	+	Missense_Mutation	SNP	G	G	A	rs111689913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	42	145	0	0.396226	0	G|0.893;A|0.107	0.107	strong	.	ODF1	55	.	NM_024410	exon2	c.G665A	p.S222N	CCTGCAGCCCCTG	.	PASS	Atlas-SNP
VLDLR	7436	hgsc.bcm.edu	37	9	2648773	2648773	+	Silent	SNP	A	A	G	rs6148	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	95	169	0	0.472637	0	A|0.874;G|0.126	0.126	strong	.	VLDLR	68	.	NM_003383	exon14	c.A2067G	p.Q689Q	TGCCCAAGACATC	.	PASS	Atlas-SNP
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	43	78	0	0.483146	0	C|0.798;G|0.202	0.202	strong	.	DEFB129	24	.	NM_080831	exon2	c.C446G	p.T149S	GTAACACCAAAGA	.	PASS	Atlas-SNP
KRT74	121391	hgsc.bcm.edu	37	12	52966390	52966390	+	Missense_Mutation	SNP	A	A	T	rs11170176	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	148	230	0	0.546125	0	A|0.812;T|0.188	0.188	strong	.	KRT74	67	.	NM_175053	exon2	c.T533A	p.L178Q	AGGTCCAGCTGCT	.	PASS	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	46	63	0	0.621622	0	T|0.613;C|0.387	0.387	strong	MAP3K5,NS,carcinoma,0,1	MAP3K5	136	1	NM_005923	exon10	c.A1557G	p.L519L	ATATATTAAAATT	.	PASS	Atlas-SNP
ARHGEF15	22899	hgsc.bcm.edu	37	17	8215534	8215534	+	Silent	SNP	C	C	T	rs3744651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	181	297	0	0.530792	0	C|0.620;T|0.380	0.380	strong	.	ARHGEF15	97	.	NM_025014	exon2	c.C177T	p.T59T	GTGCACCCCCATC	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	58	84	0	0.659091	0	T|0.662;C|0.338	0.338	strong	.	CSMD2	946	.	NM_052896	exon13	c.A1613G	p.H538R	CCGTGGTGAAACC	.	PASS	Atlas-SNP
TSC22D2	9819	hgsc.bcm.edu	37	3	150176316	150176316	+	Missense_Mutation	SNP	C	C	A	rs149526922	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	129	272	0	0.469091	0	C|0.999;A|0.001	0.001	strong	.	TSC22D2	42	.	NM_014779	exon4	c.C2236A	p.P746T	CAACTCCCAACCC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2946461	2946461	+	Silent	SNP	T	T	C	rs1124581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	200	168	0	1	0	T|0.439;C|0.561	0.561	strong	.	CARD11	339	.	NM_032415	exon25	c.A3276G	p.R1092R	CTCAGGTCGGGGC	.	PASS	Atlas-SNP
FAM207A	85395	hgsc.bcm.edu	37	21	46380068	46380068	+	Missense_Mutation	SNP	G	G	A	rs141593051	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	114	0	0.494737	0	G|0.999;A|0.001	0.001	strong	.	.	.	.	NM_058190	exon3	c.G337A	p.E113K	AGGCGTGAGCAAT	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56383744	56383744	+	Missense_Mutation	SNP	T	T	C	rs11079346	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	70	0	0.506024	0	T|0.694;C|0.306	0.306	strong	.	BZRAP1	287	.	NM_004758	exon26	c.A5183G	p.H1728R	GTTGTGTGGGCTG	.	PASS	Atlas-SNP
PSME2	5721	hgsc.bcm.edu	37	14	24615435	24615435	+	Silent	SNP	T	T	C	rs4575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	63	0	0.46988	0	T|0.531;C|0.469	0.469	strong	.	PSME2	21	.	NM_002818	exon2	c.A63G	p.R21R	ATTCTGTCTGAAG	.	PASS	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226076598	226076598	+	Missense_Mutation	SNP	C	C	T	rs35273824	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	103	187	0	0.530928	0	C|0.956;T|0.044	0.044	strong	.	LEFTY1	30	.	NM_020997	exon1	c.G169A	p.V57M	CCCTCACGTGGGT	.	PASS	Atlas-SNP
APOF	319	hgsc.bcm.edu	37	12	56755058	56755058	+	Missense_Mutation	SNP	A	A	G	rs4301822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	74	129	0	0.503401	0	A|0.818;G|0.182	0.182	strong	.	APOF	13	.	NM_001638	exon2	c.T932C	p.I311T	TTGATTATGGCCC	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43818052	43818052	+	Missense_Mutation	SNP	G	G	A	rs2245715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	134	0	0.5	0	G|0.669;A|0.331	0.331	strong	.	MAP1A	189	.	NM_002373	exon4	c.G4381A	p.D1461N	CAAAAGGATACAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677572	100677572	+	Missense_Mutation	SNP	A	A	G	rs60940057	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	55	152	0	0.237069	0	A|0.946;G|0.054	0.054	strong	.	MUC17	804	.	NM_001040105	exon3	c.A2875G	p.T959A	ACTTCTACTGAAG	.	PASS	Atlas-SNP
FGF4	2249	hgsc.bcm.edu	37	11	69588798	69588798	+	Silent	SNP	A	A	G	rs61738964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	83	131	0	0.477012	0	A|0.994;G|0.006	0.006	strong	.	FGF4	13	.	NM_002007	exon2	c.T438C	p.Y146Y	CGAGCCATAGAGC	.	PASS	Atlas-SNP
APC2	10297	hgsc.bcm.edu	37	19	1469078	1469078	+	Silent	SNP	G	G	A	rs79021820	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	19	11	0	0.655172	0	G|0.949;A|0.051	0.051	strong	.	APC2	50	.	NM_005883	exon15	c.G5778A	p.S1926S	GAGATCGCCCGTG	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19166893	19166893	+	Missense_Mutation	SNP	C	C	T	rs6662276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	60	141	0	0.491803	0	C|0.937;T|0.063	0.063	strong	TAS1R2,NS,carcinoma,+1,1	TAS1R2	134	1	NM_152232	exon6	c.G1720A	p.A574T	CCAGGGCGGCCAG	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235950284	235950284	+	Silent	SNP	A	A	C	rs3731648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	46	86	0	0.5	0	A|0.797;C|0.203	0.203	strong	SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	NM_014521	exon4	c.A871C	p.R291R	AACCACAGGAAGC	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124908352	124908352	+	Missense_Mutation	SNP	T	T	C	rs7107487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	29	155	0	0.258929	0	T|0.779;C|0.221	0.221	strong	.	CCDC15	134	.	NM_025004	exon14	c.T2437C	p.C813R	CAAGAATGTTATG	.	PASS	Atlas-SNP
SLC17A1	6568	hgsc.bcm.edu	37	6	25813150	25813150	+	Missense_Mutation	SNP	G	G	A	rs1165196	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	111	135	0	0.991071	0	G|0.298;T|0.002	.	strong	.	SLC17A1	71	.	NM_005074	exon8	c.C806T	p.T269I	CTACCAGTGGAAA	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57383315	57383315	+	Missense_Mutation	SNP	G	G	C	rs1342440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	145	283	0	0.523466	0	G|0.901;C|0.099	0.099	strong	.	C8A	103	.	NM_000562	exon11	c.G1681C	p.E561Q	AGAAGAGAGTGTG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79351542	79351542	+	Missense_Mutation	SNP	C	C	T	rs34271211	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	38	100	0	0.44186	0	C|0.992;T|0.008	0.008	strong	.	FRAS1	779	.	NM_001166133	exon37	c.C4940T	p.T1647I	AGCATACAGCTGA	.	PASS	Atlas-SNP
LRFN3	79414	hgsc.bcm.edu	37	19	36430798	36430798	+	Silent	SNP	A	A	G	rs1057265	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	24	0	1	0	A|0.872;G|0.128	0.128	strong	LRFN3,NS,carcinoma,0,1	LRFN3	43	1	NM_024509	exon2	c.A471G	p.T157T	CGAGACACTGGAG	.	PASS	Atlas-SNP
CAAP1	79886	hgsc.bcm.edu	37	9	26861106	26861106	+	Missense_Mutation	SNP	C	C	T	rs12342214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	72	175	0	0.423529	0	C|0.939;T|0.061	0.061	strong	.	.	.	.	NM_024828	exon5	c.G697A	p.V233M	CTCTCACGGATGA	.	PASS	Atlas-SNP
TXNDC5	81567	hgsc.bcm.edu	37	6	7883386	7883386	+	Silent	SNP	G	G	A	rs9502656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	25	67	0	0.384615	0	G|0.920;A|0.080	0.080	strong	.	TXNDC5	33	.	NM_030810	exon10	c.C1290T	p.D430D	AAGTTCGTCTTTC	.	PASS	Atlas-SNP
PGAM2	5224	hgsc.bcm.edu	37	7	44104805	44104805	+	Silent	SNP	C	C	T	rs112828964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	131	256	0	0.467857	0	C|0.968;T|0.032	0.032	strong	.	PGAM2	20	.	NM_000290	exon1	c.G324A	p.G108G	CTCCTCCCCGTGC	.	PASS	Atlas-SNP
PUM2	23369	hgsc.bcm.edu	37	2	20508156	20508156	+	Silent	SNP	C	C	T	rs34057700	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	85	177	0	0.472222	0	C|0.974;T|0.026	0.026	strong	.	PUM2	91	.	NM_015317	exon5	c.G708A	p.Q236Q	GTCAAACTGTAAG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187542432	187542432	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	125	244	0	0.473485	0	.	.	none	.	FAT1	500	.	NM_005245	exon10	c.T5308C	p.Y1770H	CTGTATATTCTGC	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6278425	6278425	+	Missense_Mutation	SNP	G	G	A	rs61746089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	51	91	0	0.53125	0	G|0.991;A|0.009	0.009	strong	.	RNF207	45	.	NM_207396	exon17	c.G1729A	p.A577T	GCCTCAGCCAGGT	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206012	98206012	+	Missense_Mutation	SNP	G	G	A	rs185401750	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	124	292	1	0.478764	0.00342466	G|0.989;A|0.011	0.011	strong	.	.	.	.	NM_025190	exon1	c.C137T	p.A46V	TTATTGGCGTCAT	.	PASS	Atlas-SNP
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	96	164	0	0.521739	0	T|0.663;G|0.337	0.337	strong	.	PIP4K2B	35	.	NM_003559	exon9	c.A1128C	p.T376T	CTTCTTTGTATCG	.	PASS	Atlas-SNP
SEMA3E	9723	hgsc.bcm.edu	37	7	83035289	83035289	+	Silent	SNP	A	A	G	rs28505908	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	89	0	0.490385	0	A|0.987;G|0.013	0.013	strong	.	SEMA3E	125	.	NM_012431	exon8	c.T900C	p.N300N	AATTCCATTCATT	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224754	248224754	+	Silent	SNP	T	T	C	rs76341604		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	107	304	0	0.402256	0	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.T771C	p.T257T	CTACACTTATCTA	.	PASS	Atlas-SNP
TPSB2	64499	hgsc.bcm.edu	37	16	1279623	1279623	+	Silent	SNP	G	G	A	rs72633259	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	53	134	0	0.395522	0	G|0.650;A|0.350	0.350	strong	.	TPSB2	8	.	NM_024164	exon3	c.C177T	p.C59C	GCCCCCGCAGAAG	.	PASS	Atlas-SNP
HYI	81888	hgsc.bcm.edu	37	1	43917098	43917098	+	Missense_Mutation	SNP	C	C	G	rs79439514	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	18	37	0	0.428571	0	C|0.974;G|0.026	0.026	strong	.	HYI	23	.	NM_001190880	exon7	c.G743C	p.C248S	TACTCACAGCCCA	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2039776	2039776	+	Silent	SNP	A	A	G	rs13296987	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	90	1	0.52	0.0111111	A|0.750;G|0.250	0.250	strong	SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	NM_139045	exon4	c.A666G	p.Q222Q	GCAGCAACAGCAG	.	scavenged	Atlas-SNP
MLL4	8085	hgsc.bcm.edu	37	19	36224705	36224705	+	Missense_Mutation	SNP	A	A	G	rs231591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	72	159	0	0.455696	0	A|0.441;G|0.559	0.559	strong	.	MLL4	229	.	NM_014727	exon30	c.A7091G	p.D2364G	CGGAAGATGGTCC	.	PASS	Atlas-SNP
BCLAF1	9774	hgsc.bcm.edu	37	6	136589425	136589425	+	Missense_Mutation	SNP	G	G	T	rs77081633	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	48	238	0	0.18251	0	G|0.976;T|0.024	0.024	strong	.	BCLAF1	203	.	NM_014739	exon10	c.C2272A	p.P758T	AAGAAGGTGATGC	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71841018	71841018	+	Silent	SNP	A	A	G	rs17062695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	71	235	0	0.325688	0	A|0.907;G|0.093	0.093	strong	.	TJP2	120	.	NM_001170416	exon7	c.A1230G	p.L410L	ACAGCTAGTGGTG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525780	248525780	+	Missense_Mutation	SNP	C	C	T	rs77428015		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1140	587	1097	3	0.514912	0.00273473	.	.	weak	OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.C898T	p.P300S	CACACCCCTGAGA	.	scavenged	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124288264	124288264	+	Missense_Mutation	SNP	G	G	A	rs77491573	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	26	96	0	0.4	0	G|0.882;A|0.118	0.118	strong	.	DNAH10	888	.	NM_207437	exon16	c.G2317A	p.V773I	TCTCTCGTCCACC	.	PASS	Atlas-SNP
UBA1	7317	hgsc.bcm.edu	37	X	47070468	47070468	+	Missense_Mutation	SNP	A	A	C	rs143044923	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	128	0	0.482517	0	A|0.994;C|0.006	0.006	strong	.	UBA1	89	.	NM_153280	exon20	c.A2308C	p.N770H	GCTGCCAACCTGT	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	72972770	72972770	+	Missense_Mutation	SNP	G	G	T	rs61757568	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	21	30	0	0.512195	0	G|0.986;T|0.014	0.014	strong	.	UNC5B	123	.	NM_001244889	exon1	c.G28T	p.A10S	CGGGGCGCGCTGC	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103540	53103540	+	Missense_Mutation	SNP	C	C	G	rs78135827	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	57	0	0.423077	0	C|0.965;G|0.035	0.035	strong	POM121L12,NS,carcinoma,0,1	POM121L12	146	1	NM_182595	exon1	c.C176G	p.T59S	CCCTGACTCAGAG	.	PASS	Atlas-SNP
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68344696	68344696	+	Missense_Mutation	SNP	C	C	T	rs3803650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	110	202	2	0.486726	0.00990099	C|0.334;T|0.666	0.666	strong	SLC7A6OS,NS,carcinoma,0,1	SLC7A6OS	22	1	NM_032178	exon1	c.G134A	p.G45D	TCCAAACCCTCCG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9024994	9024994	+	Missense_Mutation	SNP	C	C	T	rs67631215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	81	168	0	0.47929	0	C|0.686;T|0.314	0.314	strong	MUC16_ENST00000397910,NS,carcinoma,0,1	MUC16	4315	1	NM_024690	exon16	c.G36868A	p.E12290K	CTTTCTCGGGCCT	.	PASS	Atlas-SNP
GGA3	23163	hgsc.bcm.edu	37	17	73236124	73236124	+	Silent	SNP	A	A	G	rs28641831	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	24	66	0	0.387097	0	A|0.857;G|0.143	0.143	strong	.	GGA3	54	.	NM_138619	exon13	c.T1329C	p.D443D	AGGAGCATCGGAG	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235945294	235945294	+	Silent	SNP	T	T	C	rs6696123	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	59	110	0	0.584158	0	T|0.614;C|0.386	0.386	strong	.	LYST	370	.	NM_000081	exon15	c.A4956G	p.L1652L	GGATGATAAACAA	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27804691	27804691	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	13	169	0	0.0828025	0	.	.	none	.	C2orf16	357	.	NM_032266	exon1	c.A5252G	p.H1751R	GACATCACAGTCC	.	PASS	Atlas-SNP
HSD17B13	345275	hgsc.bcm.edu	37	4	88243832	88243832	+	Silent	SNP	A	A	G	rs137887488	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	89	173	0	0.478495	0	A|0.996;G|0.004	0.004	strong	.	HSD17B13	27	.	NM_178135	exon1	c.T162C	p.Y54Y	AAATTCATAAGTA	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112647832	112647832	+	Missense_Mutation	SNP	A	A	C	rs9826308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	143	118	0	1	0	A|0.408;C|0.592	0.592	strong	.	CD200R1	91	.	NM_138806	exon5	c.T600G	p.H200Q	GGAGATATGCGCA	.	PASS	Atlas-SNP
ZNF611	81856	hgsc.bcm.edu	37	19	53209554	53209554	+	Missense_Mutation	SNP	G	G	T	rs76627659		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	107	187	1	0.554404	0.00534759	.	.	weak	ZNF611,NS,carcinoma,+1,1	ZNF611	72	1	NM_030972	exon7	c.C754A	p.P252T	AATGGGGTATCTG	.	PASS	Atlas-SNP
SPHK2	56848	hgsc.bcm.edu	37	19	49131317	49131317	+	Silent	SNP	G	G	T	rs116785119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	37	61	0	0.569231	0	G|0.996;T|0.004	0.004	strong	.	SPHK2	62	.	NM_020126	exon5	c.G747T	p.L249L	CGGGCTGCTCCAT	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169816	113169816	+	Silent	SNP	T	T	C	rs116159392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	75	151	0	0.635593	0	T|0.959;C|0.041	0.041	strong	SVEP1,NS,carcinoma,0,1	SVEP1	326	1	NM_153366	exon38	c.A8064G	p.G2688G	TTCATATCCTGGA	.	PASS	Atlas-SNP
PARD3B	117583	hgsc.bcm.edu	37	2	205990353	205990353	+	Silent	SNP	C	C	T	rs2276676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	49	104	0	0.449541	0	T|0.294;C|0.706	0.294	strong	.	PARD3B	314	.	NM_205863	exon10	c.C1326T	p.T442T	TGTCACCGGACGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	783	344	450	1	0.439336	0.00222222	T|0.872;G|0.128	0.128	strong	FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.A6462C	p.Q2154H	TTGCTCTTGGTGG	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007680	6007680	+	Missense_Mutation	SNP	A	A	G	rs4436524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	71	163	0	0.44375	0	A|0.245;G|0.755;T|0.000	0.755	strong	OR52L1_ENST00000332249,NS,carcinoma,0,2	OR52L1	100	2	NM_001005173	exon1	c.T481C	p.C161R	CGATGCACCCTAT	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12675713	12675713	+	Missense_Mutation	SNP	T	T	C	rs17166250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	62	102	0	0.508197	0	T|0.970;C|0.030	0.030	strong	.	SCIN	105	.	NM_001112706	exon10	c.T1363C	p.F455L	TCTGCGTTCCTGA	.	PASS	Atlas-SNP
ATP11B	23200	hgsc.bcm.edu	37	3	182614493	182614493	+	Silent	SNP	T	T	C	rs4859142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	70	132	0	0.460526	0	T|0.842;C|0.158	0.158	strong	.	ATP11B	115	.	NM_014616	exon26	c.T2988C	p.F996F	GATGTTTGGAAAC	.	PASS	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64665444	64665444	+	Missense_Mutation	SNP	G	G	A	rs61740228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	12	37	0	0.5	0	G|0.957;A|0.043	0.043	strong	.	ATG2A	133	.	NM_015104	exon35	c.C4861T	p.R1621C	CGGGGCGAGCTAG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16701717	16701717	+	Silent	SNP	C	C	T	rs149110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	90	0	0.494624	0	C|0.928;T|0.072	0.072	strong	.	MYO10	198	.	NM_012334	exon25	c.G2787A	p.R929R	CTCCAGCCTGCGG	.	PASS	Atlas-SNP
CAP2	10486	hgsc.bcm.edu	37	6	17507504	17507504	+	Silent	SNP	C	C	G	rs146710056	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	66	134	0	0.515625	0	C|0.998;G|0.002	0.002	strong	.	CAP2	61	.	NM_006366	exon5	c.C405G	p.A135A	TTCGGCCGTCAGC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	141	0	0.441176	0	T|0.759;C|0.241	0.241	strong	RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	NM_001256071	exon6	c.T962C	p.M321T	ACGAGATGGCTGC	.	PASS	Atlas-SNP
ATP8B1	5205	hgsc.bcm.edu	37	18	55334339	55334339	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	4	91	0	0.0421053	0	.	.	none	.	ATP8B1	126	.	NM_005603	exon20	c.A2270G	p.Y757C	TCCCCATAGCAGA	.	PASS	Atlas-SNP
CT47B1	643311	hgsc.bcm.edu	37	X	120008932	120008932	+	Missense_Mutation	SNP	T	T	C	rs193289998	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	22	94	0	0.285714	0	T|0.985;C|0.015	0.015	strong	.	CT47B1	67	.	NM_001145718	exon1	c.A593G	p.E198G	GCGGCCTCCTGGA	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464558	39464558	+	Silent	SNP	G	G	A	rs72828117	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	44	117	0	0.423077	0	G|0.900;A|0.100	0.100	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C948T	p.P316P	GGGGCTGGGCTCA	.	PASS	Atlas-SNP
TMPRSS5	80975	hgsc.bcm.edu	37	11	113565322	113565322	+	Silent	SNP	C	C	A	rs17115841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	42	67	0	0.65625	0	C|0.913;A|0.087	0.087	strong	TMPRSS5_ENST00000299882,NS,neuroblastoma,-2,2	TMPRSS5	69	2	NM_030770	exon8	c.G663T	p.G221G	AGACTGCCCACCA	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79033306	79033306	+	Missense_Mutation	SNP	A	A	C	rs2278239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	111	1	1	0.00900901	A|0.698;C|0.302	0.302	strong	.	CMYA5	643	.	NM_153610	exon2	c.A8718C	p.K2906N	TGATAAAATGGTT	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48734136	48734136	+	Missense_Mutation	SNP	G	G	A	rs35777968	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	51	115	0	0.481132	0	G|0.987;A|0.013	0.013	strong	.	ABCC3	138	.	NM_003786	exon3	c.G296A	p.R99Q	ATGGCCGGGCCCC	.	PASS	Atlas-SNP
CAPN3	825	hgsc.bcm.edu	37	15	42652099	42652099	+	Silent	SNP	T	T	C	rs1801496	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	90	0	1	0	T|0.910;C|0.090	0.090	strong	.	CAPN3	172	.	NM_000070	exon1	c.T96C	p.T32T	GGCCACTGAGGCT	.	PASS	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32475109	32475109	+	Silent	SNP	G	G	A	rs455060	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	172	1	1	0.00581395	G|0.383;A|0.617	0.617	strong	NLRC4,NS,carcinoma,0,1	NLRC4	165	1	NM_001199138	exon4	c.C1824T	p.A608A	GTCCAGGGCACTT	.	PASS	Atlas-SNP
CCL11	6356	hgsc.bcm.edu	37	17	32612894	32612894	+	Missense_Mutation	SNP	G	G	A	rs1129844	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	16	33	0	0.571429	0	A|0.126;C|0.145;G|0.706;T|0.023	0.126	strong	.	CCL11	12	.	NM_002986	exon1	c.G67A	p.A23T	GGGCTCGCTGGGC	.	PASS	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146059006	146059006	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	4	206	0	0.0158103	0	.	.	none	OTUD4,NS,carcinoma,0,5	OTUD4	120	5	NM_001102653	exon21	c.C2726T	p.T909I	GGCACAGTTTCTC	.	scavenged	Atlas-SNP
PSG4	5672	hgsc.bcm.edu	37	19	43699417	43699417	+	Missense_Mutation	SNP	A	A	G	rs3859474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	186	100	1	1	0.01	A|0.397;G|0.603	0.603	strong	.	PSG4	129	.	NM_002780	exon4	c.G718C	p.G240R	GCTTGGACAGCTT	.	PASS	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49433356	49433356	+	Silent	SNP	G	G	A	rs116686402	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	17	30	0	0.395349	0	G|0.986;A|0.014	0.014	strong	.	MLL2	1173	.	NM_003482	exon32	c.C8091T	p.R2697R	GGTGTTGCGCTGG	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969522	49969522	+	Silent	SNP	C	C	T	rs116631301	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	16	34	0	0.470588	0	C|0.992;T|0.008	0.008	strong	.	ALDH16A1	54	.	NM_153329	exon14	c.C1920T	p.A640A	GCAGGCCCAAGGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680370	100680370	+	Silent	SNP	C	C	T	rs10257974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	68	137	0	0.511278	0	C|0.861;T|0.139	0.139	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5673T	p.P1891P	AACTCCCGCTGTC	.	PASS	Atlas-SNP
KIF12	113220	hgsc.bcm.edu	37	9	116856481	116856481	+	Missense_Mutation	SNP	C	C	A	rs35719524	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	46	64	0	0.638889	0	C|0.851;A|0.149	0.149	strong	.	KIF12	35	.	NM_138424	exon10	c.G879T	p.M293I	CTCTAGCATGAAC	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	37	14	101004432	101004432	+	Silent	SNP	G	G	A	rs7493484	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	22	41	0	0.458333	0	G|0.933;A|0.067	0.067	strong	.	BEGAIN	32	.	NM_020836	exon7	c.C1656T	p.A552A	CGGGGAGGCCTCC	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98165920	98165920	+	Missense_Mutation	SNP	A	A	G	rs200418218	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	7	6	0	0.466667	0	A|0.983;G|0.017	0.017	strong	.	.	.	.	NM_025190	exon20	c.T1439C	p.I480T	CTGGCTATATTCA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910340	29910340	+	Missense_Mutation	SNP	A	A	G	rs79326316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	54	200	0	0.203008	0	A|0.971;G|0.029	0.029	strong	.	HLA-A	89	.	NM_001242758	exon1	c.A10G	p.M4V	GCCGTCATGGCGC	.	PASS	Atlas-SNP
SOX10	6663	hgsc.bcm.edu	37	22	38379543	38379543	+	Silent	SNP	G	G	A	rs73415876	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	65	84	0	0.541667	0	A|0.044;G|0.956	0.044	strong	.	SOX10	48	.	NM_006941	exon2	c.C249T	p.Y83Y	CCAGTCGTAGCCG	.	PASS	Atlas-SNP
CLCN6	1185	hgsc.bcm.edu	37	1	11884586	11884586	+	Silent	SNP	G	G	A	rs60602304	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	53	105	0	0.535354	0	G|0.970;A|0.030	0.030	strong	.	CLCN6	77	.	NM_001286	exon8	c.G624A	p.S208S	TGGTTCGGTGGTG	.	PASS	Atlas-SNP
HNRNPH3	3189	hgsc.bcm.edu	37	10	70101417	70101417	+	Missense_Mutation	SNP	G	G	C	rs16925347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	65	104	0	0.532787	0	G|0.943;C|0.057	0.057	strong	.	HNRNPH3	33	.	NM_012207	exon8	c.G851C	p.G284A	TGGGAGGCTACGG	.	PASS	Atlas-SNP
GRIN2A	2903	hgsc.bcm.edu	37	16	9916204	9916204	+	Silent	SNP	C	C	G	rs9806806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	145	282	1	0.519713	0.0035461	C|0.671;G|0.329	0.329	strong	.	GRIN2A	366	.	NM_000833	exon11	c.G2085C	p.R695R	GTTATTCCGAATG	.	PASS	Atlas-SNP
LCN8	138307	hgsc.bcm.edu	37	9	139649612	139649612	+	Missense_Mutation	SNP	C	C	A	rs2282258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	104	130	0	0.666667	0	C|0.851;A|0.149	0.149	strong	LCN8,colon,carcinoma,0,1	LCN8	14	1	NM_178469	exon6	c.G422T	p.G141V	CACCGCCCTGCAG	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519362	43519362	+	Silent	SNP	C	C	T	rs11083680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	87	184	0	0.460317	0	C|0.424;T|0.576	0.576	strong	PSG11,right_lower_lobe,carcinoma,-2,1	PSG11	57	1	NM_002785	exon4	c.G870A	p.Q290Q	AGTAATCTGAGGG	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48134768	48134768	+	Missense_Mutation	SNP	A	A	T	rs80097705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	61	118	0	0.455224	0	A|0.965;T|0.035	0.035	strong	.	RAPGEF3	98	.	NM_001098531	exon20	c.T1979A	p.L660Q	CTCACCAGGTCCA	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109384665	109384665	+	Missense_Mutation	SNP	A	A	G	rs79989901		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	378	186	369	0	0.492063	0	.	.	weak	.	RANBP2	488	.	NM_006267	exon20	c.A7670G	p.N2557S	GTAACAATAGTGA	.	PASS	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158368846	158368846	+	Missense_Mutation	SNP	T	T	C	rs6662382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	74	139	0	0.48366	0	T|0.659;C|0.341	0.341	strong	.	OR10T2	76	.	NM_001004475	exon1	c.A411G	p.I137M	TTTGTTTATGATG	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166770120	166770120	+	Silent	SNP	A	A	G	rs10176588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	97	203	0	0.492386	0	A|0.681;G|0.319	0.319	strong	.	TTC21B	130	.	NM_024753	exon16	c.T2175C	p.F725F	GAGAAGAAAAGAC	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72294192	72294192	+	Missense_Mutation	SNP	C	C	T	rs141167395	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	40	93	0	0.434783	0	C|0.999;T|0.001	0.001	strong	.	.	.	.	NM_014431	exon9	c.C1034T	p.T345M	CCCCCACGCAGGC	.	PASS	Atlas-SNP
SLC43A2	124935	hgsc.bcm.edu	37	17	1494660	1494660	+	Silent	SNP	G	G	A	rs73976240	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	48	74	0	0.578313	0	G|0.971;A|0.029	0.029	strong	.	SLC43A2	37	.	NM_152346	exon8	c.C834T	p.S278S	CCTCATGGAGCTG	.	PASS	Atlas-SNP
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	40	88	0	0.4	0	T|0.613;A|0.387	0.387	strong	INSL4,bladder,carcinoma,+2,1	INSL4	20	1	NM_002195	exon1	c.T189A	p.R63R	TGGACGTCCCAAA	.	PASS	Atlas-SNP
APLNR	187	hgsc.bcm.edu	37	11	57003581	57003581	+	Missense_Mutation	SNP	C	C	T	rs7943508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	86	124	0	0.565789	0	C|0.986;T|0.014	0.014	strong	APLNR,caecum,carcinoma,0,2	APLNR	62	2	NM_005161	exon1	c.G898A	p.V300I	TGTTGACGTAGCT	.	PASS	Atlas-SNP
SLC4A8	9498	hgsc.bcm.edu	37	12	51855009	51855009	+	Silent	SNP	T	T	G	rs150970094	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	78	151	0	0.47561	0	T|0.997;G|0.003	0.003	strong	SLC4A8,back,malignant_melanoma,+2,1	SLC4A8	292	1	NM_001039960	exon9	c.T1035G	p.G345G	ATTGGGTCCAGTA	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79556301	79556301	+	Missense_Mutation	SNP	A	A	G	rs74140333	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	98	249	0	0.464455	0	A|0.989;G|0.011	0.011	strong	.	DLG5	154	.	NM_004747	exon28	c.T5216C	p.L1739P	GGCCTCAGAGCGG	.	PASS	Atlas-SNP
SPECC1L	23384	hgsc.bcm.edu	37	22	24761502	24761502	+	Silent	SNP	G	G	A	rs139166286	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	36	67	0	0.5	0	A|0.002;G|0.998	0.002	strong	.	SPECC1L	85	.	NM_001145468	exon12	c.G2886A	p.S962S	AGCGTCGCCAGCC	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108496435	108496435	+	Missense_Mutation	SNP	T	T	A	rs832352	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	478	415	498	1	0.868201	0.00200803	T|0.446;A|0.554	0.554	strong	RGPD4,NS,carcinoma,0,1	RGPD4	112	1	NM_182588	exon21	c.T4936A	p.W1646R	CCATTATGGCATG	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214623	45214623	+	Missense_Mutation	SNP	G	G	A	rs75637741	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	8	25	0	0.222222	0	.	.	weak	CDC27_ENST00000531206,rectum,carcinoma,0,2	CDC27	337	2	NM_001114091	exon14	c.C1826T	p.A609V	GTATAGGCATAAG	.	scavenged	Atlas-SNP
ATP6V1C1	528	hgsc.bcm.edu	37	8	104054603	104054603	+	Silent	SNP	T	T	C	rs7009365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	82	201	0	0.522293	0	T|0.922;C|0.078	0.078	strong	.	ATP6V1C1	33	.	NM_001695	exon3	c.T168C	p.D56D	GTCAGATGAACTG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56505063	56505063	+	Silent	SNP	A	A	G	rs2144407	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	74	155	0	0.468354	0	A|0.854;C|0.000;G|0.146	0.146	strong	.	DST	1427	.	NM_001723	exon4	c.T757C	p.L253L	ACTTCAAAGTTTG	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373915	27373915	+	Silent	SNP	G	G	T	rs2234898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	46	79	0	0.522727	0	G|0.756;T|0.244	0.244	strong	IL4R,NS,carcinoma,0,1	IL4R	70	1	NM_000418	exon11	c.G1242T	p.L414L	GGACCTGCTCGGA	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530534	140530534	+	Missense_Mutation	SNP	G	G	C	rs10076554	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	53	103	0	0.490741	0	G|0.986;C|0.014	0.014	strong	.	PCDHB6	161	.	NM_018939	exon1	c.G696C	p.L232F	GGTTTTGGACATC	.	PASS	Atlas-SNP
DBNL	28988	hgsc.bcm.edu	37	7	44096482	44096482	+	Missense_Mutation	SNP	G	G	A	rs61735009	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	45	66	0	0.432692	0	A|0.013;C|0.000;G|0.987	0.013	strong	.	DBNL	26	.	NM_001122956	exon5	c.G454A	p.V152M	CAGGACGTGGGAC	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	54	104	0	0.529412	0	C|0.825;T|0.175	0.175	strong	SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	NM_001034852	exon8	c.C702T	p.A234A	GAGTGCCCTGGAA	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39263422	39263422	+	Silent	SNP	C	C	T	rs41292751	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	92	0	0.515789	0	C|0.973;T|0.027	0.027	strong	.	FREM2	385	.	NM_207361	exon1	c.C1941T	p.D647D	GCAGGACATAACA	.	PASS	Atlas-SNP
VWCE	220001	hgsc.bcm.edu	37	11	61048322	61048322	+	Silent	SNP	G	G	C	rs61744427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	36	51	0	0.537313	0	G|0.971;C|0.029	0.029	strong	.	VWCE	84	.	NM_152718	exon8	c.C1173G	p.A391A	ATGCATGGCTCCC	.	PASS	Atlas-SNP
MFAP3L	9848	hgsc.bcm.edu	37	4	170912685	170912685	+	Silent	SNP	T	T	C	rs61740817	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	105	168	0	0.492958	0	T|0.933;C|0.067	0.067	strong	MFAP3L,NS,carcinoma,-2,1	MFAP3L	59	1	NM_021647	exon3	c.A1074G	p.E358E	AGAAGGTTCTGCA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910583	29910583	+	Silent	SNP	C	C	T	rs1059426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	20	87	0	0.206186	0	C|0.911;T|0.089	0.089	strong	.	HLA-A	89	.	NM_001242758	exon2	c.C123T	p.R41R	CGGCCGCGGGGAG	.	PASS	Atlas-SNP
LGI4	163175	hgsc.bcm.edu	37	19	35616316	35616316	+	Silent	SNP	C	C	T	rs12610234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	180	172	0	1	0	C|0.678;T|0.322	0.322	strong	.	LGI4	32	.	NM_139284	exon9	c.G1395A	p.Q465Q	GGCCAGCTGGTCC	.	PASS	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34814745	34814745	+	Missense_Mutation	SNP	T	T	C	rs150350937	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	150	318	0	0.515464	0	T|1.000;C|0.000	0.000	weak	RAI14,scalp,malignant_melanoma,-1,1	RAI14	100	1	NM_001145525	exon14	c.T919C	p.S307P	AAGGAATCGGTAT	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	37	MT	9540	9540	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	8	0	1	0	.	.	none	.	.	.	.	ENST00000362079	exon1	c.T334C	p.L112L	CCCCAATTAGGAG	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222825568	222825568	+	Splice_Site	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	3	182	0	0.0166667	0	.	.	none	MIA3,NS,carcinoma,0,1	MIA3	167	1	NM_198551	exon13	c.3982-2A>G	.	TGCATTAGGTTCA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512820	195512820	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	9	400	0	0.0280374	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C5631T	p.D1877D	GGAAGCGTCGGTG	.	scavenged	Atlas-SNP
ANKRD65	441869	hgsc.bcm.edu	37	1	1354515	1354515	+	Missense_Mutation	SNP	C	C	G	rs904589	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	95	202	0	0.458937	0	C|0.714;G|0.286	0.286	strong	.	ANKRD65	4	.	NM_001145210	exon4	c.G1165C	p.E389Q	CCTTCTCCCCCCC	.	PASS	Atlas-SNP
ZNF808	388558	hgsc.bcm.edu	37	19	53057031	53057031	+	Missense_Mutation	SNP	A	A	G	rs116132766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	53	162	0	0.350993	0	A|0.996;G|0.004	0.004	strong	.	ZNF808	81	.	NM_001039886	exon5	c.A862G	p.K288E	CCTTACAAGTGTA	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53675381	53675381	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	2	110	0	0.0169492	0	.	.	none	ESPL1,colon,carcinoma,-1,1	ESPL1	158	1	NM_012291	exon13	c.C2590T	p.R864X	CTGCTTCGAAGTC	.	scavenged	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818514	55818514	+	Missense_Mutation	SNP	C	C	T	rs59719421	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	97	200	0	0.434978	0	C|0.979;T|0.021	0.021	strong	.	FBXO34	61	.	NM_017943	exon2	c.C1406T	p.S469F	AGCCTTCCATTTT	.	PASS	Atlas-SNP
SYBU	55638	hgsc.bcm.edu	37	8	110587222	110587222	+	Silent	SNP	A	A	G	rs35039797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	105	0	1	0	A|0.972;G|0.028	0.028	strong	.	SYBU	71	.	NM_001099752	exon8	c.T1905C	p.P635P	ATACACAGGATCC	.	PASS	Atlas-SNP
DHX36	170506	hgsc.bcm.edu	37	3	154002774	154002774	+	Silent	SNP	G	G	A	rs114098462	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	75	155	0	0.436047	0	G|0.992;A|0.008	0.008	strong	.	DHX36	98	.	NM_020865	exon18	c.C2034T	p.N678N	CAAAGCGTTCTGT	.	PASS	Atlas-SNP
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	138	134	0	0.992806	0	A|0.527;G|0.473	0.473	strong	.	SLC29A3	51	.	NM_018344	exon2	c.A52G	p.R18G	ACCTACAGAACCA	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38129311	38129311	+	Silent	SNP	C	C	T	rs200990219	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	80	171	0	0.470588	0	C|0.998;T|0.002	0.002	strong	.	TRIOBP	262	.	NM_001039141	exon8	c.C3954T	p.S1318S	GAAGTCCGAGGCA	.	PASS	Atlas-SNP
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731159	140731159	+	Silent	SNP	T	T	C	rs78745319	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	70	107	0	0.486111	0	T|0.959;C|0.041	0.041	strong	.	PCDHGB1	198	.	NM_018922	exon1	c.T1332C	p.N444N	CGACAATGCACCT	.	PASS	Atlas-SNP
PRIMA1	145270	hgsc.bcm.edu	37	14	94187816	94187816	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	29	65	0	0.42029	0	.	.	none	.	PRIMA1	21	.	NM_178013	exon5	c.G436C	p.V146L	CGTCTACTCCTTT	.	PASS	Atlas-SNP
UNC5D	137970	hgsc.bcm.edu	37	8	35624434	35624434	+	Silent	SNP	C	C	A	rs16884404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	51	135	0	0.418033	0	C|0.891;A|0.109	0.109	strong	.	UNC5D	393	.	NM_080872	exon15	c.C2328A	p.S776S	GTTCTCCCGCGTG	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139698977	139698977	+	Silent	SNP	G	G	A	rs11145892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	27	31	0	0.675	0	G|0.993;A|0.007	0.007	strong	.	KIAA1984	39	.	NM_001039374	exon7	c.G690A	p.A230A	GGAGGCGTCCTTC	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31603189	31603189	+	Missense_Mutation	SNP	G	G	A	rs11538264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	110	278	0	0.497738	0	G|0.943;A|0.057	0.057	strong	.	PRRC2A	152	.	NM_004638	exon23	c.G5320A	p.V1774M	CGCCTAGTGGTAG	.	PASS	Atlas-SNP
CSF1R	1436	hgsc.bcm.edu	37	5	149460544	149460544	+	Silent	SNP	G	G	A	rs41424646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	94	136	1	0.505376	0.00735294	T|0.000;G|0.999;A|0.001	0.001	strong	CSF1R_ENST00000286301,caecum,carcinoma,-1,2	CSF1R	250	2	NM_005211	exon3	c.C93T	p.V31V	CTTCACGACCAGC	.	scavenged	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344238	72344238	+	Silent	SNP	C	C	T	rs17817969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	59	122	0	0.522124	0	C|0.907;T|0.093	0.093	strong	.	ZNF407	231	.	NM_001146190	exon1	c.C1263T	p.L421L	TATTCTCGTGTTG	.	PASS	Atlas-SNP
TBX22	50945	hgsc.bcm.edu	37	X	79283509	79283509	+	Silent	SNP	T	T	C	rs195293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	84	91	0	0.988235	0	T|0.847;0|0.016	.	strong	.	TBX22	118	.	NM_016954	exon7	c.T883C	p.L295L	GGGCTTTTAGAGA	.	PASS	Atlas-SNP
CDK11A	728642	hgsc.bcm.edu	37	1	1635565	1635565	+	Silent	SNP	C	C	T	rs11488591	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	132	238	0	0.532258	0	C|0.822;T|0.178	0.178	strong	CDK11B,NS,carcinoma,0,2	CDK11A	38	2	NM_024011	exon16	c.G1707A	p.A569A	CTCCCGCGCCAGC	.	PASS	Atlas-SNP
ZNF765	91661	hgsc.bcm.edu	37	19	53901281	53901281	+	Missense_Mutation	SNP	C	C	G	rs141876832	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	68	0	0.468354	0	C|0.962;G|0.038	0.038	strong	ZNF765_ENST00000396408,NS,carcinoma,-2,1	ZNF765	61	1	NM_001040185	exon2	c.C13G	p.Q5E	CTTCCTCAGGTGA	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918135	51918135	+	Missense_Mutation	SNP	G	G	T	rs1833785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	105	0	0.5	0	G|0.776;T|0.224	0.224	strong	.	SIGLEC10	112	.	NM_033130	exon8	c.C1558A	p.R520S	CACAGCGGAGCCT	.	PASS	Atlas-SNP
NEUROG1	4762	hgsc.bcm.edu	37	5	134871280	134871280	+	Missense_Mutation	SNP	C	C	T	rs34137563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	13	23	0	0.433333	0	C|0.993;T|0.007	0.007	strong	.	NEUROG1	18	.	NM_006161	exon1	c.G101A	p.R34K	TGGAGTCTGGCAC	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154275786	154275786	+	Missense_Mutation	SNP	G	G	A	rs6865950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	96	191	0	0.527473	0	G|0.891;A|0.109	0.109	strong	.	GEMIN5	120	.	NM_015465	exon24	c.C3463T	p.P1155S	CGAAAGGCCCTTC	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30793532	30793532	+	Missense_Mutation	SNP	G	G	A	rs76338133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	71	0	0.460526	0	G|0.984;A|0.016	0.016	strong	.	INMT	38	.	NM_006774	exon2	c.G340A	p.A114T	AAATTCGCCTGTG	.	PASS	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	37	12	56815717	56815717	+	Missense_Mutation	SNP	T	T	C	rs61733875	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	57	71	0	0.5	0	T|0.947;C|0.053	0.053	strong	.	TIMELESS	107	.	NM_003920	exon21	c.A2608G	p.M870V	GTCCCATCTGTAC	.	PASS	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90760810	90760810	+	Silent	SNP	C	C	T	rs74037028	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	61	162	0	0.458647	0	C|0.977;T|0.023	0.023	strong	.	SEMA4B	51	.	NM_020210	exon3	c.C297T	p.F99F	CAGCTTCCTGCCA	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1421531	1421531	+	Silent	SNP	C	C	A	rs819976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	90	231	0	0.436893	0	C|0.587;A|0.413	0.413	strong	.	ATAD3B	68	.	NM_031921	exon10	c.C1005A	p.T335T	AGCAACCAGGAAC	.	PASS	Atlas-SNP
OR6Y1	391112	hgsc.bcm.edu	37	1	158517099	158517099	+	Missense_Mutation	SNP	C	C	A	rs113154921	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	68	152	0	0.478873	0	A|0.018;C|0.982;G|0.000	0.018	strong	.	OR6Y1	73	.	NM_001005189	exon1	c.G797T	p.R266L	TTGGGACGGGCAT	.	PASS	Atlas-SNP
RPE65	6121	hgsc.bcm.edu	37	1	68904645	68904645	+	Silent	SNP	C	C	A	rs61752907	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	72	128	0	0.503497	0	C|0.998;A|0.002	0.002	strong	.	RPE65	87	.	NM_000329	exon9	c.G978T	p.V326V	GAGATCCACAATC	.	PASS	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169566308	169566308	+	Silent	SNP	G	G	A	rs6132	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	92	194	0	0.464646	0	G|0.764;A|0.236	0.236	strong	.	SELP	132	.	NM_003005	exon11	c.C1812T	p.N604N	AAAGCCGTTGTCA	.	PASS	Atlas-SNP
C8orf31	286122	hgsc.bcm.edu	37	8	144126087	144126087	+	Missense_Mutation	SNP	C	C	A	rs73717943	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	33	57	0	0.559322	0	C|0.973;A|0.027	0.027	strong	.	C8orf31	18	.	NM_173687	exon4	c.C208A	p.P70T	CTGGCACCCCAGG	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29240783	29240783	+	Missense_Mutation	SNP	A	A	G	rs1109758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	48	117	0	0.387097	0	A|0.599;G|0.401	0.401	strong	.	FAM179A	106	.	NM_199280	exon10	c.A1321G	p.I441V	ATCCCCATCAGCC	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778694	84778694	+	Missense_Mutation	SNP	T	T	C	rs2326391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	105	191	0	0.502392	0	T|0.774;C|0.226	0.226	strong	.	USP10	51	.	NM_001272075	exon5	c.T619C	p.S207P	CCCCCGTCAGTTA	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	6995315	6995315	+	Silent	SNP	C	C	T	rs2379206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	112	189	0	0.480687	0	C|0.347;T|0.653	0.653	strong	.	HDHD1	21	.	NM_001135565	exon4	c.G525A	p.P175P	GATGTCCGGGTCT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535832	+	Missense_Mutation	SNP	A	A	G	rs201553143	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	364	58	349	0	0.159341	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.A2018G	p.D673G	GCAGTGATAGCAG	.	PASS	Atlas-SNP
C2CD4C	126567	hgsc.bcm.edu	37	19	408200	408200	+	Silent	SNP	G	G	C	rs7252178	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	98	150	0	0.544444	0	G|0.971;C|0.029	0.029	strong	C2CD4C,NS,carcinoma,0,1	C2CD4C	13	1	NM_001136263	exon2	c.C162G	p.P54P	CAGCTTGGGGGGG	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	36	58	0	0.553846	0	C|0.791;T|0.209	0.209	strong	TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	NM_001248006	exon6	c.G1125A	p.P375P	TGGCACCGGAAGG	.	PASS	Atlas-SNP
PIP4K2B	8396	hgsc.bcm.edu	37	17	36936846	36936846	+	Silent	SNP	C	C	T	rs16968328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	71	0	0.423077	0	C|0.931;T|0.069	0.069	strong	.	PIP4K2B	35	.	NM_003559	exon4	c.G366A	p.T122T	GCTGCGCGTCACT	.	PASS	Atlas-SNP
DPP8	54878	hgsc.bcm.edu	37	15	65793060	65793060	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	62	190	0	0.346369	0	.	.	none	DPP8,colon,carcinoma,+1,1	DPP8	78	1	NM_197960	exon5	c.C478T	p.R160C	CAATGCGTTTTCT	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81960783	81960783	+	Silent	SNP	G	G	A	rs115583707	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	81	0	0.527027	0	G|0.984;A|0.016	0.016	strong	.	PLCG2	276	.	NM_002661	exon23	c.G2514A	p.Q838Q	AAAGCAGGTGAGT	.	PASS	Atlas-SNP
GPR171	29909	hgsc.bcm.edu	37	3	150917000	150917000	+	Silent	SNP	T	T	G	rs3773614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	88	220	0	0.508671	0	T|0.882;G|0.118	0.118	strong	.	GPR171	36	.	NM_013308	exon3	c.A174C	p.T58T	ATCGGCTGTAAGC	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77170477	77170477	+	Missense_Mutation	SNP	C	C	A	rs1051978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	55	123	0	0.539216	0	C|0.931;A|0.069	0.069	strong	.	NFATC1	105	.	NM_172390	exon2	c.C202A	p.P68T	CCGGCCCCGTGCC	.	PASS	Atlas-SNP
C2orf91	400950	hgsc.bcm.edu	37	2	42165754	42165754	+	Splice_Site	SNP	C	C	T	rs10192292	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	102	170	0	0.542553	0	C|0.732;T|0.268	0.268	strong	.	.	.	.	NM_001242815	exon5	c.386-1G>A	.	TGGAACCTGCAAG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169116	113169116	+	Missense_Mutation	SNP	T	T	C	rs16914996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	52	66	0	0.702703	0	T|0.943;C|0.057	0.057	strong	.	SVEP1	326	.	NM_153366	exon38	c.A8764G	p.I2922V	GCAAGATGTAGCC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	28	18	0	0.736842	0	C|0.975;A|0.025	0.025	strong	.	NAV2	255	.	NM_145117	exon1	c.C84A	p.P28P	CGTGCCCCCGGCC	.	PASS	Atlas-SNP
OLFML2B	25903	hgsc.bcm.edu	37	1	161993192	161993192	+	Missense_Mutation	SNP	T	T	C	rs12130792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	132	148	0	0.985075	0	T|0.895;C|0.105	0.105	strong	.	OLFML2B	114	.	NM_015441	exon1	c.A29G	p.Y10C	GCGAAGTAGAGAA	.	PASS	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87717863	87717863	+	Missense_Mutation	SNP	C	C	T	rs138328691	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	121	192	0	0.555046	0	C|0.999;T|0.001	0.001	strong	JPH3,NS,carcinoma,-2,1	JPH3	95	1	NM_020655	exon3	c.C1276T	p.R426W	CAGCACCGGGAAA	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12420145	12420145	+	Silent	SNP	T	T	C	rs146236000	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	42	47	0	0.552632	0	T|0.994;C|0.006	0.006	strong	VWDE_ENST00000275358,NS,carcinoma,-2,1	VWDE	123	1	NM_001135924	exon5	c.A756G	p.E252E	ATCAAGTTCTAAA	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23556550	23556550	+	Missense_Mutation	SNP	G	G	A	rs148956643	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	58	132	0	0.453125	0	G|0.992;A|0.008	0.008	strong	.	ZNF91	349	.	NM_003430	exon3	c.C247T	p.P83S	CTGTGGGTTCATC	.	PASS	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120803654	120803654	+	Silent	SNP	C	C	T	rs11996390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	119	0	0.523364	0	C|0.777;T|0.223	0.223	strong	.	TAF2	204	.	NM_003184	exon11	c.G1323A	p.L441L	CCAGGACAGTGTA	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519267	113519267	+	Missense_Mutation	SNP	C	C	T	rs35067467	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	121	253	0	0.508403	0	C|0.959;T|0.041	0.041	strong	.	PPP1R3A	317	.	NM_002711	exon4	c.G1880A	p.R627K	TCATTCCTCAAAA	.	PASS	Atlas-SNP
PATZ1	23598	hgsc.bcm.edu	37	22	31737436	31737436	+	Silent	SNP	G	G	A	rs62236170	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	45	124	0	0.375	0	G|0.963;A|0.037	0.037	strong	.	PATZ1	24	.	NM_032051	exon3	c.C1569T	p.T523T	TGGGGTGGTCCAG	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29783908	29783908	+	Missense_Mutation	SNP	A	A	G	rs78773460	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	71	155	0	0.269962	0	A|0.500;G|0.500	0.500	strong	SVIL,NS,carcinoma,0,2	SVIL	226	2	NM_021738	exon20	c.T3776C	p.M1259T	AACTGCATATCTG	.	PASS	Atlas-SNP
MCM5	4174	hgsc.bcm.edu	37	22	35806815	35806815	+	Silent	SNP	T	T	C	rs133417	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	92	131	0	0.484211	0	T|0.893;C|0.107	0.107	strong	.	MCM5	54	.	NM_006739	exon7	c.T831C	p.T277T	CCTGACTACCAGC	.	PASS	Atlas-SNP
FAM71B	153745	hgsc.bcm.edu	37	5	156589937	156589937	+	Missense_Mutation	SNP	G	G	A	rs115938677	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	24	78	0	0.375	0	G|0.995;A|0.005	0.005	strong	FAM71B,NS,carcinoma,0,1	FAM71B	145	1	NM_130899	exon2	c.C1339T	p.R447C	CCTTGCGGTGATG	.	PASS	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	37	5	57751443	57751443	+	Silent	SNP	A	A	G	rs1042994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	93	200	0	0.455882	0	A|0.873;G|0.127	0.127	strong	.	PLK2	71	.	NM_006622	exon11	c.T1548C	p.F516F	GTACCCAAAGCCA	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5410814	5410814	+	Silent	SNP	G	G	C	rs114987874	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	33	79	0	0.39759	0	G|0.984;C|0.016	0.016	strong	.	TNRC18	311	.	NM_001080495	exon11	c.C3411G	p.P1137P	CTTGGAGGGGGAC	.	PASS	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	37	5	140209593	140209593	+	Silent	SNP	A	A	G	rs61730636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	72	140	1	0.489796	0.00714286	A|0.940;G|0.060	0.060	strong	PCDHA6_ENST00000529310,NS,carcinoma,+2,6	PCDHA6	442	6	NM_018909	exon1	c.A1917G	p.E639E	GGACGAAGCGGAC	.	scavenged	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	154	232	1	0.613546	0.00431034	C|0.831;T|0.169	0.169	strong	.	GRIN3A	186	.	NM_133445	exon9	c.G3122A	p.R1041Q	TGGATCCGGATGC	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120139701	120139701	+	Silent	SNP	T	T	G	rs34140357	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	60	107	0	0.425532	0	T|0.947;G|0.053	0.053	strong	.	CIT	535	.	NM_001206999	exon42	c.A5367C	p.G1789G	ATTGGTTCCAATG	.	PASS	Atlas-SNP
C19orf21	126353	hgsc.bcm.edu	37	19	757354	757354	+	Silent	SNP	G	G	A	rs35090443	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	95	0	0.484127	0	G|0.982;A|0.018	0.018	strong	.	C19orf21	56	.	NM_173481	exon2	c.G408A	p.L136L	GAGGCTGTGTGAC	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85435730	85435730	+	Silent	SNP	C	C	T	rs550404	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	99	113	0	0.99	0	C|0.366;T|0.634	0.634	strong	.	SYTL2	231	.	NM_206927	exon1	c.G1770A	p.P590P	TATTAACGGAGCC	.	PASS	Atlas-SNP
UBA6	55236	hgsc.bcm.edu	37	4	68500171	68500171	+	Silent	SNP	A	A	G	rs10008910	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	31	57	0	0.837838	0	A|0.851;G|0.149	0.149	strong	.	UBA6	98	.	NM_018227	exon21	c.T1908C	p.H636H	TATGGTATGTTCA	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	32	68	0	0.410256	0	C|0.819;A|0.181	0.181	strong	DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	NM_130810	exon10	c.G1249T	p.E417X	TTAGTTCTGTTCC	.	PASS	Atlas-SNP
IL17REL	400935	hgsc.bcm.edu	37	22	50439194	50439194	+	Missense_Mutation	SNP	C	C	T	rs9617090	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	49	110	0	0.494949	0	C|0.696;T|0.304	0.304	strong	.	IL17REL	21	.	NM_001001694	exon5	c.G208A	p.G70R	GCCCCCCCTGCTG	.	PASS	Atlas-SNP
ZNF836	162962	hgsc.bcm.edu	37	19	52658510	52658510	+	Missense_Mutation	SNP	T	T	C	rs8113504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	107	0	1	0	T|0.735;C|0.265	0.265	strong	.	ZNF836	158	.	NM_001102657	exon5	c.A2426G	p.N809S	CACTCATTACACA	.	PASS	Atlas-SNP
CCNB2	9133	hgsc.bcm.edu	37	15	59406674	59406674	+	Missense_Mutation	SNP	T	T	C	rs16941036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	102	0	0.484127	0	T|0.994;C|0.006	0.006	strong	.	CCNB2	23	.	NM_004701	exon4	c.T299C	p.M100T	TCTCCATGAAGGA	.	PASS	Atlas-SNP
ARID1B	57492	hgsc.bcm.edu	37	6	157505478	157505478	+	Silent	SNP	G	G	A	rs61745451	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	75	150	0	0.462963	0	G|0.989;A|0.011	0.011	strong	.	ARID1B	320	.	NM_020732	exon13	c.G3459A	p.E1153E	CTTTGAGTGCAAG	.	PASS	Atlas-SNP
STH	246744	hgsc.bcm.edu	37	17	44076711	44076711	+	Silent	SNP	G	G	A	rs73317018	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	90	164	0	0.5	0	A|0.027;C|0.000;G|0.972;T|0.000	0.027	strong	.	STH	14	.	NM_001007532	exon1	c.G66A	p.P22P	GTGGCCGGCCCTC	.	PASS	Atlas-SNP
VLDLR	7436	hgsc.bcm.edu	37	9	2645719	2645719	+	Silent	SNP	C	C	T	rs6143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	51	91	0	0.579545	0	C|0.945;T|0.055	0.055	strong	.	VLDLR	68	.	NM_003383	exon10	c.C1458T	p.A486A	CTGGGCCGATCTA	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107978343	107978343	+	Missense_Mutation	SNP	C	C	T	rs41307415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	67	97	0	0.582609	0	C|0.950;T|0.050	0.050	strong	.	IRS4	253	.	NM_003604	exon1	c.G1232A	p.R411Q	CTTCCTCGCCTGG	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115002305	115002305	+	Silent	SNP	G	G	A	rs8002514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	63	110	0	0.477273	0	G|0.678;A|0.322	0.322	strong	.	CDC16	50	.	NM_003903	exon3	c.G135A	p.Q45Q	GGCTCAGTGTCTT	.	PASS	Atlas-SNP
WSB2	55884	hgsc.bcm.edu	37	12	118474238	118474238	+	Silent	SNP	G	G	A	rs34253698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	59	140	0	0.44697	0	G|0.985;A|0.015	0.015	strong	.	WSB2	32	.	NM_018639	exon6	c.C738T	p.D246D	GGAGAAGTCACAA	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	846012	846012	+	Silent	SNP	C	C	T	rs114461038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	40	92	0	0.444444	0	C|0.979;T|0.021	0.021	strong	.	CHTF18	52	.	NM_022092	exon18	c.C2391T	p.L797L	GATGCTCGCTTAC	.	PASS	Atlas-SNP
CXorf27	25763	hgsc.bcm.edu	37	X	37850385	37850385	+	Missense_Mutation	SNP	C	C	T	rs61737321	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	105	152	0	0.502392	0	C|0.994;T|0.006	0.006	strong	.	CXorf27	14	.	NM_012274	exon1	c.C293T	p.A98V	ACAGCGCTGAGAG	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	6	13	0	0.26087	0	T|0.651;C|0.349	0.349	strong	.	WDR18	20	.	NM_024100	exon8	c.T945C	p.N315N	CACCAATGCCGCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414629	105414629	+	Missense_Mutation	SNP	G	G	A	rs72702027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	229	234	0	1	0	G|0.479;A|0.521	0.521	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C7159T	p.P2387S	CCTCTGGGAGTTT	.	PASS	Atlas-SNP
CHMP6	79643	hgsc.bcm.edu	37	17	78972902	78972902	+	Silent	SNP	C	C	T	rs35687235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	52	93	0	0.58427	0	C|0.968;T|0.032	0.032	strong	.	CHMP6	16	.	NM_024591	exon8	c.C555T	p.N185N	AGAAAACGTCCCT	.	PASS	Atlas-SNP
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	333	166	312	0	0.498498	0	A|0.827;G|0.173	0.173	strong	.	TBC1D4	142	.	NM_014832	exon21	c.T3824C	p.V1275A	CAATTGACTAGAG	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6480013	6480013	+	Missense_Mutation	SNP	C	C	T	rs10416003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	77	102	0	0.531034	0	C|0.991;T|0.009	0.009	strong	.	DENND1C	93	.	NM_024898	exon2	c.G67A	p.A23T	GGGAGGCAGGGCA	.	PASS	Atlas-SNP
NPY	4852	hgsc.bcm.edu	37	7	24329133	24329133	+	Silent	SNP	C	C	T	rs5574	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	23	47	0	0.433962	0	C|0.579;A|0.002	.	strong	.	NPY	25	.	NM_000905	exon3	c.C204T	p.S68S	ACGATCCAGCCCA	.	PASS	Atlas-SNP
EAF1	85403	hgsc.bcm.edu	37	3	15476011	15476011	+	Silent	SNP	C	C	G	rs1563415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	34	83	0	0.395349	0	C|0.796;G|0.204	0.204	strong	.	EAF1	16	.	NM_033083	exon4	c.C492G	p.P164P	TAACCCCTCACCT	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22940659	22940659	+	Silent	SNP	C	C	T	rs59621958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	53	61	0	1	0	C|0.826;T|0.174	0.174	strong	.	ZNF99	273	.	NM_001080409	exon4	c.G2052A	p.K684K	AAAAGCCTTGCCA	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	75	76	0	1	0	T|0.541;C|0.459	0.459	strong	.	GPATCH1	79	.	NM_018025	exon11	c.T1427C	p.L476P	CCCAGCTCTCCCC	.	PASS	Atlas-SNP
SEC62	7095	hgsc.bcm.edu	37	3	169700525	169700525	+	Silent	SNP	C	C	G	rs35176867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	98	176	0	0.502564	0	C|0.983;G|0.017	0.017	strong	.	SEC62	27	.	NM_003262	exon4	c.C282G	p.A94A	CCGAGCCCTAAAA	.	PASS	Atlas-SNP
PRKCG	5582	hgsc.bcm.edu	37	19	54410114	54410114	+	Missense_Mutation	SNP	A	A	G	rs73937614	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	89	180	0	0.427885	0	A|0.993;G|0.007	0.007	strong	.	PRKCG	246	.	NM_002739	exon18	c.A2059G	p.S687G	GCCCGCAGCCCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505863	195505863	+	Silent	SNP	G	G	A	rs113561118		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	15	198	0	0.050505	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C12588T	p.T4196T	AGTGTCGGTGACA	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179428061	179428061	+	Missense_Mutation	SNP	C	C	T	rs11896637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	115	198	0	0.483193	0	C|0.965;T|0.035	0.035	strong	.	TTN	18412	.	NM_001267550	exon326	c.G82798A	p.A27600T	CAGGTGCGCCACC	.	PASS	Atlas-SNP
KIF26B	55083	hgsc.bcm.edu	37	1	245530282	245530282	+	Silent	SNP	G	G	A	rs61734839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	62	111	0	0.54386	0	G|0.953;A|0.047	0.047	strong	.	KIF26B	343	.	NM_018012	exon3	c.G612A	p.T204T	GCTGACGTTGGAG	.	PASS	Atlas-SNP
EGR4	1961	hgsc.bcm.edu	37	2	73518716	73518716	+	Missense_Mutation	SNP	C	C	T	rs141733943		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	99	146	0	0.5625	0	C|1.000;T|0.000	0.000	weak	.	EGR4	52	.	NM_001965	exon2	c.G1639A	p.G547S	GGCGGCCGCACAC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32041621	32041621	+	Missense_Mutation	SNP	G	G	A	rs6910390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	100	182	0	0.526316	0	G|0.992;A|0.008	0.008	strong	.	TNXB	553	.	NM_019105	exon12	c.C4484T	p.T1495I	GGGACTGTCCAGG	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31729359	31729359	+	Silent	SNP	A	A	G	rs707938	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	58	71	0	0.644444	0	A|0.573;G|0.427	0.427	strong	.	MSH5	108	.	NM_025259	exon22	c.A2202G	p.Q734Q	GCTACAACTGCTG	.	PASS	Atlas-SNP
SPINK1	6690	hgsc.bcm.edu	37	5	147207605	147207605	+	Silent	SNP	G	G	A	rs35737774	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	41	42	0	1	0	G|0.956;A|0.044	0.044	strong	.	SPINK1	9	.	NM_003122	exon3	c.C174T	p.C58C	TAACACGCATTCA	.	PASS	Atlas-SNP
CSNK2A3	283106	hgsc.bcm.edu	37	11	11373631	11373631	+	Missense_Mutation	SNP	C	C	T	rs74507390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	126	0	0.5	0	C|0.965;T|0.035	0.035	strong	.	.	.	.	NM_001256686	exon1	c.G1036A	p.V346I	TGCTGACGGGCGT	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36678816	36678816	+	Silent	SNP	C	C	A	rs80050551	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	26	28	0	0.619048	0	C|0.969;A|0.031	0.031	strong	MYH9,NS,NS,0,1	MYH9	225	1	NM_002473	exon41	c.G5781T	p.P1927P	GACAAACGGCAGG	.	PASS	Atlas-SNP
DCTN4	51164	hgsc.bcm.edu	37	5	150097883	150097883	+	Missense_Mutation	SNP	G	G	C	rs11954652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	115	1	1	0.00869565	G|0.780;C|0.220	0.220	strong	.	DCTN4	35	.	NM_001135643	exon12	c.C1047G	p.F349L	ACACTCGAAGAGA	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993990	45993990	+	Missense_Mutation	SNP	T	T	C	rs79601471	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	530	140	575	0	0.264151	0	T|0.955;C|0.045	0.045	strong	.	KRTAP10-4	44	.	NM_198687	exon1	c.T355C	p.C119R	ACTGTCTGCTGCA	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324516	31324516	+	Missense_Mutation	SNP	C	C	A	rs1131215	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	66	40	40	0.985075	1	C|0.415;A|0.585	0.585	strong	HLA-B,colon,carcinoma,0,1	HLA-B	54	1	NM_005514	exon2	c.G292T	p.D98Y	CTCGGTCAGTCTG	.	scavenged	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116032519	116032519	+	Missense_Mutation	SNP	A	A	G	rs597371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	109	0	0.990291	0	A|0.454;G|0.546	0.546	strong	.	VWA2	64	.	NM_001272046	exon6	c.A392G	p.E131G	AGACGGAACTTGC	.	PASS	Atlas-SNP
OPN4	94233	hgsc.bcm.edu	37	10	88416963	88416963	+	Missense_Mutation	SNP	G	G	A	rs7901458	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	50	105	0	0.442478	0	G|0.949;A|0.051	0.051	strong	OPN4,NS,carcinoma,+1,1	OPN4	61	1	NM_001030015	exon3	c.G302A	p.R101H	TGCTTCGTGGAGT	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3670646	3670646	+	Silent	SNP	C	C	T	rs8115679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	75	178	0	0.421348	0	C|0.974;T|0.026	0.026	strong	.	SIGLEC1	210	.	NM_023068	exon18	c.G4857A	p.L1619L	AGAGCCCAGGACA	.	PASS	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34687817	34687817	+	Missense_Mutation	SNP	T	T	C	rs10521016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	180	150	0	0.994475	0	T|0.955;C|0.045	0.045	strong	.	RAI14	100	.	NM_001145523	exon1	c.T2C	p.M1T	ATTAGATGGAAGC	.	PASS	Atlas-SNP
NTF3	4908	hgsc.bcm.edu	37	12	5603632	5603632	+	Silent	SNP	G	G	A	rs6332	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	19	32	0	0.452381	0	G|0.498;A|0.502	0.502	strong	.	NTF3	50	.	NM_001102654	exon2	c.G291A	p.P97P	CCAGCCGGTGATT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47754449	47754449	+	Missense_Mutation	SNP	G	G	A	rs59183158	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	14	262	2	0.0465116	0.00763359	.	.	weak	PCNT,NS,carcinoma,0,1	PCNT	283	1	NM_006031	exon3	c.G406A	p.G136S	ACAGTCGGTGACC	.	scavenged	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6896483	6896483	+	Missense_Mutation	SNP	G	G	A	rs330877	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	81	168	1	0.50625	0.00595238	G|0.675;A|0.325	0.325	strong	EMR1,NS,carcinoma,-1,1	EMR1	153	1	NM_001256252	exon3	c.G169A	p.A57T	TATTGCGCTTGCA	.	scavenged	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155219373	155219373	+	Silent	SNP	A	A	G	rs17031391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	98	199	0	0.457944	0	A|0.913;G|0.087	0.087	strong	.	DCHS2	594	.	NM_017639	exon18	c.T4728C	p.V1576V	GTCATTAACATCA	.	PASS	Atlas-SNP
OR5B2	390190	hgsc.bcm.edu	37	11	58190228	58190228	+	Silent	SNP	G	G	A	rs77952368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	43	60	0	0.597222	0	G|0.993;A|0.007	0.007	strong	OR5B2,NS,carcinoma,-1,1	OR5B2	75	1	NM_001005566	exon1	c.C507T	p.S169S	CAGATTGGATTTA	.	PASS	Atlas-SNP
IFNA5	3442	hgsc.bcm.edu	37	9	21305048	21305048	+	Missense_Mutation	SNP	G	G	C	rs138121530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	138	332	0	0.479167	0	G|0.984;C|0.016	0.016	strong	.	IFNA5	21	.	NM_002169	exon1	c.C208G	p.Q70E	GGAACTGGTTGCC	.	PASS	Atlas-SNP
OPRM1	4988	hgsc.bcm.edu	37	6	154428666	154428666	+	Nonsense_Mutation	SNP	C	C	T	rs677830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	70	0	0.471429	0	C|0.837;T|0.163	0.163	strong	.	OPRM1	241	.	NM_001145286	exon4	c.C1231T	p.Q411X	GCAGGGCAGTCTC	.	PASS	Atlas-SNP
NUDT8	254552	hgsc.bcm.edu	37	11	67397251	67397251	+	Silent	SNP	G	G	C	rs17851655	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	5	1	0	1	0	G|0.869;C|0.131	0.131	strong	.	NUDT8	12	.	NM_181843	exon1	c.C132G	p.V44V	CGCCGGGACCCCA	.	PASS	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31399988	31399988	+	Missense_Mutation	SNP	C	C	T	rs4592896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	178	164	0	0.994413	0	C|0.689;T|0.311	0.311	strong	.	CAPN14	36	.	NM_001145122	exon20	c.G1876A	p.V626I	GACAGACGTCATC	.	PASS	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51729594	51729594	+	Missense_Mutation	SNP	T	T	C	rs11882250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	94	0	0.518519	0	T|0.958;C|0.042	0.042	strong	.	CD33	55	.	NM_001772	exon4	c.T727C	p.F243L	GGTATCTTTCCAG	.	PASS	Atlas-SNP
PDE3A	5139	hgsc.bcm.edu	37	12	20522487	20522487	+	Missense_Mutation	SNP	A	A	G	rs372953537		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	68	0	0.459459	0	.	.	weak	.	PDE3A	184	.	NM_000921	exon1	c.A269G	p.E90G	ACCTGGAGCAGTG	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26774089	26774089	+	Missense_Mutation	SNP	T	T	G	rs2230373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	139	254	1	0.494662	0.00393701	T|0.944;G|0.056	0.056	strong	.	ITPR2	270	.	NM_002223	exon26	c.A3429C	p.E1143D	TTGACTTTCCCCT	.	PASS	Atlas-SNP
PLA2G4E	123745	hgsc.bcm.edu	37	15	42289456	42289456	+	Missense_Mutation	SNP	G	G	C	rs79040960	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	53	125	0	0.5	0	G|0.982;C|0.018	0.018	strong	.	PLA2G4E	60	.	NM_001206670	exon11	c.C976G	p.P326A	TCTCAGGGCTGGA	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	104	202	0	0.490566	0	C|0.771;T|0.229	0.229	strong	.	FBXO39	50	.	NM_153230	exon3	c.C1086T	p.I362I	CCTCATCATATCC	.	PASS	Atlas-SNP
ZP4	57829	hgsc.bcm.edu	37	1	238049143	238049143	+	Missense_Mutation	SNP	G	G	A	rs34811980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	51	73	0	0.542553	0	G|0.973;A|0.027	0.027	strong	.	ZP4	161	.	NM_021186	exon7	c.C883T	p.P295S	TGATTGGGAGAGA	.	PASS	Atlas-SNP
PHPT1	29085	hgsc.bcm.edu	37	9	139745012	139745012	+	Missense_Mutation	SNP	G	G	T	rs149543778	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	36	50	0	0.590164	0	G|0.996;T|0.004	0.004	strong	.	PHPT1	14	.	NM_001135861	exon3	c.G340T	p.G114C	CATCAAGGTTTGC	.	PASS	Atlas-SNP
PRSS35	167681	hgsc.bcm.edu	37	6	84233325	84233325	+	Silent	SNP	G	G	A	rs147168330	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	84	209	0	0.424242	0	G|0.997;A|0.003	0.003	strong	.	PRSS35	60	.	NM_153362	exon2	c.G165A	p.K55K	TGCTAAGATGATG	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48697713	48697713	+	Missense_Mutation	SNP	C	C	T	rs140292897	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	232	248	0	0.995708	0	C|0.998;T|0.002	0.002	strong	.	SLC5A9	82	.	NM_001135181	exon8	c.C862T	p.R288W	CTCCCACGGCCCG	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	44	122	0	0.392857	0	T|0.988;C|0.012	0.012	strong	.	FER	100	.	NM_005246	exon13	c.T1587C	p.D529D	TATAGATCATCAC	.	PASS	Atlas-SNP
ADAM8	101	hgsc.bcm.edu	37	10	135077265	135077265	+	Missense_Mutation	SNP	A	A	G	rs3008319	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	22	58	0	0.423077	0	A|0.917;G|0.083	0.083	strong	ADAM8,NS,carcinoma,0,1	ADAM8	41	1	NM_001109	exon22	c.T2324C	p.I775T	GGCTTGATGACCT	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31380194	31380194	+	Missense_Mutation	SNP	T	T	C	rs41554412	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	92	0	1	0	T|0.773;C|0.227	0.227	strong	MICA,NS,carcinoma,-2,1	MICA	21	1	NM_001177519	exon5	c.T985C	p.C329R	TTTCTATGTCCGT	.	PASS	Atlas-SNP
MYH15	22989	hgsc.bcm.edu	37	3	108147543	108147543	+	Silent	SNP	C	C	A	rs61745179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	125	197	0	0.538793	0	C|0.934;A|0.066	0.066	strong	.	MYH15	223	.	NM_014981	exon28	c.G3558T	p.L1186L	TCGGTGCAGCTTC	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106815517	106815517	+	Silent	SNP	C	C	T	rs11995760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	56	122	0	0.414815	0	C|0.884;T|0.116	0.116	strong	.	ZFPM2	219	.	NM_012082	exon8	c.C3207T	p.H1069H	TCAGCACGAAGAC	.	PASS	Atlas-SNP
ARFGEF1	10565	hgsc.bcm.edu	37	8	68178397	68178397	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	4	296	0	0.0132013	0	.	.	none	ARFGEF1,NS,carcinoma,0,1	ARFGEF1	196	1	NM_006421	exon14	c.C1967T	p.P656L	GTCTCAGGGTGTT	.	scavenged	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156641537	156641537	+	Missense_Mutation	SNP	C	C	T	rs951781	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	94	181	1	0.497355	0.00552486	C|0.783;T|0.217	0.217	strong	NES,NS,carcinoma,0,1	NES	196	1	NM_006617	exon4	c.G2443A	p.V815I	CCTCTACGCTCTC	.	scavenged	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160737717	160737717	+	Silent	SNP	G	G	A	rs79199281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	23	88	0	0.258427	0	G|0.994;A|0.006	0.006	strong	.	LY75	151	.	NM_002349	exon8	c.C1281T	p.N427N	GTTTATGTTCTTA	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102751276	102751276	+	Silent	SNP	C	C	T	rs10516486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	25	64	0	0.367647	0	C|0.514;T|0.486	0.486	strong	.	BANK1	95	.	NM_017935	exon2	c.C382T	p.L128L	GAATTACTAAATA	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11164	11164	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	15	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.A405G	p.R135R	CACCCGATGAGGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	5	95	0	0.037037	0	.	.	none	MUC17,NS,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.G4291A	p.A1431T	ACTTCTGCTGAAG	.	scavenged	Atlas-SNP
CACNA2D3	55799	hgsc.bcm.edu	37	3	55108149	55108149	+	Silent	SNP	A	A	G	rs17054785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	56	126	0	0.491228	0	A|0.895;G|0.105	0.105	strong	.	CACNA2D3	159	.	NM_018398	exon38	c.A3192G	p.A1064A	GAATGCAAGGGAG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	52	134	0	0.356164	0	C|0.746;G|0.254	0.254	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon31	c.G14716C	p.D4906H	GGAGATCTCCAGC	.	PASS	Atlas-SNP
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	155	116	0	0.99359	0	C|0.399;A|0.601	0.601	strong	.	ZNF512	54	.	NM_032434	exon11	c.C1155A	p.L385L	AGGGCTCCCTACC	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7246994	7246994	+	Silent	SNP	C	C	T	rs187908583	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	10	14	0	0.625	0	C|0.993;T|0.007	0.007	strong	.	RREB1	242	.	NM_001003699	exon12	c.C4311T	p.G1437G	GGCAGGCGCCGGG	.	PASS	Atlas-SNP
LRRIQ3	127255	hgsc.bcm.edu	37	1	74575141	74575141	+	Silent	SNP	G	G	A	rs182798407	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	59	98	0	0.491667	0	G|0.997;A|0.003	0.003	strong	LRRIQ3,right_upper_lobe,carcinoma,-1,1	LRRIQ3	146	1	NM_001105659	exon5	c.C804T	p.L268L	CTTAAGGAGCTTA	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38592406	38592406	+	Silent	SNP	A	A	G	rs1805126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	48	73	0	0.539326	0	A|0.498;G|0.502	0.502	strong	.	SCN5A	634	.	NM_198056	exon28	c.T5457C	p.D1819D	CAGGGCATCGGCA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911086	29911086	+	Missense_Mutation	SNP	T	T	C	rs1136700	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	44	79	0	0.619718	0	C|0.299;T|0.701	0.299	strong	HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	NM_001242758	exon3	c.T385C	p.S129P	GTGGGGTCGGACG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107336	55107336	+	Silent	SNP	C	C	T	rs34058364	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	172	273	0	0.92973	0	C|0.851;T|0.149	0.149	strong	.	LILRA1	105	.	NM_006863	exon6	c.C894T	p.S298S	ATGCTCCGGTGCA	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77415284	77415284	+	Silent	SNP	A	A	C	rs7859201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	81	116	0	0.637795	0	A|0.532;C|0.468	0.468	strong	.	TRPM6	377	.	NM_017662	exon17	c.T2124G	p.L708L	CAGTTTAAGGCAG	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16248791	16248791	+	Missense_Mutation	SNP	C	C	T	rs57695665	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	58	115	0	0.537037	0	C|0.994;T|0.006	0.006	strong	.	ABCC6	110	.	NM_001171	exon28	c.G3980A	p.G1327E	GGGACCCCGTCGA	.	PASS	Atlas-SNP
RBBP4	5928	hgsc.bcm.edu	37	1	33134865	33134865	+	Silent	SNP	A	A	C	rs11551266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	94	236	1	0.437209	0.00423729	A|0.925;C|0.075	0.075	strong	.	RBBP4	38	.	NM_005610	exon7	c.A795C	p.P265P	CAAACCAAGCCAC	.	PASS	Atlas-SNP
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	52	104	0	0.472727	0	C|0.785;G|0.000;T|0.215	0.215	strong	.	NMT1	31	.	NM_021079	exon4	c.C487T	p.L163L	TTGGACCTGGGCG	.	PASS	Atlas-SNP
PSG9	5678	hgsc.bcm.edu	37	19	43773532	43773532	+	Missense_Mutation	SNP	G	G	C	rs8101191	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	24	54	0	0.358209	0	G|0.866;C|0.134	0.134	strong	.	PSG9	77	.	NM_002784	exon1	c.C52G	p.L18V	GCAGGAGCCCCTT	.	PASS	Atlas-SNP
MAST1	22983	hgsc.bcm.edu	37	19	12978556	12978556	+	Silent	SNP	C	C	G	rs202159363	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	33	61	0	0.532258	0	C|0.995;G|0.005	0.005	strong	.	MAST1	214	.	NM_014975	exon20	c.C2331G	p.S777S	ATTCTCCGCGTCC	.	PASS	Atlas-SNP
PNPLA3	80339	hgsc.bcm.edu	37	22	44322922	44322922	+	Missense_Mutation	SNP	T	T	G	rs2076213	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	84	137	0	0.56	0	T|0.924;G|0.076;C|0.000	0.076	strong	.	PNPLA3	53	.	NM_025225	exon2	c.T295G	p.C99G	GGTCTCTGCAAAT	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152527608	152527608	+	Missense_Mutation	SNP	C	C	T	rs34577613	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	253	250	0	0.992157	0	C|0.705;T|0.295	0.295	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_004543	exon38	c.G4435A	p.V1479I	ACTTGACGGTATC	.	PASS	Atlas-SNP
NEDD9	4739	hgsc.bcm.edu	37	6	11190859	11190859	+	Missense_Mutation	SNP	G	G	A	rs61755989	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	51	95	0	0.485714	0	G|0.981;A|0.019	0.019	strong	.	NEDD9	191	.	NM_001142393	exon6	c.C1243T	p.R415W	GGAGCCGCTGAAG	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175105996	175105996	+	Missense_Mutation	SNP	C	C	T	rs2072036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	31	79	0	0.430556	0	C|0.889;T|0.111	0.111	strong	TNN,bladder,carcinoma,-1,1	TNN	297	1	NM_022093	exon17	c.C3467T	p.A1156V	CTCCAGCGCGGTA	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	1004554	1004554	+	Silent	SNP	C	C	T	rs3751667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	47	75	0	0.474747	0	C|0.674;T|0.326	0.326	strong	LMF1,NS,carcinoma,-1,3	LMF1	42	3	NM_022773	exon2	c.G306A	p.T102T	CCAGCTCGTCCTG	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133815981	133815981	+	Silent	SNP	C	C	G	rs10894768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	59	176	0	0.40411	0	C|0.633;G|0.367	0.367	strong	.	IGSF9B	290	.	NM_014987	exon2	c.G237C	p.P79P	GTGCGGCGGGTAG	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786888	75786888	+	Missense_Mutation	SNP	C	C	T	rs1615736	bycluster;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	54	50	0	0.465517	0	C|0.618;T|0.382	0.382	strong	.	ZNF717	160	.	NM_001128223	exon5	c.G1886A	p.R629H	TTCTGACGAAAGG	.	PASS	Atlas-SNP
KCNK18	338567	hgsc.bcm.edu	37	10	118969353	118969353	+	Missense_Mutation	SNP	C	C	T	rs363360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	56	110	1	0.466667	0.00909091	A|0.000;C|0.963;T|0.037	0.037	strong	KCNK18,colon,carcinoma,0,1	KCNK18	70	1	NM_181840	exon3	c.C698T	p.A233V	CTCATGCGCTAGA	.	scavenged	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9334571	9334571	+	Silent	SNP	C	C	T	rs3741849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	76	102	0	0.567164	0	C|0.886;T|0.114	0.114	strong	PZP_ENST00000381997,colon,carcinoma,-1,2	PZP	422	2	NM_002864	exon14	c.G1689A	p.K563K	GCTCACCTTGTTG	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77413223	77413223	+	Missense_Mutation	SNP	T	T	C	rs78433827	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	162	256	1	0.5625	0.00390625	T|0.992;C|0.008	0.008	strong	RSF1,caecum,carcinoma,+2,1	RSF1	105	1	NM_016578	exon6	c.A1051G	p.I351V	ATTCGATCCTTTC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74287389	74287389	+	Missense_Mutation	SNP	T	T	C	rs2279053	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	74	110	0	0.587302	0	T|0.545;C|0.455	0.455	strong	.	QRICH2	143	.	NM_032134	exon4	c.A2921G	p.H974R	ATTCCATGTCGGT	.	PASS	Atlas-SNP
FAM86C1	55199	hgsc.bcm.edu	37	11	71507186	71507186	+	Missense_Mutation	SNP	T	T	C	rs74830167	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	22	238	2	0.0745763	0.00840336	T|0.940;C|0.060	0.060	strong	FAM86C1_ENST00000426628,brain,glioma,0,3	FAM86C1	27	3	NM_018172	exon4	c.T385C	p.C129R	CAGAGATGTGCCA	.	scavenged	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	37	6	145051594	145051594	+	Silent	SNP	G	G	A	rs4305737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	6	42	0	0.171429	0	G|0.490;A|0.510	0.510	strong	.	UTRN	327	.	NM_007124	exon53	c.G7911A	p.E2637E	TGAAGAGCCAAGA	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31768491	31768491	+	Silent	SNP	G	G	A	rs139947200	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	27	63	0	0.409091	0	G|0.999;A|0.001	0.001	strong	.	TSHZ3	549	.	NM_020856	exon2	c.C2208T	p.A736A	CTTGGCGGCCTTG	.	PASS	Atlas-SNP
SWAP70	23075	hgsc.bcm.edu	37	11	9769483	9769483	+	Silent	SNP	C	C	T	rs34696762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	61	101	0	0.469231	0	C|0.889;T|0.111	0.111	strong	.	SWAP70	40	.	NM_015055	exon10	c.C1434T	p.T478T	GACAACCGAGGCG	.	PASS	Atlas-SNP
CSF2RA	1438	hgsc.bcm.edu	37	X	1401646	1401646	+	Missense_Mutation	SNP	C	C	G	rs67006588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	593	281	589	0	0.473862	0	C|0.794;G|0.206	0.206	strong	.	CSF2RA	153	.	NM_172247	exon1	c.C50G	p.A17G	ACCCAGCATTCCT	.	PASS	Atlas-SNP
FBXO44	93611	hgsc.bcm.edu	37	1	11721321	11721321	+	Missense_Mutation	SNP	G	G	A	rs12057383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	66	128	0	0.468085	0	G|0.924;A|0.076	0.076	strong	.	FBXO44	20	.	NM_183412	exon5	c.G634A	p.A212T	GCCCCCGCTGCCC	.	PASS	Atlas-SNP
CCDC17	149483	hgsc.bcm.edu	37	1	46086588	46086588	+	Missense_Mutation	SNP	T	T	C	rs16832629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	57	128	0	0.407143	0	T|0.993;C|0.007	0.007	strong	.	CCDC17	54	.	NM_001114938	exon11	c.A1586G	p.N529S	ATCCCATTCAGCT	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33755763	33755763	+	Silent	SNP	G	G	A	rs2833795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	86	0	1	0	G|0.471;A|0.529	0.529	strong	URB1_ENST00000382751,NS,carcinoma,0,2	URB1	176	2	NM_014825	exon4	c.C535T	p.L179L	TGTACAGGGTCTT	.	PASS	Atlas-SNP
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	96	0	0.526882	0	C|0.955;G|0.045	0.045	strong	.	ENOX1	158	.	NM_017993	exon4	c.G48C	p.E16D	AGGAAGCTCCTGG	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13671402	13671402	+	Silent	SNP	C	C	T	rs41283999	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	78	164	0	0.47561	0	C|0.965;T|0.035	0.035	strong	.	FBLN2	137	.	NM_001004019	exon14	c.C2925T	p.C975C	TTCCTGCGCCTCC	.	PASS	Atlas-SNP
STAG3	10734	hgsc.bcm.edu	37	7	99796146	99796146	+	Silent	SNP	A	A	C	rs3735241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	410	207	347	0	0.504878	0	C|0.482;N|0.000	0.482	strong	.	STAG3	121	.	NM_012447	exon13	c.A1293C	p.P431P	CTACCCAGTTGTG	.	PASS	Atlas-SNP
CGN	57530	hgsc.bcm.edu	37	1	151493098	151493098	+	Silent	SNP	C	C	T	rs141884525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	101	192	0	0.515306	0	C|0.997;T|0.003	0.003	strong	.	CGN	106	.	NM_020770	exon5	c.C1071T	p.A357A	TAAGGCCGTGGCA	.	PASS	Atlas-SNP
UNC5A	90249	hgsc.bcm.edu	37	5	176305523	176305523	+	Silent	SNP	C	C	T	rs146460064	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	116	223	1	0.522523	0.00448431	C|0.996;T|0.004	0.004	strong	.	UNC5A	76	.	NM_133369	exon13	c.C2067T	p.H689H	CTTGCACTGCACC	.	PASS	Atlas-SNP
SPATA4	132851	hgsc.bcm.edu	37	4	177113956	177113956	+	Silent	SNP	A	A	G	rs2291244	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	30	60	0	0.46875	0	A|0.801;G|0.199	0.199	strong	.	SPATA4	44	.	NM_144644	exon4	c.T510C	p.Y170Y	GTAGCTATAGTCC	.	PASS	Atlas-SNP
IFT80	57560	hgsc.bcm.edu	37	3	159997061	159997061	+	Missense_Mutation	SNP	T	T	A	rs6778728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	75	182	0	0.416667	0	T|0.699;A|0.301	0.301	strong	.	IFT80	68	.	NM_020800	exon16	c.A1756T	p.T586S	ATGGTGTTATGCT	.	PASS	Atlas-SNP
CCDC84	338657	hgsc.bcm.edu	37	11	118886117	118886117	+	Silent	SNP	C	C	T	rs10111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	55	170	0	0.429688	0	C|0.763;T|0.237	0.237	strong	.	CCDC84	21	.	NM_198489	exon10	c.C906T	p.R302R	TGGCCGCGTCTGG	.	PASS	Atlas-SNP
COPE	11316	hgsc.bcm.edu	37	19	19017862	19017862	+	Missense_Mutation	SNP	G	G	A	rs10330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	59	97	0	0.561905	0	G|0.804;A|0.196	0.196	strong	.	COPE	26	.	NM_007263	exon4	c.C350T	p.T117I	AAGGTGGTGTTGG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50532155	50532155	+	Missense_Mutation	SNP	T	T	G	rs61453891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	45	82	0	0.511364	0	T|0.977;G|0.023	0.023	strong	.	C10orf71	179	.	NM_001135196	exon3	c.T1565G	p.V522G	TGAAAGTGCTTGA	.	PASS	Atlas-SNP
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	69	0	1	0	G|0.579;A|0.421	0.421	strong	.	KCNMA1	370	.	NM_001161352	exon4	c.C687T	p.F229F	CAAGCCGAAGTAG	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32822957	32822957	+	Silent	SNP	G	G	A	rs2710625	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	25	71	0	0.373134	0	G|0.624;A|0.376	0.376	strong	BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	2	NM_016252	exon69	c.G13752A	p.T4584T	TGTGACGCTTTCA	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43970658	43970658	+	Missense_Mutation	SNP	T	T	A	rs115402675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	15	33	0	0.405405	0	T|0.955;A|0.045	0.045	strong	C6orf223,NS,carcinoma,0,1	C6orf223	14	1	NM_153246	exon4	c.T524A	p.L175H	CCCTTCTTCGCGG	.	PASS	Atlas-SNP
ZNF229	7772	hgsc.bcm.edu	37	19	44934653	44934653	+	Silent	SNP	T	T	C	rs8113370	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	61	103	0	0.476562	0	T|0.846;C|0.154	0.154	strong	.	ZNF229	123	.	NM_014518	exon6	c.A303G	p.K101K	GAGCTCTTTGTGT	.	PASS	Atlas-SNP
SLC22A14	9389	hgsc.bcm.edu	37	3	38347633	38347633	+	Missense_Mutation	SNP	G	G	A	rs34043027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	87	193	0	0.508772	0	G|0.933;A|0.067	0.067	strong	SLC22A14,NS,lymphoid_neoplasm,+1,1	SLC22A14	64	1	NM_004803	exon1	c.G116A	p.R39H	TGTTACGCAGATT	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632744	32632744	+	Silent	SNP	C	C	T	rs1049082	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	20	41	0	1	0	C|0.668;T|0.332	0.332	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G210A	p.A70A	GAAGCGCGCGTAC	.	PASS	Atlas-SNP
HIST3H3	8290	hgsc.bcm.edu	37	1	228612934	228612934	+	Silent	SNP	A	A	G	rs61740979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	24	93	0	0.375	0	A|0.981;G|0.019	0.019	strong	.	HIST3H3	20	.	NM_003493	exon1	c.T93C	p.P31P	AGTGGCAGGTGCG	.	PASS	Atlas-SNP
UPK1A	11045	hgsc.bcm.edu	37	19	36168914	36168914	+	Missense_Mutation	SNP	T	T	C	rs2285421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	71	0	1	0	T|0.391;C|0.609	0.609	strong	.	UPK1A	23	.	NM_007000	exon7	c.T770C	p.M257T	ACACCATGCTCTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228494696	228494696	+	Silent	SNP	G	G	A	rs4653939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	269	240	0	1	0	G|0.667;A|0.333	0.333	strong	.	OBSCN	2142	.	NM_001271223	exon56	c.G14892A	p.A4964A	GGGTGCGAGCGTG	.	PASS	Atlas-SNP
SECTM1	6398	hgsc.bcm.edu	37	17	80280054	80280054	+	Missense_Mutation	SNP	A	A	C	rs61738919	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	44	87	0	0.52381	0	A|0.935;C|0.065	0.065	strong	.	SECTM1	14	.	NM_003004	exon5	c.T730G	p.Y244D	CGGCATATGGAAA	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30795146	30795146	+	Silent	SNP	C	C	T	rs6966180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	23	33	0	0.45098	0	C|0.962;T|0.038	0.038	strong	.	INMT	38	.	NM_006774	exon3	c.C471T	p.A157A	TCTCGCCGACTGT	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	55999879	55999879	+	Silent	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	94	197	1	0.429224	0.00507614	.	.	none	OR5T2,NS,carcinoma,0,1	OR5T2	107	1	NM_001004746	exon1	c.G783T	p.L261L	GGCCAACAGAATC	.	scavenged	Atlas-SNP
LMTK3	114783	hgsc.bcm.edu	37	19	49001600	49001600	+	Missense_Mutation	SNP	A	A	G	rs61745738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	87	0	1	0	A|0.922;G|0.078	0.078	strong	.	LMTK3	125	.	NM_001080434	exon12	c.T2813C	p.V938A	CCCAGGACTGTCG	.	PASS	Atlas-SNP
GRHL1	29841	hgsc.bcm.edu	37	2	10101289	10101289	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	80	177	0	0.441989	0	.	.	none	.	GRHL1	95	.	NM_198182	exon4	c.C393T	p.G131G	GCTGGGCATTGAT	.	PASS	Atlas-SNP
MYO19	80179	hgsc.bcm.edu	37	17	34856697	34856697	+	Missense_Mutation	SNP	A	A	G	rs56919948	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	26	73	0	0.361111	0	A|0.996;G|0.004	0.004	strong	.	MYO19	130	.	NM_001163735	exon24	c.T2350C	p.W784R	CCCGCCACTGCCG	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33588874	33588874	+	Silent	SNP	G	G	A	rs76931580	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	198	0	0.442708	0	G|0.996;A|0.004	0.004	strong	.	MYH7B	145	.	NM_020884	exon41	c.G5514A	p.T1838T	GCAGACGGTGCGC	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38592356	38592356	+	Missense_Mutation	SNP	A	A	G	rs45563942	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	37	72	0	0.513889	0	A|0.999;G|0.001	0.001	strong	.	SCN5A	634	.	NM_198056	exon28	c.T5507C	p.I1836T	ATGTTGATGAGGC	.	PASS	Atlas-SNP
GALM	130589	hgsc.bcm.edu	37	2	38916970	38916970	+	Missense_Mutation	SNP	A	A	T	rs6741892	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	175	0	1	0	A|0.849;T|0.151	0.151	strong	.	GALM	20	.	NM_138801	exon4	c.A568T	p.N190Y	AATATAAATGACC	.	PASS	Atlas-SNP
EIF2B3	8891	hgsc.bcm.edu	37	1	45444038	45444038	+	Silent	SNP	G	G	A	rs11556200	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	63	113	0	0.504	0	G|0.714;A|0.286	0.286	strong	.	EIF2B3	43	.	NM_020365	exon3	c.C243T	p.D81D	GTCAGCGTCATCA	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34831866	34831866	+	Silent	SNP	G	G	A	rs3734264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	49	130	0	0.382812	0	G|0.537;A|0.463	0.463	strong	.	UHRF1BP1	102	.	NM_017754	exon15	c.G3303A	p.T1101T	GAGGACGGTATCT	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113285272	113285272	+	Silent	SNP	A	A	C	rs61734094	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	72	133	0	0.517986	0	A|0.978;C|0.022	0.022	strong	.	SIDT1	99	.	NM_017699	exon2	c.A228C	p.T76T	GGTGACAGCCGTG	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855647	12855647	+	Silent	SNP	C	C	T	rs200536957		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	39	376	61	0.0915493	0.162234	C|0.999;T|0.001	0.001	weak	PRAMEF1,NS,carcinoma,+2,2	PRAMEF1	78	2	NM_023013	exon4	c.C927T	p.D309D	AGAAGACATGAAG	.	scavenged	Atlas-SNP
MNS1	55329	hgsc.bcm.edu	37	15	56735674	56735674	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	2	106	0	0.0185185	0	.	.	none	MNS1,colon,carcinoma,-1,1	MNS1	39	1	NM_018365	exon7	c.A965G	p.E322G	TATAATTCTTGTC	.	scavenged	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	37	18	77473127	77473127	+	Missense_Mutation	SNP	C	C	T	rs2279103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	65	134	0	0.590909	0	C|0.885;T|0.115	0.115	strong	.	CTDP1	67	.	NM_004715	exon7	c.C1019T	p.T340M	CTCAGACGAGAAA	.	PASS	Atlas-SNP
C15orf43	145645	hgsc.bcm.edu	37	15	45253735	45253735	+	Missense_Mutation	SNP	A	A	T	rs77033860	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	10	193	0	0.0543478	0	A|0.989;T|0.011	0.011	strong	C15orf43,NS,haematopoietic_neoplasm,0,2	C15orf43	19	2	NM_152448	exon4	c.A301T	p.I101F	AGAAAAATTGGTA	.	scavenged	Atlas-SNP
FURIN	5045	hgsc.bcm.edu	37	15	91419098	91419098	+	Missense_Mutation	SNP	C	C	T	rs16944971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	59	0	1	0	C|0.968;T|0.032	0.032	strong	.	FURIN	85	.	NM_002569	exon2	c.C128T	p.A43V	GCCCAGCGGTGGC	.	PASS	Atlas-SNP
VPS54	51542	hgsc.bcm.edu	37	2	64189566	64189566	+	Silent	SNP	A	A	G	rs17028275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	69	0	1	0	A|0.893;G|0.107	0.107	strong	.	VPS54	57	.	NM_016516	exon7	c.T636C	p.Y212Y	ATCCAGATAATGG	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104089586	104089586	+	Silent	SNP	C	C	T	rs17034395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	52	142	0	0.422764	0	C|0.930;T|0.070	0.070	strong	.	STAB2	370	.	NM_017564	exon33	c.C3546T	p.I1182I	TGCCATCGAGAAT	.	PASS	Atlas-SNP
MAPK13	5603	hgsc.bcm.edu	37	6	36104468	36104468	+	Silent	SNP	C	C	G	rs115013068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	98	169	0	0.524064	0	C|0.990;G|0.010	0.010	strong	.	MAPK13	65	.	NM_002754	exon7	c.C531G	p.A177A	AGACGCCGAGATG	.	PASS	Atlas-SNP
USP8	9101	hgsc.bcm.edu	37	15	50776525	50776525	+	Silent	SNP	T	T	C	rs10220843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	81	0	0.441176	0	T|0.906;C|0.094	0.094	strong	.	USP8	90	.	NM_001128610	exon12	c.T1857C	p.F619F	AACTTTTAGAGAG	.	PASS	Atlas-SNP
DEFB136	613210	hgsc.bcm.edu	37	8	11831557	11831557	+	Silent	SNP	G	G	A	rs73538682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	173	1	1	0.00578035	G|0.980;A|0.020	0.020	strong	.	DEFB136	16	.	NM_001033018	exon2	c.C126T	p.F42F	ACACCCGAAGAAA	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132020983	132020983	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	694	85	573	1	0.122478	0.0017452	.	.	none	ENSG00000188219,NS,carcinoma,+1,1	.	.	1	NM_001083538	exon15	c.G1955A	p.R652Q	CGTTGCGGGAAGA	.	scavenged	Atlas-SNP
HSD17B4	3295	hgsc.bcm.edu	37	5	118860938	118860938	+	Missense_Mutation	SNP	T	T	C	rs11539471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	42	83	0	0.518519	0	T|0.864;C|0.136	0.136	strong	.	HSD17B4	63	.	NM_001199291	exon19	c.T1606C	p.W536R	GGAGACTGGAATC	.	PASS	Atlas-SNP
PTPRE	5791	hgsc.bcm.edu	37	10	129866449	129866449	+	Silent	SNP	C	C	G	rs7100666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	37	75	0	0.552239	0	C|0.880;G|0.120	0.120	strong	PTPRE_ENST00000306042,NS,carcinoma,0,4	PTPRE	132	4	NM_006504	exon12	c.C906G	p.P302P	CTGGCCCGACTTC	.	PASS	Atlas-SNP
EMX2	2018	hgsc.bcm.edu	37	10	119305282	119305282	+	Silent	SNP	C	C	A	rs424112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	95	159	0	0.533708	0	C|0.962;A|0.038	0.038	strong	.	EMX2	25	.	NM_004098	exon2	c.C546A	p.A182A	GGGCGCCGAAAGG	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70406747	70406747	+	Missense_Mutation	SNP	A	A	G	rs144156611	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	54	140	0	0.425197	0	A|0.995;G|0.005	0.005	strong	.	TET1	255	.	NM_030625	exon4	c.A4261G	p.T1421A	CTGCCCACCTGCA	.	PASS	Atlas-SNP
PHYH	5264	hgsc.bcm.edu	37	10	13330402	13330402	+	Silent	SNP	T	T	C	rs473407	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	33	85	0	0.464789	0	T|0.728;C|0.272	0.272	strong	.	PHYH	50	.	NM_006214	exon6	c.A636G	p.T212T	CTTGTGTGTGCCT	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464437	39464437	+	Missense_Mutation	SNP	G	G	C	rs72828116	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	103	0	0.509804	0	G|0.900;C|0.100	0.100	strong	KRTAP16-1,NS,carcinoma,0,1	KRTAP16-1	12	1	NM_001146182	exon1	c.C1069G	p.L357V	AGGAAAGAGGTCG	.	PASS	Atlas-SNP
ISY1	57461	hgsc.bcm.edu	37	3	128853738	128853738	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	4	162	0	0.0204082	0	.	.	none	ISY1,NS,carcinoma,+1,1	ISY1	36	1	NM_001199469	exon9	c.T544C	p.Y182H	AACCATAGTACTC	.	scavenged	Atlas-SNP
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661691	31661691	+	Missense_Mutation	SNP	A	A	G	rs8127420	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	99	227	0	0.402439	0	A|0.520;G|0.480	0.480	strong	.	KRTAP25-1	13	.	NM_001128598	exon1	c.T118C	p.S40P	TCCTGGACACAAA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	501	97	507	1	0.193613	0.00197239	T|0.993;C|0.007	0.007	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.A10703G	p.Q3568R	TGCTCCTGAGCAG	.	scavenged	Atlas-SNP
SERPINB2	5055	hgsc.bcm.edu	37	18	61565014	61565014	+	Silent	SNP	C	C	T	rs6106	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	106	212	0	0.495327	0	C|0.933;T|0.067	0.067	strong	.	SERPINB2	63	.	NM_002575	exon5	c.C471T	p.D157D	AGTAGACTTCCTA	.	PASS	Atlas-SNP
KNTC1	9735	hgsc.bcm.edu	37	12	123030788	123030788	+	Missense_Mutation	SNP	G	G	T	rs7968222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	63	130	0	0.443662	0	G|0.867;T|0.133	0.133	strong	.	KNTC1	182	.	NM_014708	exon9	c.G735T	p.K245N	AGTTAAGAACCTT	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48058071	48058071	+	Missense_Mutation	SNP	G	G	A	rs532598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	52	124	0	0.412698	0	G|0.549;N|0.000	.	strong	.	SEMA6D	322	.	NM_153617	exon14	c.G1433A	p.S478N	GGTGCAGTGCTGA	.	PASS	Atlas-SNP
ERCC4	2072	hgsc.bcm.edu	37	16	14038659	14038659	+	Missense_Mutation	SNP	T	T	C	rs2020955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	61	168	0	0.458647	0	T|0.934;C|0.066	0.066	strong	.	ERCC4	100	.	NM_005236	exon10	c.T1984C	p.S662P	ACAGCATCTGCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507060	195507060	+	Missense_Mutation	SNP	G	G	T	rs202129071	byfrequency;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	15	159	0	0.0955414	0	G|0.956;A|0.044	.	alt	MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.C11391A	p.D3797E	GGAAGTGTCGGTG	.	scavenged	Atlas-SNP
CATSPER3	347732	hgsc.bcm.edu	37	5	134343766	134343766	+	Missense_Mutation	SNP	T	T	G	rs3896260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	145	249	0	0.478548	0	T|0.860;G|0.140	0.140	strong	.	CATSPER3	38	.	NM_178019	exon4	c.T612G	p.N204K	AGACAATGGTGAC	.	PASS	Atlas-SNP
ZNF618	114991	hgsc.bcm.edu	37	9	116810204	116810204	+	Silent	SNP	G	G	A	rs12378906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	57	121	0	0.471074	0	G|0.927;A|0.073	0.073	strong	.	ZNF618	184	.	NM_133374	exon13	c.G999A	p.Q333Q	CAACCAGTCCCGA	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88396213	88396213	+	Silent	SNP	G	G	A	rs13403507	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	58	156	0	0.504348	0	G|0.992;A|0.008	0.008	strong	.	SMYD1	95	.	NM_198274	exon6	c.G798A	p.L266L	GCAGCTGAAGAAG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	57	0	1	0	C|0.493;T|0.507	0.507	strong	.	ZNF804B	322	.	NM_181646	exon4	c.C1704T	p.F568F	TACTTTCAGTGCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677944	100677944	+	Missense_Mutation	SNP	T	T	C	rs10264727	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	203	137	0	0.590116	0	T|0.902;C|0.098	0.098	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3247C	p.S1083P	TCATCTTCTACAA	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47261017	47261017	+	Silent	SNP	T	T	C	rs6066802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	78	0	1	0	T|0.728;C|0.272	0.272	strong	PREX1,NS,carcinoma,0,1	PREX1	441	1	NM_020820	exon27	c.A3531G	p.R1177R	CGAGTCTCGATTG	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130762324	130762324	+	Silent	SNP	A	A	G	rs35085916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	67	102	0	0.603604	0	A|0.981;G|0.019	0.019	strong	.	GSDMC	71	.	NM_031415	exon12	c.T1125C	p.G375G	GATGGCACCACCA	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124731689	124731689	+	Missense_Mutation	SNP	T	T	A	rs78680419	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	157	283	0	0.493711	0	T|0.772;A|0.228	0.228	strong	.	HEG1	109	.	NM_020733	exon6	c.A2734T	p.T912S	ATCCAGTGGTAGC	.	PASS	Atlas-SNP
CDK12	51755	hgsc.bcm.edu	37	17	37619038	37619038	+	Silent	SNP	G	G	A	rs35896550	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	29	45	0	0.508772	0	G|0.933;A|0.067	0.067	strong	CDK12,NS,carcinoma,+1,1	CDK12	161	1	NM_016507	exon1	c.G714A	p.S238S	CCCCTCGGGAGCT	.	PASS	Atlas-SNP
ETV7	51513	hgsc.bcm.edu	37	6	36341251	36341251	+	Missense_Mutation	SNP	G	G	A	rs9470262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	63	130	0	0.443662	0	G|0.988;A|0.012	0.012	strong	.	ETV7	31	.	NM_001207035	exon4	c.C412T	p.H138Y	GAGAGTGCTGGGT	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	134	329	0	0.455782	0	C|0.867;T|0.133	0.133	strong	.	XRN1	138	.	NM_001042604	exon16	c.G1791A	p.E597E	TAGGCACTCACTA	.	PASS	Atlas-SNP
PIWIL3	440822	hgsc.bcm.edu	37	22	25119210	25119210	+	Silent	SNP	A	A	C	rs56199175	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	14	32	0	0.451613	0	A|0.945;C|0.055	0.055	strong	.	PIWIL3	115	.	NM_001008496	exon19	c.T2271G	p.A757A	AATGAAAGCTAGA	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	37	9	20764870	20764870	+	Missense_Mutation	SNP	T	T	C	rs10511687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	136	0	0.441176	0	T|0.745;C|0.255	0.255	strong	.	.	.	.	NM_017794	exon9	c.T497C	p.L166S	ATAGGTTAGAAGT	.	PASS	Atlas-SNP
LRP6	4040	hgsc.bcm.edu	37	12	12336966	12336966	+	Silent	SNP	A	A	G	rs7978064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	76	159	0	0.567164	0	A|0.850;G|0.150	0.150	strong	.	LRP6	170	.	NM_002336	exon5	c.T924C	p.C308C	GCAAGCACACTGA	.	PASS	Atlas-SNP
AMOTL1	154810	hgsc.bcm.edu	37	11	94533373	94533373	+	Silent	SNP	C	C	T	rs2303960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	59	0	0.542857	0	C|0.744;T|0.256	0.256	strong	AMOTL1,colon,carcinoma,+2,1	AMOTL1	95	1	NM_130847	exon3	c.C1017T	p.P339P	GCACCCCGGGATG	.	PASS	Atlas-SNP
SEMA6C	10500	hgsc.bcm.edu	37	1	151107277	151107277	+	Missense_Mutation	SNP	C	C	T	rs149398166	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	107	178	0	0.519417	0	C|0.995;T|0.005	0.005	strong	.	SEMA6C	70	.	NM_001178061	exon16	c.G1655A	p.G552D	TACCCACCAGATC	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61906397	61906397	+	Missense_Mutation	SNP	A	A	G	rs138049815	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	68	64	0	0.548387	0	A|0.996;G|0.004	0.004	strong	.	INCENP	122	.	NM_001040694	exon7	c.A1211G	p.N404S	CCCACAATGACAC	.	PASS	Atlas-SNP
ICT1	3396	hgsc.bcm.edu	37	17	73008804	73008804	+	Missense_Mutation	SNP	G	G	T	rs3744206	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	14	9	0	0.823529	0	C|0.010;G|0.987;T|0.003	0.003	strong	ICT1,NS,carcinoma,0,1	ICT1	17	1	NM_001545	exon1	c.G23T	p.R8L	GCCTGCGCTGGGG	.	PASS	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46401243	46401243	+	Silent	SNP	A	A	G	rs3918386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	32	87	0	0.432432	0	A|0.940;G|0.060	0.060	strong	.	CCR2	103	.	NM_001123041	exon3	c.A1017G	p.P339P	GAGACCAGGAAAG	.	PASS	Atlas-SNP
CLEC14A	161198	hgsc.bcm.edu	37	14	38724043	38724043	+	Silent	SNP	G	G	A	rs78287081	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	38	72	0	0.5	0	G|0.992;A|0.008	0.008	strong	.	CLEC14A	83	.	NM_175060	exon1	c.C1185T	p.S395S	GGCAGAGGAGGAG	.	PASS	Atlas-SNP
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316482	39316482	+	Missense_Mutation	SNP	C	C	G	rs366700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	250	218	0	0.996016	0	C|0.938;G|0.062	0.062	strong	.	KRTAP4-4	21	.	NM_032524	exon1	c.G462C	p.R154S	GTAGCACCTGGAC	.	PASS	Atlas-SNP
DSE	29940	hgsc.bcm.edu	37	6	116758004	116758004	+	Silent	SNP	C	C	T	rs367781233		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	64	113	0	0.450704	0	.	.	weak	.	DSE	98	.	NM_001080976	exon6	c.C2373T	p.D791D	CATTGACAGGATT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100128003	100128003	+	Missense_Mutation	SNP	C	C	G	rs148165882	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	37	82	0	0.336364	0	C|0.994;G|0.006	0.006	strong	KIAA1529,NS,haematopoietic_neoplasm,0,2	.	.	2	NM_020893	exon30	c.C4161G	p.N1387K	TGAGAACCTGCTG	.	PASS	Atlas-SNP
TGM2	7052	hgsc.bcm.edu	37	20	36770588	36770588	+	Silent	SNP	C	C	T	rs2076390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	110	212	0	0.555556	0	C|0.831;T|0.169	0.169	strong	.	TGM2	88	.	NM_198951	exon7	c.G873A	p.L291L	GATGCCCAGGCAC	.	PASS	Atlas-SNP
GIMAP8	155038	hgsc.bcm.edu	37	7	150163837	150163837	+	Silent	SNP	A	A	G	rs2140595	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	29	78	0	0.414286	0	A|0.649;G|0.351	0.351	strong	GIMAP8,trunk,malignant_melanoma,+1,1	GIMAP8	136	1	NM_175571	exon2	c.A51G	p.G17G	CCTGGGAAAATGC	.	PASS	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64675074	64675074	+	Missense_Mutation	SNP	G	G	A	rs61741398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	47	89	0	0.398305	0	G|0.984;A|0.016	0.016	strong	.	ATG2A	133	.	NM_015104	exon18	c.C2570T	p.A857V	GGCTGGGCGGCGG	.	PASS	Atlas-SNP
CIAPIN1	57019	hgsc.bcm.edu	37	16	57468110	57468110	+	Silent	SNP	G	G	A	rs77773186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	56	122	0	0.583333	0	G|0.993;A|0.007	0.007	strong	.	CIAPIN1	17	.	NM_020313	exon5	c.C402T	p.P134P	GGTTAGGGGCTCC	.	PASS	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76754367	76754367	+	Silent	SNP	C	C	T	rs2927258	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	55	84	0	0.585106	0	C|0.930;T|0.070	0.070	strong	SALL3,NS,carcinoma,0,1	SALL3	162	1	NM_171999	exon2	c.C2376T	p.T792T	GGAGACCCTGAGC	.	PASS	Atlas-SNP
FAM114A2	10827	hgsc.bcm.edu	37	5	153382518	153382518	+	Silent	SNP	G	G	A	rs34136150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	91	0	0.494737	0	G|0.880;A|0.120	0.120	strong	.	FAM114A2	51	.	NM_018691	exon10	c.C1005T	p.T335T	GTGGGCGGTATTT	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	86	199	0	0.480447	0	A|0.922;T|0.078	0.078	strong	.	C1orf127	134	.	NM_001170754	exon12	c.T1598A	p.V533D	CCTGAGACCAGAA	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3481531	3481531	+	Silent	SNP	T	T	C	rs11548215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	115	230	0	0.416667	0	T|0.889;C|0.111	0.111	strong	.	.	.	.	NM_016030	exon10	c.T1842C	p.D614D	ATTAGATGGACTA	.	PASS	Atlas-SNP
ZBTB24	9841	hgsc.bcm.edu	37	6	109787596	109787596	+	Missense_Mutation	SNP	C	C	T	rs2232448	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	77	112	0	0.583333	0	C|0.918;T|0.082	0.082	strong	.	ZBTB24	64	.	NM_014797	exon7	c.G1552A	p.A518T	CTGAAGCATGCTT	.	PASS	Atlas-SNP
OR2A2	442361	hgsc.bcm.edu	37	7	143806688	143806688	+	Missense_Mutation	SNP	C	C	A	rs10230228	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	127	232	0	0.445614	0	C|0.826;A|0.174	0.174	strong	OR2A2,rectum,carcinoma,-2,1	OR2A2	48	1	NM_001005480	exon1	c.C13A	p.Q5K	GGCAACCAGACAT	.	PASS	Atlas-SNP
ZNF432	9668	hgsc.bcm.edu	37	19	52538278	52538278	+	Silent	SNP	A	A	C	rs6509616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	89	0	0.504951	0	A|0.946;C|0.054	0.054	strong	.	ZNF432	172	.	NM_014650	exon5	c.T654G	p.S218S	GAGCTGAGACTTC	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55578991	55578991	+	Silent	SNP	C	C	T	rs66537410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	66	117	0	0.564103	0	C|0.899;T|0.101	0.101	strong	OR5L1,NS,carcinoma,0,1	OR5L1	145	1	NM_001004738	exon1	c.C49T	p.L17L	CTTGGACTATCAG	.	PASS	Atlas-SNP
ENDOG	2021	hgsc.bcm.edu	37	9	131584649	131584649	+	Silent	SNP	C	C	T	rs55985529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	66	105	0	0.616822	0	C|0.970;T|0.030	0.030	strong	.	ENDOG	8	.	NM_004435	exon3	c.C654T	p.I218I	GGTCATCGGCAAG	.	PASS	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169824983	169824983	+	Missense_Mutation	SNP	T	T	C	rs11568364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	58	135	0	0.439394	0	T|0.937;C|0.063	0.063	strong	.	ABCB11	136	.	NM_003742	exon17	c.A2029G	p.M677V	CAAGCATGTCATC	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158533140	158533140	+	Silent	SNP	A	A	G	rs12080815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	31	79	0	0.43662	0	A|0.465;G|0.535	0.535	strong	OR6P1,NS,carcinoma,0,1	OR6P1	47	1	NM_001160325	exon1	c.T255C	p.F85F	GGTAAGAAAGGCT	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17049245	17049245	+	Silent	SNP	G	G	A	rs61133226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	20	51	0	0.540541	0	G|0.961;A|0.039	0.039	strong	.	CPAMD8	192	.	NM_015692	exon23	c.C2946T	p.V982V	CCGGGGGACTCCT	.	PASS	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	37	3	361508	361508	+	Missense_Mutation	SNP	C	C	T	rs2272522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	46	0	0.45	0	C|0.678;T|0.322	0.322	strong	CHL1,caecum,carcinoma,0,2	CHL1	242	2	NM_001253388	exon1	c.C49T	p.L17F	ATGTTCCTCCTGT	.	PASS	Atlas-SNP
LRRTM1	347730	hgsc.bcm.edu	37	2	80529706	80529706	+	Silent	SNP	A	A	G	rs35054232	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	13	33	0	0.351351	0	A|0.958;G|0.042	0.042	strong	.	LRRTM1	251	.	NM_178839	exon2	c.T1239C	p.L413L	GCCTGGAAGAGCC	.	PASS	Atlas-SNP
GPAM	57678	hgsc.bcm.edu	37	10	113935379	113935379	+	Missense_Mutation	SNP	T	T	C	rs10787428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	87	0	1	0	C|0.558;N|0.000	0.558	strong	.	GPAM	68	.	NM_001244949	exon6	c.A392G	p.E131G	ACATTTTCAGTCA	.	PASS	Atlas-SNP
DPYSL4	10570	hgsc.bcm.edu	37	10	134017388	134017388	+	Silent	SNP	C	C	G	rs1052556	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	67	178	0	0.378531	0	C|0.865;G|0.135	0.135	strong	.	DPYSL4	91	.	NM_006426	exon13	c.C1584G	p.V528V	CTCCGTCCCTCCT	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671318	31671318	+	Silent	SNP	T	T	C	rs144729538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	74	113	0	0.564885	0	T|0.986;C|0.014	0.014	strong	.	.	.	.	NM_182519	exon3	c.T315C	p.Y105Y	CCGATATGGTGAG	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43836237	43836237	+	Missense_Mutation	SNP	T	T	A	rs61729393	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	92	157	0	0.476684	0	T|0.988;A|0.012	0.012	strong	.	SEMG1	71	.	NM_003007	exon2	c.T299A	p.L100Q	GACATCTAGGTGG	.	PASS	Atlas-SNP
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	69	0	1	0	C|0.611;T|0.389	0.389	strong	.	ABCC8	170	.	NM_000352	exon31	c.G3819A	p.R1273R	GAGCTCCCTGTGC	.	PASS	Atlas-SNP
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	109	0	0.523364	0	C|0.728;A|0.272	0.272	strong	.	ZNF683	51	.	NM_173574	exon4	c.G863T	p.R288L	CCACCACGCTCCA	.	PASS	Atlas-SNP
AGT	183	hgsc.bcm.edu	37	1	230846305	230846305	+	Missense_Mutation	SNP	C	C	T	rs11568032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	86	193	0	0.469945	0	C|0.994;T|0.006	0.006	strong	.	AGT	62	.	NM_000029	exon2	c.G292A	p.E98K	TGTCTTCGGTGTC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901722	129901722	+	Silent	SNP	G	G	A	rs10082432	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	106	281	1	0.445378	0.00355872	G|0.782;A|0.218	0.218	strong	.	MKI67	363	.	NM_002417	exon13	c.C8382T	p.A2794A	GGCTTGGGCACTT	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44086831	44086831	+	Silent	SNP	C	C	T	rs1143702	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	267	235	0	1	0	A|0.000;C|0.380;T|0.620	0.620	strong	.	PTPRF	172	.	NM_002840	exon33	c.C5583T	p.Y1861Y	GCGCTACGAGGGC	.	PASS	Atlas-SNP
ARHGEF2	9181	hgsc.bcm.edu	37	1	155931630	155931630	+	Silent	SNP	G	G	A	rs143812169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	95	201	0	0.502645	0	G|0.995;A|0.005	0.005	strong	.	ARHGEF2	81	.	NM_001162383	exon11	c.C1290T	p.D430D	ACCCTCGTCCACA	.	PASS	Atlas-SNP
SPOCK1	6695	hgsc.bcm.edu	37	5	136448208	136448208	+	Silent	SNP	A	A	G	rs17170968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	25	75	0	0.403226	0	A|0.924;G|0.076	0.076	strong	.	SPOCK1	58	.	NM_004598	exon5	c.T390C	p.P130P	ATTCGAAGGTCCA	.	PASS	Atlas-SNP
PITX1	5307	hgsc.bcm.edu	37	5	134364996	134364996	+	Silent	SNP	G	G	T	rs1131611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	31	49	0	0.574074	0	G|0.809;T|0.191	0.191	strong	.	PITX1	31	.	NM_002653	exon3	c.C418A	p.R140R	CTCGCCGGTTCTT	.	PASS	Atlas-SNP
ABHD2	11057	hgsc.bcm.edu	37	15	89738475	89738475	+	Missense_Mutation	SNP	A	A	C	rs147106119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	55	115	0	0.478261	0	A|0.999;C|0.001	0.001	strong	.	ABHD2	55	.	NM_007011	exon15	c.A1099C	p.M367L	AACGTCATGTTTG	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58743454	58743454	+	Missense_Mutation	SNP	A	A	C	rs30842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	54	59	0	0.6	0	A|0.252;C|0.748	0.748	strong	.	GOT2	42	.	NM_002080	exon9	c.T1037G	p.V346G	GCCATGACTTTCA	.	PASS	Atlas-SNP
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	108	109	0	0.990826	0	A|0.455;G|0.545	0.545	strong	CST5,NS,carcinoma,0,1	CST5	24	1	NM_001900	exon1	c.T136C	p.C46R	GGGCACACTGCAC	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186459475	186459475	+	Missense_Mutation	SNP	C	C	G	rs5030084	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	48	124	0	0.403361	0	C|0.964;G|0.036	0.036	strong	.	KNG1	129	.	NM_001102416	exon10	c.C1290G	p.D430E	ACATGACTGGGGC	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	73051440	73051440	+	Missense_Mutation	SNP	G	G	A	rs10509332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	75	0	0.517241	0	G|0.960;A|0.040	0.040	strong	.	UNC5B	123	.	NM_170744	exon10	c.G1546A	p.A516T	GATTTCGCCCGGG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	78987157	78987157	+	Missense_Mutation	SNP	A	A	G	rs4859905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	394	182	402	1	0.461929	0.00248756	A|0.473;G|0.527	0.527	strong	.	FRAS1	779	.	NM_001166133	exon2	c.A95G	p.D32G	ATCAGGATTCCTT	.	PASS	Atlas-SNP
LRRC18	474354	hgsc.bcm.edu	37	10	50121785	50121785	+	Missense_Mutation	SNP	G	G	A	rs11101561	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	62	181	0	0.424658	0	G|0.891;A|0.109	0.109	strong	.	LRRC18	52	.	NM_001006939	exon1	c.C416T	p.T139I	CCCAGTGTGGTGG	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825662	34825662	+	Silent	SNP	T	T	C	rs16894959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	63	100	0	0.533898	0	T|0.852;C|0.148	0.148	strong	.	UHRF1BP1	102	.	NM_017754	exon13	c.T1735C	p.L579L	GAACACTTGGACA	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1647186	1647186	+	Silent	SNP	G	G	A	rs111450110	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	31	65	0	0.43662	0	G|0.992;A|0.008	0.008	strong	.	PXDN	255	.	NM_012293	exon19	c.C3906T	p.D1302D	GATCTCGTCACAG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	66	137	0	0.289474	0	A|0.749;T|0.251	0.251	strong	.	PSPH	23	.	NM_004577	exon4	c.T120A	p.V40V	GTCCTCAACGCCA	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140603248	140603248	+	Silent	SNP	G	G	A	rs7713000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	106	188	0	0.517073	0	G|0.975;A|0.025	0.025	strong	.	PCDHB14	132	.	NM_018934	exon1	c.G171A	p.E57E	GGTGGAGGAGCTG	.	PASS	Atlas-SNP
CCT5	22948	hgsc.bcm.edu	37	5	10262607	10262607	+	Silent	SNP	G	G	A	rs113262482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	68	120	0	0.475524	0	G|0.992;A|0.008	0.008	strong	.	CCT5	49	.	NM_012073	exon9	c.G1194A	p.A398A	GGAGGCGAAACGA	.	PASS	Atlas-SNP
GALNT10	55568	hgsc.bcm.edu	37	5	153792453	153792453	+	Missense_Mutation	SNP	G	G	A	rs142635658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	17	41	0	0.548387	0	G|0.997;A|0.003	0.003	strong	.	GALNT10	70	.	NM_198321	exon10	c.G1391A	p.R464Q	AGATCCGAAATGT	.	PASS	Atlas-SNP
ZNF600	162966	hgsc.bcm.edu	37	19	53270460	53270460	+	Silent	SNP	G	G	A	rs56336133		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	72	188	0	0.4	0	.	.	weak	.	ZNF600	75	.	NM_198457	exon3	c.C549T	p.P183P	TAAATGGGGTATC	.	PASS	Atlas-SNP
CEP78	84131	hgsc.bcm.edu	37	9	80881357	80881357	+	Splice_Site	SNP	G	G	C	rs146563928	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	10	34	0	0.344828	0	G|0.999;C|0.001	0.001	strong	.	CEP78	79	.	NM_001098802	exon16	c.1849-1G>C	.	CTTCTAGTTTCAG	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821576	100821576	+	Missense_Mutation	SNP	G	G	A	rs7496668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	45	46	0	0.978261	0	G|0.589;A|0.411	0.411	strong	ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	NM_139057	exon4	c.C647T	p.S216L	TCCCGCGAAGGCC	.	PASS	Atlas-SNP
AGMO	392636	hgsc.bcm.edu	37	7	15458194	15458194	+	Missense_Mutation	SNP	T	T	A	rs146442781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	81	140	1	0.5	0.00714286	T|0.997;A|0.003	0.003	strong	AGMO,NS,carcinoma,0,1	AGMO	98	1	NM_001004320	exon5	c.A598T	p.I200F	TATGGATCCAAAA	.	scavenged	Atlas-SNP
DEFB1	1672	hgsc.bcm.edu	37	8	6728298	6728298	+	Missense_Mutation	SNP	C	C	T	rs2738047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	71	122	0	0.554688	0	T|0.041;C|0.959	0.041	strong	.	DEFB1	4	.	NM_005218	exon2	c.G112A	p.V38I	TGCTGACGCAATT	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23751736	23751736	+	Silent	SNP	A	A	G	rs7779633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	143	166	0	0.993056	0	A|0.618;G|0.382	0.382	strong	STK31,NS,carcinoma,+1,1	STK31	175	1	NM_031414	exon2	c.A69G	p.Q23Q	TGTTCAAATGGAT	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	26	28	1	1	0.0357143	T|0.772;G|0.228	0.228	strong	KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	NM_001039374	exon4	c.T338G	p.L113R	TCCACCTGGTGCG	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149498945	149498945	+	Missense_Mutation	SNP	C	C	T	rs73727615	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	44	105	0	0.564103	0	C|0.982;T|0.018	0.018	strong	.	.	.	.	NM_198455	exon50	c.C7397T	p.P2466L	GTTCCCCGAGCCA	.	PASS	Atlas-SNP
CHRNB4	1143	hgsc.bcm.edu	37	15	78921762	78921762	+	Silent	SNP	G	G	A	rs3743072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	70	124	0	0.546875	0	G|0.962;A|0.038	0.038	strong	.	CHRNB4	59	.	NM_000750	exon5	c.C885T	p.I295I	CTTGCCGATGAGA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107738948	107738948	+	Silent	SNP	G	G	A	rs451252	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	73	144	0	0.52518	0	G|0.674;A|0.326	0.326	strong	.	LAMB4	253	.	NM_007356	exon11	c.C1260T	p.A420A	CTGGCCGGCCACA	.	PASS	Atlas-SNP
CLDN6	9074	hgsc.bcm.edu	37	16	3065924	3065924	+	Silent	SNP	G	G	A	rs2269911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	106	210	1	0.449153	0.0047619	G|0.811;A|0.189	0.189	strong	CLDN6,NS,carcinoma,0,1	CLDN6	31	1	NM_021195	exon2	c.C99T	p.T33T	GAAAGCGGTCACC	.	scavenged	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29226417	29226417	+	Silent	SNP	C	C	T	rs76285160	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	125	240	1	0.518672	0.00416667	C|0.929;T|0.071	0.071	strong	.	FAM179A	106	.	NM_199280	exon6	c.C699T	p.G233G	CCTGGGCGCCATC	.	PASS	Atlas-SNP
ALPI	248	hgsc.bcm.edu	37	2	233323000	233323000	+	Silent	SNP	C	C	T	rs10195208	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	128	240	1	0.481203	0.00416667	C|0.950;T|0.050	0.050	strong	ALPI,NS,carcinoma,+2,1	ALPI	64	1	NM_001631	exon9	c.C1065T	p.D355D	CGACGACGCCATT	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125591687	125591687	+	Silent	SNP	A	A	G	rs3733471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	103	237	0	0.438298	0	A|0.742;G|0.258	0.258	strong	.	ANKRD50	136	.	NM_020337	exon4	c.T2745C	p.N915N	CAGTGCATTTCTT	.	PASS	Atlas-SNP
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570951	186570951	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	128	235	1	0.53112	0.00425532	.	.	none	.	ADIPOQ	35	.	NM_001177800	exon3	c.C104T	p.A35V	AGGGGGCCTGCAC	.	PASS	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67265360	67265360	+	Silent	SNP	C	C	A	rs6499118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	80	136	0	0.493827	0	C|0.755;A|0.245	0.245	strong	.	FHOD1	86	.	NM_013241	exon16	c.G2478T	p.A826A	GCCCACCGCTAGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149486726	149486726	+	Silent	SNP	T	T	C	rs855695	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	77	140	0	0.606299	0	T|0.974;C|0.026	0.026	strong	.	.	.	.	NM_198455	exon31	c.T4500C	p.V1500V	CTGTGTTGATGGC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	Silent	SNP	C	C	T	rs3795280	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	86	194	0	0.547771	0	C|0.606;T|0.394	0.394	strong	.	KIAA1751	92	.	NM_001080484	exon6	c.G435A	p.L145L	TGCAAACAGGCGT	.	PASS	Atlas-SNP
JMJD7-PLA2G4B	8681	hgsc.bcm.edu	37	15	42138572	42138572	+	Missense_Mutation	SNP	C	C	T	rs36126315	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	55	114	0	0.491071	0	C|0.985;T|0.015	0.015	strong	.	JMJD7-PLA2G4B	90	.	NM_005090	exon22	c.C2465T	p.T822I	TCTCCACATGGAA	.	PASS	Atlas-SNP
IMP4	92856	hgsc.bcm.edu	37	2	131103479	131103479	+	Silent	SNP	C	C	T	rs34942992	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	83	176	0	0.497006	0	C|0.934;T|0.066	0.066	strong	.	IMP4	35	.	NM_033416	exon6	c.C567T	p.H189H	CACACACGGCTTC	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77376647	77376647	+	Missense_Mutation	SNP	T	T	C	rs2274924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	135	215	0	0.658537	0	T|0.756;C|0.244	0.244	strong	TRPM6,caecum,carcinoma,+2,2	TRPM6	377	2	NM_017662	exon27	c.A4750G	p.K1584E	TTTTCTTTGACAG	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2813177	2813177	+	Missense_Mutation	SNP	C	C	G	rs17136053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	47	0	0.428571	0	C|0.969;G|0.031	0.031	strong	.	SRRM2	263	.	NM_016333	exon11	c.C2648G	p.S883C	TGAAATCTAGGAC	.	PASS	Atlas-SNP
HSPB8	26353	hgsc.bcm.edu	37	12	119631654	119631654	+	Silent	SNP	C	C	T	rs4628742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	74	156	0	0.4625	0	C|0.917;T|0.083	0.083	strong	.	HSPB8	45	.	NM_014365	exon3	c.C582T	p.T194T	AGTCACCTGTACC	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98709684	98709684	+	Silent	SNP	T	T	C	rs298917	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	92	232	0	0.467005	0	T|0.871;C|0.129	0.129	strong	.	VWA3B	138	.	NM_144992	exon2	c.T129C	p.H43H	ACTGCATGGGCTT	.	PASS	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31410653	31410653	+	Missense_Mutation	SNP	C	C	T	rs7422120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	142	155	0	0.993007	0	C|0.732;T|0.268	0.268	strong	.	CAPN14	36	.	NM_001145122	exon15	c.G1558A	p.D520N	ATTCATCCTGCCT	.	PASS	Atlas-SNP
GJA4	2701	hgsc.bcm.edu	37	1	35259961	35259961	+	Silent	SNP	A	A	G	rs1764390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	163	186	0	0.993902	0	A|0.319;C|0.000;G|0.681;T|0.000	0.681	strong	.	GJA4	25	.	NM_002060	exon2	c.A147G	p.Q49Q	CGAGCAATCAGAT	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106155751	106155751	+	Missense_Mutation	SNP	G	G	A	rs6843141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	64	0	0.545455	0	G|0.879;A|0.121	0.121	strong	.	TET2	1762	.	NM_001127208	exon3	c.G652A	p.V218M	TCTTCCGTGGAAC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058043	46058043	+	Missense_Mutation	SNP	C	C	T	rs77109703	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	380	84	218	0	0.221053	0	C|0.966;T|0.034	0.034	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C709T	p.R237C	TGCTCCCGCCCTG	.	PASS	Atlas-SNP
SOGA3	387104	hgsc.bcm.edu	37	6	127797389	127797389	+	Silent	SNP	C	C	T	rs61741826	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	38	89	0	0.447059	0	C|0.999;T|0.001	0.001	strong	.	.	.	.	NM_001012279	exon6	c.G1782A	p.V594V	TTCCTCCACCAGC	.	PASS	Atlas-SNP
LY6H	4062	hgsc.bcm.edu	37	8	144239859	144239859	+	Silent	SNP	A	A	G	rs10109061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	86	1	1	0.0116279	A|0.509;G|0.491	0.491	strong	LY6H,NS,carcinoma,0,1	LY6H	12	1	NM_001135655	exon4	c.T294C	p.C98C	GAAGTCACAGGAG	.	scavenged	Atlas-SNP
TRIM41	90933	hgsc.bcm.edu	37	5	180661274	180661274	+	Missense_Mutation	SNP	C	C	G	rs78013120	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	28	40	0	0.56	0	C|0.995;G|0.005	0.005	strong	.	TRIM41	96	.	NM_201627	exon6	c.C1392G	p.D464E	TGCTGACCATCCC	.	PASS	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	37	16	1584294	1584294	+	Silent	SNP	C	C	T	rs79579867	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	98	182	0	0.485149	0	C|0.979;T|0.021	0.021	strong	.	TMEM204	29	.	NM_024600	exon1	c.C18T	p.L6L	GAGACTCGTGGCC	.	PASS	Atlas-SNP
ABCA12	26154	hgsc.bcm.edu	37	2	215876371	215876371	+	Silent	SNP	T	T	C	rs10198064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	112	253	0	0.506787	0	T|0.734;C|0.266	0.266	strong	ABCA12,NS,carcinoma,-1,1	ABCA12	368	1	NM_173076	exon17	c.A2124G	p.A708A	GTACATTGCCTGT	.	PASS	Atlas-SNP
ZBTB38	253461	hgsc.bcm.edu	37	3	141163975	141163975	+	Silent	SNP	G	G	A	rs61732448	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	31	76	0	0.402597	0	G|0.989;A|0.011	0.011	strong	ZBTB38,NS,carcinoma,0,1	ZBTB38	92	1	NM_001080412	exon8	c.G2745A	p.P915P	CAAACCGTGGCGC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525647	248525647	+	Silent	SNP	C	C	A	rs28405645	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	919	438	890	1	0.476605	0.0011236	C|0.790;A|0.210	0.210	strong	.	OR2T4	126	.	NM_001004696	exon1	c.C765A	p.L255L	CCTCCTCACCATC	.	PASS	Atlas-SNP
CYP4F3	4051	hgsc.bcm.edu	37	19	15763721	15763721	+	Silent	SNP	G	G	A	rs1805042	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	79	171	0	0.411458	0	G|0.523;A|0.477	0.477	strong	CYP4F3,NS,carcinoma,0,1	CYP4F3	69	1	NM_001199209	exon9	c.G1074A	p.V358V	GGAGGTGCAAGAG	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59481016	59481016	+	Silent	SNP	C	C	T	rs537595	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	43	90	0	0.462366	0	C|0.894;T|0.106	0.106	strong	.	OR10V1	40	.	NM_001005324	exon1	c.G303A	p.Q101Q	AAACATCTGGGTG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656511	46656511	+	Silent	SNP	A	A	G	rs9627324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	55	115	0	0.544554	0	A|0.733;G|0.267	0.267	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T2709C	p.I903I	TGTAGAAATGGGA	.	PASS	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11224265	11224265	+	Silent	SNP	A	A	G	rs5930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	36	91	0	0.461538	0	A|0.345;G|0.655	0.655	strong	LDLR,NS,carcinoma,0,1	LDLR	72	1	NM_001195798	exon10	c.A1413G	p.R471R	CAGCAGAGACATC	.	PASS	Atlas-SNP
ARHGEF40	55701	hgsc.bcm.edu	37	14	21546354	21546354	+	Missense_Mutation	SNP	C	C	T	rs61744857	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	58	83	0	0.585859	0	C|0.939;T|0.061	0.061	strong	ARHGEF40_ENST00000298694,NS,carcinoma,-1,1	ARHGEF40	84	1	NM_018071	exon9	c.C2053T	p.R685C	CTATGTCGCCTGT	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71248046	71248046	+	Silent	SNP	A	A	G	rs9455152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	96	204	0	0.551724	0	A|0.974;G|0.026	0.026	strong	.	FAM135A	181	.	NM_001162529	exon18	c.A4170G	p.T1390T	GCTGACATGTCGA	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37280711	37280711	+	Silent	SNP	T	T	C	rs10202107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	101	221	0	0.515306	0	T|0.989;C|0.011	0.011	strong	.	HEATR5B	185	.	NM_019024	exon17	c.A2439G	p.Q813Q	TTTAGCTTGTTTA	.	PASS	Atlas-SNP
DLK1	8788	hgsc.bcm.edu	37	14	101201219	101201219	+	Missense_Mutation	SNP	G	G	C	rs115349979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	10	26	0	0.5	0	G|0.988;C|0.012	0.012	strong	DLK1,NS,carcinoma,-2,2	DLK1	57	2	NM_003836	exon5	c.G1138C	p.D380H	GCCGGCGACGAGG	.	PASS	Atlas-SNP
GHRHR	2692	hgsc.bcm.edu	37	7	31008686	31008686	+	Missense_Mutation	SNP	G	G	A	rs4988496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	45	63	0	0.548781	0	G|0.861;A|0.139	0.139	strong	.	GHRHR	55	.	NM_000823	exon3	c.G169A	p.A57T	TGCCCTGCGACCT	.	PASS	Atlas-SNP
ZFP36	7538	hgsc.bcm.edu	37	19	39898667	39898667	+	Silent	SNP	C	C	T	rs3746083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	35	0	1	0	A|0.000;C|0.959;G|0.000;T|0.041	0.041	strong	.	ZFP36	19	.	NM_003407	exon2	c.C327T	p.R109R	CTCGCGCTACAAG	.	PASS	Atlas-SNP
HELQ	113510	hgsc.bcm.edu	37	4	84350870	84350870	+	Silent	SNP	A	A	G	rs59255439	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	42	84	0	0.512195	0	A|0.908;G|0.092	0.092	strong	.	HELQ	95	.	NM_133636	exon12	c.T2325C	p.H775H	CATGAAATGATAG	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129291751	129291751	+	Silent	SNP	T	T	C	rs2244708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	31	71	0	0.476923	0	T|0.572;C|0.428	0.428	strong	PLXND1,colon,carcinoma,0,1	PLXND1	149	1	NM_015103	exon14	c.A2871G	p.P957P	TGAGAGTGGTCCT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057636	46057636	+	Missense_Mutation	SNP	T	T	A	rs115298124	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	120	205	0	0.43956	0	T|0.928;A|0.072	0.072	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.T302A	p.V101E	GCTGTGTGCCCGT	.	PASS	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51795172	51795172	+	Silent	SNP	G	G	A	rs12592889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	42	79	0	0.518519	0	G|0.548;A|0.452	0.452	strong	DMXL2,NS,carcinoma,0,1	DMXL2	262	1	NM_001174116	exon17	c.C2823T	p.N941N	ATCTACGTTCTTC	.	PASS	Atlas-SNP
CELF2	10659	hgsc.bcm.edu	37	10	11356160	11356160	+	Silent	SNP	C	C	T	rs2246449	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	94	228	1	0.537143	0.00438596	C|0.603;T|0.397	0.397	strong	.	CELF2	78	.	NM_006561	exon10	c.C1035T	p.L345L	CTCTCTCGGGACT	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	37	6	97512577	97512577	+	Missense_Mutation	SNP	A	A	G	rs2294763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	64	131	0	0.426667	0	A|0.940;G|0.060	0.060	strong	KLHL32,NS,carcinoma,0,1	KLHL32	85	1	NM_052904	exon5	c.A386G	p.N129S	TTCTCAATTTATG	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36997655	36997655	+	Missense_Mutation	SNP	C	C	T	rs2232613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	99	0	0.476744	0	C|0.926;T|0.074	0.074	strong	.	LBP	60	.	NM_004139	exon10	c.C998T	p.P333L	TCTACCCCAACAT	.	PASS	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	720152	720152	+	Silent	SNP	T	T	C	rs3752487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	29	38	0	0.557692	0	T|0.850;C|0.150	0.150	strong	.	RHOT2	35	.	NM_138769	exon6	c.T306C	p.N102N	GGTGAATGGGGGG	.	PASS	Atlas-SNP
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	63	118	0	0.5	0	A|0.941;G|0.059	0.059	strong	.	ALDH7A1	57	.	NM_001202404	exon3	c.T354C	p.T118T	CTTTACAGTTTCT	.	PASS	Atlas-SNP
RINT1	60561	hgsc.bcm.edu	37	7	105177041	105177041	+	Missense_Mutation	SNP	A	A	T	rs11556986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	60	86	0	0.521739	0	A|0.809;T|0.191	0.191	strong	RINT1,NS,carcinoma,-2,1	RINT1	65	1	NM_021930	exon3	c.A118T	p.S40C	ATTGGAAGTAAAC	.	PASS	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	37	5	137708434	137708434	+	Silent	SNP	C	C	T	rs4835678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	100	199	0	0.473934	0	C|0.379;T|0.621	0.621	strong	.	KDM3B	177	.	NM_016604	exon2	c.C264T	p.I88I	AGTTATCGTGCTT	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138584014	138584014	+	Missense_Mutation	SNP	C	C	G	rs116596107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	65	142	0	0.532787	0	C|0.998;G|0.002	0.002	strong	.	KIAA1244	236	.	NM_020340	exon12	c.C1394G	p.A465G	ATGGGGCTGAGTG	.	PASS	Atlas-SNP
MED13	9969	hgsc.bcm.edu	37	17	60040329	60040329	+	Silent	SNP	C	C	T	rs2278812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	26	51	0	0.5	0	C|0.741;T|0.259	0.259	strong	MED13,colon,carcinoma,0,1	MED13	181	1	NM_005121	exon21	c.G4848A	p.T1616T	ATCCATCGTGCTA	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	66	120	0	0.468085	0	C|0.301;N|0.000	0.301	strong	GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	NM_148963	exon6	c.A2433G	p.P811P	CACAGCTGGTACA	.	PASS	Atlas-SNP
ARHGAP17	55114	hgsc.bcm.edu	37	16	24965975	24965975	+	Silent	SNP	C	C	G	rs111986765	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	43	91	0	0.494253	0	C|0.999;G|0.001	0.001	strong	.	ARHGAP17	138	.	NM_001006634	exon10	c.G801C	p.L267L	AATGGGCAGCGCA	.	PASS	Atlas-SNP
ATP8	0	hgsc.bcm.edu	37	MT	8468	8468	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	6	4	0	1	0	.	.	none	.	.	.	.	ENST00000361851	exon1	c.C103T	p.L35L	TACCACCTACCTC	.	PASS	Atlas-SNP
UQCC	55245	hgsc.bcm.edu	37	20	33981906	33981906	+	Missense_Mutation	SNP	G	G	C	rs75909303	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	77	0	0.466667	0	G|0.994;C|0.006	0.006	strong	UQCC,NS,carcinoma,0,1	UQCC	41	1	NM_018244	exon2	c.C118G	p.R40G	AAGTGCGAGACAG	.	PASS	Atlas-SNP
PNPO	55163	hgsc.bcm.edu	37	17	46023295	46023295	+	Silent	SNP	C	C	G	rs35974730	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	30	71	0	0.555556	0	C|0.980;G|0.020	0.020	strong	.	PNPO	18	.	NM_018129	exon5	c.C486G	p.P162P	CCGCCCCAAGAGC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525657	248525657	+	Missense_Mutation	SNP	G	G	A	rs28718027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	927	457	902	2	0.492988	0.00221729	G|0.795;A|0.205	0.205	strong	OR2T4,right_upper_lobe,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.G775A	p.G259R	ATCCACGGGATGA	.	scavenged	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117810651	117810651	+	Silent	SNP	G	G	A	rs146504512	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	68	0	0.468354	0	G|0.996;A|0.004	0.004	strong	.	TNC	282	.	NM_002160	exon16	c.C4740T	p.T1580T	CCTCTGGGTTCCT	.	PASS	Atlas-SNP
IRAK3	11213	hgsc.bcm.edu	37	12	66641813	66641813	+	Silent	SNP	C	C	T	rs11465988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	110	1	1	0.00909091	C|0.968;T|0.032	0.032	strong	.	IRAK3	75	.	NM_007199	exon12	c.C1653T	p.S551S	TCCATCCCAGGAC	.	PASS	Atlas-SNP
AQP8	343	hgsc.bcm.edu	37	16	25228566	25228566	+	Silent	SNP	G	G	A	rs139992979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	111	233	0	0.466387	0	G|0.993;A|0.007	0.007	strong	.	AQP8	75	.	NM_001169	exon2	c.G60A	p.P20P	GGAGCCGAGCGTG	.	PASS	Atlas-SNP
OR3A2	4995	hgsc.bcm.edu	37	17	3181677	3181677	+	Missense_Mutation	SNP	G	G	C	rs73977611	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	140	274	1	0.474576	0.00364964	G|0.991;C|0.009	0.009	strong	.	OR3A2	36	.	NM_002551	exon1	c.C553G	p.H185D	AGAAGTGATTGAC	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131190696	131190696	+	Silent	SNP	T	T	C	rs6651125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	77	0	0.417582	0	T|0.657;C|0.343	0.343	strong	.	PODXL	53	.	NM_001018111	exon8	c.A1410G	p.A470A	GAATGATGCCATG	.	PASS	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	87	0	0.473684	0	C|0.810;T|0.190	0.190	strong	.	KCNG4	71	.	NM_172347	exon3	c.G973A	p.G325R	AGCTCCCGCTCGG	.	PASS	Atlas-SNP
MAT1A	4143	hgsc.bcm.edu	37	10	82040052	82040052	+	Silent	SNP	A	A	G	rs1143694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	66	80	0	1	0	A|0.209;G|0.791	0.791	strong	.	MAT1A	52	.	NM_000429	exon5	c.T426C	p.A142A	GTCGGTAGCATAG	.	PASS	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67992279	67992279	+	Silent	SNP	G	G	A	rs2231562	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	16	56	0	0.280702	0	G|0.878;A|0.122	0.122	strong	.	SOCS6	54	.	NM_004232	exon2	c.G375A	p.T125T	GTCCACGTCGCTC	.	PASS	Atlas-SNP
SLC26A11	284129	hgsc.bcm.edu	37	17	78199666	78199666	+	Missense_Mutation	SNP	C	C	G	rs115961261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	65	116	0	0.496183	0	C|0.990;G|0.010	0.010	strong	SLC26A11,NS,carcinoma,-1,2	SLC26A11	60	2	NM_173626	exon6	c.C544G	p.P182A	CCCAGGCCGTTCT	.	PASS	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40498503	40498503	+	Missense_Mutation	SNP	T	T	C	rs1801528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	86	167	0	0.488636	0	T|0.917;C|0.083	0.083	strong	BUB1B,NS,carcinoma,+1,1	BUB1B	71	1	NM_001211	exon15	c.T1853C	p.V618A	GTTTTGTATCCAC	.	PASS	Atlas-SNP
MTFR2	113115	hgsc.bcm.edu	37	6	136570221	136570221	+	Missense_Mutation	SNP	T	T	C	rs147085272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	16	47	0	0.380952	0	T|0.988;C|0.012	0.012	strong	.	.	.	.	NM_138419	exon2	c.A17G	p.N6S	AAGATATTCAGTA	.	PASS	Atlas-SNP
CDK7	1022	hgsc.bcm.edu	37	5	68531253	68531253	+	Silent	SNP	C	C	T	rs2972388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	310	284	1	0.996785	0.00352113	C|0.407;T|0.593	0.593	strong	.	CDK7	48	.	NM_001799	exon2	c.C99T	p.N33N	TAAGAACACCAAC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79025317	79025317	+	Silent	SNP	A	A	G	rs1366270	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	85	0	1	0	A|0.700;G|0.300	0.300	strong	.	CMYA5	643	.	NM_153610	exon2	c.A729G	p.Q243Q	TCTACAATTTTAT	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860087	16860087	+	Missense_Mutation	SNP	G	G	A	rs61750949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	87	0	0.504951	0	G|0.983;A|0.017	0.017	strong	.	NWD1	303	.	NM_001007525	exon6	c.G634A	p.A212T	CGGCTCGCGGATG	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124360032	124360032	+	Silent	SNP	C	C	T	rs11834289	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	48	91	0	0.475248	0	C|0.924;T|0.076	0.076	strong	.	DNAH10	888	.	NM_207437	exon46	c.C7839T	p.H2613H	AGGCCACACCTCG	.	PASS	Atlas-SNP
CRISP2	7180	hgsc.bcm.edu	37	6	49666100	49666100	+	Missense_Mutation	SNP	T	T	C	rs34457011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	59	113	0	0.430657	0	T|0.991;C|0.009	0.009	strong	.	CRISP2	53	.	NM_001142408	exon7	c.A392G	p.N131S	ACTGCATTGGGAC	.	PASS	Atlas-SNP
DQX1	165545	hgsc.bcm.edu	37	2	74746322	74746322	+	Silent	SNP	A	A	T	rs6546909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	147	140	0	0.993243	0	A|0.580;T|0.420	0.420	strong	.	DQX1	95	.	NM_133637	exon11	c.T1842A	p.L614L	TAGGAGAAGGTAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415299	105415299	+	Silent	SNP	A	A	G	rs59107644	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	358	185	336	0	0.51676	0	A|0.823;G|0.177	0.177	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T6489C	p.F2163F	CACCCCAAACGAC	.	PASS	Atlas-SNP
USP44	84101	hgsc.bcm.edu	37	12	95927087	95927087	+	Missense_Mutation	SNP	C	C	G	rs7305024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	31	60	0	0.484375	0	C|0.955;G|0.045	0.045	strong	.	USP44	83	.	NM_032147	exon2	c.G946C	p.E316Q	TCTTCTCGCTAGC	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89849480	89849480	+	Missense_Mutation	SNP	C	C	T	rs2239359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	112	229	0	0.486957	0	C|0.439;N|0.001	.	strong	.	FANCA	99	.	NM_000135	exon16	c.G1501A	p.G501S	ACTTGCCGGGAAC	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373872	27373872	+	Missense_Mutation	SNP	A	A	C	rs1805011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	46	92	0	0.522727	0	A|0.756;C|0.244	0.244	strong	IL4R,NS,carcinoma,0,1	IL4R	70	1	NM_000418	exon11	c.A1199C	p.E400A	GAAGGGAGGGCAT	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247021040	247021040	+	Silent	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	4	306	1	0.0133779	0.00326797	.	.	none	AHCTF1,NS,carcinoma,-1,1	AHCTF1	187	1	NM_015446	exon30	c.G4236T	p.P1412P	TTGAACCGGGCTT	.	scavenged	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20662938	20662938	+	Missense_Mutation	SNP	A	A	G	rs10916769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	123	188	1	0.539474	0.00531915	A|0.767;G|0.233	0.233	strong	.	VWA5B1	44	.	NM_001039500	exon13	c.A1901G	p.K634R	AGGCCAAAAATGC	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71058184	71058184	+	Silent	SNP	C	C	T	rs13421115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	42	117	0	0.403846	0	C|0.806;T|0.194	0.194	strong	.	CD207	47	.	NM_015717	exon6	c.G984A	p.P328P	CTGTCACGGTTCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124323011	124323011	+	Silent	SNP	T	T	C	rs116167096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	35	51	0	0.486111	0	T|0.983;C|0.017	0.017	strong	.	DNAH10	888	.	NM_207437	exon28	c.T4557C	p.G1519G	CATGGGTGAGACC	.	PASS	Atlas-SNP
PCDHA2	56146	hgsc.bcm.edu	37	5	140176840	140176840	+	Missense_Mutation	SNP	C	C	T	rs6858913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	143	269	0	0.468852	0	C|0.982;T|0.018	0.018	strong	.	PCDHA2	404	.	NM_031495	exon1	c.C2291T	p.P764L	AGGACCCCCCCAA	.	PASS	Atlas-SNP
VIPR1	7433	hgsc.bcm.edu	37	3	42568929	42568929	+	Silent	SNP	T	T	C	rs2229722	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	78	0	0.487805	0	T|0.722;C|0.278	0.278	strong	.	VIPR1	45	.	NM_004624	exon5	c.T444C	p.I148I	CACCATTGGCTAC	.	PASS	Atlas-SNP
ZBTB22	9278	hgsc.bcm.edu	37	6	33283945	33283945	+	Missense_Mutation	SNP	C	C	G	rs35663442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	25	60	0	0.347222	0	C|0.989;G|0.011	0.011	strong	.	ZBTB22	48	.	NM_001145338	exon2	c.G749C	p.G250A	GCCCCTCCACTGC	.	PASS	Atlas-SNP
GJA4	2701	hgsc.bcm.edu	37	1	35260760	35260760	+	Missense_Mutation	SNP	G	G	A	rs140949366	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	43	0	0.490196	0	G|0.989;A|0.011	0.011	strong	.	GJA4	25	.	NM_002060	exon2	c.G946A	p.G316S	CAGAATGGCCAAA	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120145987	120145987	+	Silent	SNP	G	G	C	rs56158046	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	84	0	0.986667	0	G|0.901;C|0.099	0.099	strong	.	CIT	535	.	NM_001206999	exon40	c.C5208G	p.G1736G	TACCTTGCCTGCC	.	PASS	Atlas-SNP
AGL	178	hgsc.bcm.edu	37	1	100335977	100335977	+	Missense_Mutation	SNP	A	A	G	rs17121403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	74	135	0	0.5	0	A|0.959;G|0.041	0.041	strong	.	AGL	137	.	NM_000644	exon6	c.A686G	p.Q229R	GGATCCAGGAACA	.	PASS	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	37	9	37745562	37745562	+	Missense_Mutation	SNP	C	C	T	rs62640016	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	41	75	0	0.525641	0	C|0.986;T|0.014	0.014	strong	FRMPD1,scalp,carcinoma,+1,1	FRMPD1	237	1	NM_014907	exon16	c.C3533T	p.P1178L	ATCCCCCTAGAGA	.	PASS	Atlas-SNP
EQTN	54586	hgsc.bcm.edu	37	9	27296705	27296705	+	Silent	SNP	A	A	G	rs3824406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	106	209	0	0.50237	0	A|0.873;G|0.127	0.127	strong	.	.	.	.	NM_001161585	exon2	c.T108C	p.D36D	ATTAACATCTTCA	.	PASS	Atlas-SNP
C1orf52	148423	hgsc.bcm.edu	37	1	85724328	85724328	+	Silent	SNP	C	C	T	rs4949926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	34	90	0	0.365591	0	C|0.810;T|0.190	0.190	strong	.	C1orf52	16	.	NM_198077	exon2	c.G354A	p.P118P	TGGAGGCGGAGGC	.	PASS	Atlas-SNP
MTERFD1	51001	hgsc.bcm.edu	37	8	97263180	97263180	+	Missense_Mutation	SNP	T	T	G	rs112357919	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	82	169	0	0.503067	0	T|0.958;G|0.042	0.042	strong	.	MTERFD1	50	.	NM_015942	exon4	c.A631C	p.K211Q	GATTTTTTGTCAG	.	PASS	Atlas-SNP
FMNL3	91010	hgsc.bcm.edu	37	12	50043687	50043687	+	Silent	SNP	A	A	G	rs61733848	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	39	35	1	0.672414	0.0285714	A|0.985;G|0.015	0.015	strong	FMNL3,face,carcinoma,-2,1	FMNL3	137	1	NM_175736	exon18	c.T2022C	p.P674P	GTCCACAGGTAGT	.	scavenged	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107357	55107357	+	Silent	SNP	C	C	T	rs35066441	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	68	260	0	0.444444	0	C|0.920;T|0.080	0.080	strong	.	LILRA1	105	.	NM_006863	exon6	c.C915T	p.S305S	CTCCTCCGAGTGG	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53994083	53994083	+	Silent	SNP	T	T	C	rs150664026	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	119	249	0	0.479839	0	T|0.999;C|0.001	0.001	strong	ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	NM_001004301	exon4	c.T597C	p.S199S	GAATTCTTCGTTA	.	PASS	Atlas-SNP
TMEM206	55248	hgsc.bcm.edu	37	1	212538572	212538572	+	Silent	SNP	C	C	T	rs12087727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	59	143	0	0.433824	0	C|0.908;T|0.092	0.092	strong	TMEM206,NS,carcinoma,-1,1	TMEM206	41	1	NM_001198862	exon9	c.G1221A	p.T407T	GTGGCTCGTTGCC	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38860809	38860809	+	Silent	SNP	G	G	T	rs77229707	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	43	84	0	0.573333	0	G|0.978;T|0.022	0.022	strong	.	VPS41	102	.	NM_014396	exon6	c.C378A	p.P126P	TTTAATGGGACAG	.	PASS	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220404648	220404648	+	Silent	SNP	C	C	T	rs1043833	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	235	227	2	1	0.00881057	C|0.645;T|0.355	0.355	strong	.	CHPF	56	.	NM_024536	exon4	c.G1785A	p.L595L	GAGGCGCAGTGGT	.	PASS	Atlas-SNP
VN1R4	317703	hgsc.bcm.edu	37	19	53770846	53770846	+	Missense_Mutation	SNP	C	C	G	rs148896466	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	394	192	332	0	0.48731	0	C|0.953;G|0.047	0.047	strong	.	VN1R4	65	.	NM_173857	exon1	c.G73C	p.V25L	GAAGAACAGAGAA	.	PASS	Atlas-SNP
ZCCHC2	54877	hgsc.bcm.edu	37	18	60227833	60227833	+	Silent	SNP	T	T	C	rs17070100	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	74	158	0	0.4625	0	T|0.893;C|0.107	0.107	strong	.	ZCCHC2	64	.	NM_017742	exon8	c.T1506C	p.H502H	GCAGCATGCCATA	.	PASS	Atlas-SNP
DPY19L1	23333	hgsc.bcm.edu	37	7	34978926	34978926	+	Silent	SNP	G	G	A	rs377307859		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	71	113	0	0.514493	0	.	.	weak	.	DPY19L1	56	.	NM_015283	exon20	c.C1707T	p.P569P	CACAATGGGCCGA	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161032668	161032668	+	Silent	SNP	A	A	G	rs80331546		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	8	64	0	0.275862	0	A|0.250;G|0.750	0.750	weak	LPA,NS,carcinoma,0,1	LPA	237	1	NM_005577	exon17	c.T2529C	p.T843T	TCTTCCAGTGACA	.	scavenged	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85403104	85403104	+	Missense_Mutation	SNP	G	G	A	rs114686452	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	46	102	0	0.446602	0	G|0.998;A|0.002	0.002	strong	.	ALPK3	289	.	NM_020778	exon8	c.G4669A	p.A1557T	GGCTCGGCCTCCA	.	PASS	Atlas-SNP
HDGFRP2	0	hgsc.bcm.edu	37	19	4488718	4488718	+	Missense_Mutation	SNP	G	G	A	rs147061912	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	16	27	0	0.571429	0	G|0.994;A|0.006	0.006	strong	.	.	.	.	NM_032631	exon4	c.G334A	p.D112N	CCCGCCGACGGCA	.	PASS	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76855412	76855412	+	Silent	SNP	G	G	A	rs3740317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	124	122	2	0.992	0.0163934	G|0.642;A|0.358	0.358	strong	DUSP13_ENST00000356369,NS,carcinoma,0,1	DUSP13	82	1	NM_001007273	exon5	c.C594T	p.D198D	GTTGTCGTCCGCC	.	scavenged	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242004866	242004866	+	Silent	SNP	A	A	G	rs2286321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	52	85	0	0.514852	0	A|0.630;G|0.370	0.370	strong	.	SNED1	76	.	NM_001080437	exon21	c.A2865G	p.T955T	CCGCACAGACTTT	.	PASS	Atlas-SNP
C5orf46	389336	hgsc.bcm.edu	37	5	147286013	147286013	+	Missense_Mutation	SNP	A	A	T	rs7722926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	368	361	0	1	0	A|0.710;T|0.290	0.290	strong	.	C5orf46	8	.	NM_206966	exon1	c.T52A	p.F18I	TCAGGAATAAGAC	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3188976	3188976	+	Missense_Mutation	SNP	A	A	G	rs1962519	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	83	213	0	0.408867	0	A|0.536;G|0.464	0.464	strong	.	MYOM1	192	.	NM_003803	exon4	c.T541C	p.S181P	GTTTAGATGTTGT	.	PASS	Atlas-SNP
TSKS	60385	hgsc.bcm.edu	37	19	50248556	50248556	+	Missense_Mutation	SNP	C	C	T	rs34082111	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	38	26	0	0.622951	0	C|0.991;T|0.009	0.009	strong	.	TSKS	97	.	NM_021733	exon7	c.G1090A	p.G364S	GGAAGCCGTCGAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408315	105408315	+	Silent	SNP	T	T	C	rs28600075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	249	262	0	1	0	T|0.466;C|0.534	0.534	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A13473G	p.P4491P	CATCTTTGGCGCA	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242021742	242021742	+	Missense_Mutation	SNP	G	G	T	rs2108485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	115	120	0	0.982906	0	G|0.576;T|0.424	0.424	strong	.	SNED1	76	.	NM_001080437	exon29	c.G4084T	p.A1362S	ACAAAGGCCTTTC	.	PASS	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47575279	47575279	+	Silent	SNP	G	G	C	rs76187449	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	131	0	0.523364	0	.	.	weak	.	ZC3H4	96	.	NM_015168	exon13	c.C1902G	p.P634P	CATGTCGGGGTGC	.	PASS	Atlas-SNP
MBOAT2	129642	hgsc.bcm.edu	37	2	8998971	8998971	+	Silent	SNP	T	T	C	rs35943010	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	45	130	0	0.424528	0	T|0.994;C|0.006	0.006	strong	.	MBOAT2	36	.	NM_138799	exon13	c.A1401G	p.K467K	TTGAGTTTTTTTC	.	PASS	Atlas-SNP
CHST5	23563	hgsc.bcm.edu	37	16	75563746	75563746	+	Silent	SNP	T	T	G	rs8048818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	21	53	0	0.368421	0	T|0.771;G|0.229	0.229	strong	.	CHST5	47	.	NM_024533	exon3	c.A537C	p.P179P	GCTGAATGGCTGC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725019	54725019	+	Silent	SNP	G	G	A	rs78279726	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	122	129	0	0.406667	0	G|0.702;A|0.298	0.298	strong	.	LILRB3	67	.	NM_006864	exon5	c.C891T	p.Y297Y	TGCACCGTAGCAC	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70858194	70858194	+	Silent	SNP	C	C	T	rs277941	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	90	0	0.486486	0	C|0.662;T|0.338	0.338	strong	.	BDP1	204	.	NM_018429	exon38	c.C7590T	p.R2530R	GAAACGCCTAAAA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	29	258	0	0.088685	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.C2646T	p.S882S	TGATAGCAGTGAC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs56376819		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	50	0	1	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.A1778G	p.H593R	GCCAGATGAAGAG	.	PASS	Atlas-SNP
GBX1	2636	hgsc.bcm.edu	37	7	150846188	150846188	+	Missense_Mutation	SNP	C	C	T	rs11975799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	15	21	0	0.625	0	C|0.979;T|0.021	0.021	strong	.	GBX1	21	.	NM_001098834	exon2	c.G580A	p.A194T	CTGATGCCTCCAG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160673405	160673405	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	3	184	0	0.0205479	0	.	.	none	LY75,NS,carcinoma,-1,1	LY75	151	1	NM_002349	exon30	c.G4292A	p.S1431N	TGAACGCTTGCCA	.	scavenged	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150657173	150657173	+	Silent	SNP	T	T	C	rs56998614	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	34	69	0	0.435897	0	T|0.911;C|0.089	0.089	strong	.	SLC36A3	54	.	NM_001145017	exon11	c.A1317G	p.V439V	GGAGCCTACCAGG	.	PASS	Atlas-SNP
SHISA6	388336	hgsc.bcm.edu	37	17	11461483	11461483	+	Silent	SNP	C	C	T	rs148413919	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	28	61	0	0.411765	0	C|0.994;T|0.006	0.006	strong	.	SHISA6	44	.	NM_207386	exon6	c.C1518T	p.Y506Y	CTCATACGCCACC	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127624905	127624905	+	Missense_Mutation	SNP	T	T	A	rs149071226	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	43	82	0	0.390909	0	T|0.998;A|0.002	0.002	strong	.	FBN2	858	.	NM_001999	exon52	c.A6551T	p.N2184I	TGACCATTTGAAC	.	PASS	Atlas-SNP
ACSM2B	348158	hgsc.bcm.edu	37	16	20554582	20554582	+	Missense_Mutation	SNP	T	T	G	rs9941182	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	110	366	48	0.428016	0.131148	.	.	weak	ACSM2B,NS,carcinoma,-2,1	ACSM2B	121	1	NM_182617	exon12	c.A1284C	p.E428D	GGGATTTTCCTGG	.	scavenged	Atlas-SNP
GNAI1	2770	hgsc.bcm.edu	37	7	79840339	79840339	+	Silent	SNP	C	C	T	rs12721454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	85	137	0	0.586207	0	C|0.935;T|0.065	0.065	strong	.	GNAI1	44	.	NM_002069	exon6	c.C645T	p.F215F	TTGCTTCGAAGGA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228560181	228560181	+	Silent	SNP	G	G	A	rs62640372	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	44	94	0	0.478261	0	G|0.996;A|0.004	0.004	strong	.	OBSCN	2142	.	NM_001271223	exon105	c.G24573A	p.S8191S	CCAGTCGGAGGAG	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	25	0	1	0	G|0.766;A|0.234	0.234	strong	.	CDAN1	70	.	NM_138477	exon2	c.C477T	p.P159P	GCGGCTGGGGCTG	.	PASS	Atlas-SNP
TCN2	6948	hgsc.bcm.edu	37	22	31011350	31011350	+	Missense_Mutation	SNP	C	C	T	rs35838082	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	208	183	0	1	0	C|0.925;T|0.075	0.075	strong	.	TCN2	44	.	NM_000355	exon5	c.C643T	p.R215W	CCTGGTCGGAGAC	.	PASS	Atlas-SNP
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	177	150	0	0.994382	0	C|0.504;T|0.496	0.496	strong	MB_ENST00000447607,caecum,carcinoma,0,2	MB	7	2	NM_203377	exon3	c.G174A	p.A58A	CTCAGACGCCTTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100683156	100683156	+	Missense_Mutation	SNP	C	C	T	rs79046921	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	77	117	1	0.538462	0.00854701	A|0.000;C|0.960;T|0.040	0.040	strong	MUC17,colon,carcinoma,-1,2	MUC17	804	2	NM_001040105	exon3	c.C8459T	p.T2820M	ACCACACGCCAGT	.	scavenged	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	88	154	0	0.54321	0	G|0.705;A|0.295	0.295	strong	.	WDR67	97	.	NM_001145088	exon13	c.G1812A	p.L604L	CCTTCTGATGACT	.	PASS	Atlas-SNP
EPB41L1	2036	hgsc.bcm.edu	37	20	34782171	34782171	+	Silent	SNP	T	T	C	rs2295568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	87	149	0	0.472826	0	T|0.886;C|0.114	0.114	strong	.	EPB41L1	111	.	NM_001258329	exon13	c.T1338C	p.H446H	GAACCATGATGCA	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs78240139		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	561	299	779	0	0.532977	0	G|0.500;C|0.500	0.500	weak	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G1557C	p.K519N	TGCAAAGATTTCC	.	scavenged	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188326955	188326955	+	Missense_Mutation	SNP	A	A	G	rs35417432	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	46	86	0	0.422018	0	A|0.939;G|0.061	0.061	strong	.	LPP	72	.	NM_005578	exon6	c.A436G	p.T146A	AGCTCCACTGGTT	.	PASS	Atlas-SNP
HDAC8	55869	hgsc.bcm.edu	37	X	71791912	71791912	+	Silent	SNP	C	C	T	rs11093377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	133	196	0	0.487179	0	C|0.654;0|0.003	.	strong	.	HDAC8	18	.	NM_018486	exon2	c.G159A	p.Q53Q	CCTCATCTGCTTA	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200819	67200819	+	Silent	SNP	C	C	T	rs4930427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	42	0	1	0	A|0.000;C|0.599;T|0.400	0.400	strong	RPS6KB2_ENST00000312629,NS,carcinoma,0,1	RPS6KB2	92	1	NM_003952	exon10	c.C807T	p.F269F	GCCCTTCACCGCA	.	PASS	Atlas-SNP
C10orf12	26148	hgsc.bcm.edu	37	10	98742088	98742088	+	Missense_Mutation	SNP	T	T	C	rs7082522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	36	96	0	0.439024	0	T|0.994;C|0.006	0.006	strong	.	C10orf12	94	.	NM_015652	exon1	c.T941C	p.L314P	CTCACCTTCCTGA	.	PASS	Atlas-SNP
AP1G2	8906	hgsc.bcm.edu	37	14	24033027	24033027	+	Missense_Mutation	SNP	G	G	A	rs12897422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	48	113	0	0.457143	0	G|0.919;A|0.081	0.081	strong	.	AP1G2	75	.	NM_003917	exon12	c.C1130T	p.S377F	ACATTGGAGCTAT	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184299167	184299167	+	Silent	SNP	T	T	C	rs1138510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	305	229	1	0.996732	0.00436681	T|0.632;C|0.368	0.368	strong	.	EPHB3	114	.	NM_004443	exon15	c.T2859C	p.S953S	TGCATCTTTTGAC	.	PASS	Atlas-SNP
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	72	196	0	0.45283	0	A|0.814;G|0.186	0.186	strong	.	SP1	57	.	NM_138473	exon3	c.A1440G	p.Q480Q	AGCCCAAACAATC	.	PASS	Atlas-SNP
NUP155	9631	hgsc.bcm.edu	37	5	37310765	37310765	+	Silent	SNP	A	A	G	rs53429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	54	112	0	0.465517	0	A|0.962;C|0.000	.	strong	.	NUP155	116	.	NM_153485	exon23	c.T2517C	p.A839A	AAGAGAAGCAATT	.	PASS	Atlas-SNP
TDP2	51567	hgsc.bcm.edu	37	6	24653273	24653273	+	Missense_Mutation	SNP	G	G	C	rs2294689	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	91	0	0.486842	0	G|0.830;C|0.170	0.170	strong	.	TDP2	29	.	NM_016614	exon6	c.C745G	p.Q249E	CCTCTTGCATTTT	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7033037	7033037	+	Silent	SNP	G	G	A	rs621993	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	37	0	1	0	G|0.542;A|0.458	0.458	strong	LAMA1,brain,glioma,-1,1	LAMA1	458	1	NM_005559	exon15	c.C2109T	p.A703A	ATCAGCGGCCACC	.	PASS	Atlas-SNP
C22orf42	150297	hgsc.bcm.edu	37	22	32554985	32554985	+	Missense_Mutation	SNP	A	A	G	rs5998267	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	296	275	0	0.996633	0	A|0.432;G|0.568	0.568	strong	.	C22orf42	37	.	NM_001010859	exon1	c.T218C	p.L73P	ATCTTCAGCATCT	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152511874	152511874	+	Missense_Mutation	SNP	A	A	C	rs78733601	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	8	30	0	0.296296	0	A|0.970;C|0.030	0.030	strong	.	NEB	1697	.	NM_004543	exon51	c.T6717G	p.I2239M	CCAATCAATGGTG	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178262683	178262683	+	Silent	SNP	T	T	C	rs17676249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	28	52	0	0.459016	0	T|0.826;C|0.174	0.174	strong	.	NEIL3	89	.	NM_018248	exon6	c.T756C	p.P252P	GCGTCCTAATTGT	.	PASS	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	129	128	0	1	0	C|0.449;T|0.551	0.551	strong	OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	NM_145798	exon23	c.G2430A	p.T810T	GCTATCCGTCTGC	.	PASS	Atlas-SNP
DOCK4	9732	hgsc.bcm.edu	37	7	111512589	111512589	+	Silent	SNP	G	G	A	rs10257550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	61	0	0.439394	0	G|0.930;A|0.070	0.070	strong	.	DOCK4	365	.	NM_014705	exon18	c.C1776T	p.T592T	TGGGTGGGTTCTC	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	988894	988894	+	Silent	SNP	G	G	A	rs9804992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	82	129	0	0.460674	0	G|0.860;A|0.140	0.140	strong	WNK1,NS,carcinoma,0,2	WNK1	403	2	NM_018979	exon11	c.G2529A	p.Q843Q	CTCTCAGATTCCC	.	PASS	Atlas-SNP
SREBF2	6721	hgsc.bcm.edu	37	22	42276742	42276742	+	Missense_Mutation	SNP	G	G	C	rs2228314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	112	220	0	0.497778	0	G|0.627;C|0.373	0.373	strong	SREBF2,NS,carcinoma,+1,1	SREBF2	99	1	NM_004599	exon10	c.G1784C	p.G595A	CTGCCGGCAACCT	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	37	19	42863035	42863035	+	Missense_Mutation	SNP	A	A	G	rs1206038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	123	251	0	0.514644	0	A|0.900;G|0.100	0.100	strong	.	MEGF8	358	.	NM_001271938	exon30	c.A5272G	p.K1758E	AGGAAGAAGATGG	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17084066	17084066	+	Missense_Mutation	SNP	G	G	A	rs201206414		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1552	122	1264	1	0.0786082	0.000791139	G|0.999;A|0.001	0.001	weak	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon14	c.C1855T	p.R619W	TCTCCCGCACATG	.	scavenged	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16354590	16354590	+	Missense_Mutation	SNP	A	A	T	rs12126269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	106	220	0	0.447257	0	A|0.809;T|0.191	0.191	strong	.	CLCNKA	56	.	NM_004070	exon10	c.A944T	p.Y315F	ATCGGTACAGCTC	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	83	86	0	0.988095	0	T|0.741;C|0.259	0.259	strong	EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	NM_001205301	exon6	c.T685C	p.W229R	CGCAGCTGGCCCA	.	PASS	Atlas-SNP
PPP1R10	5514	hgsc.bcm.edu	37	6	30570374	30570374	+	Silent	SNP	G	G	A	rs35689098	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	13	20	0	0.5	0	G|0.970;A|0.030	0.030	strong	.	PPP1R10	60	.	NM_002714	exon19	c.C2052T	p.G684G	AGGGTCGCCCGGG	.	PASS	Atlas-SNP
CHCHD10	400916	hgsc.bcm.edu	37	22	24108438	24108438	+	Missense_Mutation	SNP	G	G	T	rs111677724	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	65	0	0.5	0	G|0.957;T|0.043	0.043	strong	.	CHCHD10	4	.	NM_213720	exon3	c.C286A	p.P96T	GCAGGGGCTGGGG	.	PASS	Atlas-SNP
CDA	978	hgsc.bcm.edu	37	1	20945055	20945055	+	Silent	SNP	C	C	T	rs1048977	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	39	94	0	0.414894	0	C|0.671;T|0.329	0.329	strong	CDA,NS,carcinoma,0,1	CDA	19	1	NM_001785	exon4	c.C435T	p.T145T	GAAGACCCAGTGA	.	PASS	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	37	22	19121872	19121872	+	Missense_Mutation	SNP	G	G	A	rs712965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	351	165	346	0	0.470085	0	G|0.894;T|0.002	.	strong	.	DGCR14	43	.	NM_022719	exon10	c.C1268T	p.A423V	GAGCGTGCTGGGG	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139576736	139576736	+	Missense_Mutation	SNP	C	C	T	rs17068451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	106	0	1	0	C|0.754;T|0.246	0.246	strong	.	TXLNB	96	.	NM_153235	exon7	c.G1042A	p.V348M	TCAGCACTTTCGC	.	PASS	Atlas-SNP
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31691993	31691993	+	Missense_Mutation	SNP	C	C	T	rs77018583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	77	106	0	0.513333	0	C|0.989;T|0.011	0.011	strong	KRTAP26-1,colon,carcinoma,+1,1	KRTAP26-1	58	1	NM_203405	exon1	c.G361A	p.G121S	GACAGCCGCTGGA	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66364804	66364804	+	Missense_Mutation	SNP	T	T	C	rs1558878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	46	129	0	0.425926	0	T|0.602;C|0.398	0.398	strong	.	ARSG	55	.	NM_001267727	exon7	c.T820C	p.W274R	GGGCTCTGGGAGA	.	PASS	Atlas-SNP
G6PD	2539	hgsc.bcm.edu	37	X	153763492	153763492	+	Missense_Mutation	SNP	T	T	C	rs1050829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	78	184	0	0.331915	0	T|0.844;0|0.051	.	strong	.	G6PD	73	.	NM_000402	exon5	c.A466G	p.N156D	GGGCATTCATGTG	.	PASS	Atlas-SNP
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458476	39458476	+	Missense_Mutation	SNP	A	A	T	rs1001191	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	118	0	0.439024	0	A|0.766;T|0.234	0.234	strong	.	KRTAP29-1	2	.	NM_001257309	exon1	c.T628A	p.C210S	TATAGCAGATGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515126	195515126	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	37	167	0	0.104816	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.G3325T	p.D1109Y	AAGTGTCGGTGAC	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	69	0	0.486842	0	G|0.795;A|0.205	0.205	strong	.	DHRS4	22	.	NM_021004	exon1	c.G10A	p.A4T	CACAAGGCGGGGC	.	PASS	Atlas-SNP
CLDN16	10686	hgsc.bcm.edu	37	3	190106074	190106074	+	Missense_Mutation	SNP	G	G	C	rs3214506	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	106	205	0	0.443515	0	G|0.753;C|0.247	0.247	strong	.	CLDN16	59	.	NM_006580	exon1	c.G166C	p.A56P	GCCAGGGCTGGTG	.	PASS	Atlas-SNP
CYP11B1	1584	hgsc.bcm.edu	37	8	143957163	143957163	+	Silent	SNP	C	C	G	rs6403	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	148	237	0	0.554307	0	C|0.948;G|0.052	0.052	strong	.	CYP11B1	128	.	NM_000497	exon6	c.G1086C	p.L362L	CAAGGGCAGCTCG	.	PASS	Atlas-SNP
GRB10	2887	hgsc.bcm.edu	37	7	50672017	50672017	+	Silent	SNP	G	G	A	rs200886440	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	63	115	0	0.473684	0	G|0.999;A|0.001	0.001	strong	.	GRB10	155	.	NM_005311	exon13	c.C1447T	p.L483L	TACTTAGGGTAGA	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	37	6	46976924	46976924	+	Silent	SNP	G	G	A	rs45511696	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	69	126	0	0.511111	0	G|0.952;A|0.048	0.048	strong	.	GPR110	102	.	NM_153840	exon11	c.C2247T	p.V749V	TGCAGGGACAACA	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11289129	11289129	+	Missense_Mutation	SNP	G	G	A	rs114414326	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	39	64	0	0.4875	0	G|0.990;A|0.010	0.010	strong	.	KANK2	47	.	NM_015493	exon4	c.C1436T	p.P479L	CCTGGAGGGGAGG	.	PASS	Atlas-SNP
PSEN2	5664	hgsc.bcm.edu	37	1	227076671	227076671	+	Silent	SNP	T	T	C	rs61730652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	141	241	0	0.477966	0	T|0.969;C|0.031	0.031	strong	.	PSEN2	55	.	NM_012486	exon8	c.T708C	p.S236S	GATCAGTGCGCTC	.	PASS	Atlas-SNP
GAPVD1	26130	hgsc.bcm.edu	37	9	128099784	128099784	+	Missense_Mutation	SNP	C	C	T	rs62637637	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	33	119	0	0.242647	0	C|0.993;T|0.007	0.007	strong	.	GAPVD1	124	.	NM_015635	exon16	c.C2872T	p.P958S	CTCCCTCCAGCTG	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16979661	16979661	+	Silent	SNP	T	T	C	rs1801234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	40	95	0	0.571429	0	T|0.475;C|0.525	0.525	strong	.	CUBN	515	.	NM_001081	exon39	c.A5856G	p.S1952S	CTTCCCTGAGATT	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16338814	16338814	+	Missense_Mutation	SNP	T	T	C	rs9975169	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	118	223	1	0.508621	0.00448431	T|0.973;C|0.027	0.027	strong	.	NRIP1	103	.	NM_003489	exon4	c.A1700G	p.N567S	GAGAGATTGATGG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931151	157931151	+	Missense_Mutation	SNP	C	C	G	rs150508509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	35	93	0	0.346535	0	C|0.981;G|0.019	0.019	strong	.	PTPRN2	243	.	NM_130843	exon7	c.G967C	p.G323R	TCAGGCCCCTCAC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2959172	2959172	+	Silent	SNP	G	G	A	rs3735126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	99	220	0	0.507692	0	G|0.880;A|0.120	0.120	strong	.	CARD11	339	.	NM_032415	exon18	c.C2344T	p.L782L	TGTTCAGGTTCAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179598399	179598399	+	Silent	SNP	C	C	T	rs72648932	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	82	125	0	0.535948	0	C|0.980;T|0.020	0.020	strong	.	TTN	18412	.	NM_001267550	exon53	c.G15717A	p.T5239T	CAGGCACGTGTAT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	61	118	0	0.508333	0	G|0.737;C|0.263	0.263	strong	.	EPPK1	199	.	NM_031308	exon1	c.C6241G	p.L2081V	ACAGCAGCCAGCC	.	PASS	Atlas-SNP
SLC14A1	6563	hgsc.bcm.edu	37	18	43307246	43307246	+	Missense_Mutation	SNP	C	C	T	rs11877062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	143	1	1	0.00699301	C|0.593;T|0.407	0.407	strong	.	SLC14A1	84	.	NM_001146037	exon1	c.C10T	p.R4W	AATGGACGGTCTT	.	PASS	Atlas-SNP
TRIM49B	283116	hgsc.bcm.edu	37	11	49053390	49053390	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	4	308	0	0.0138889	0	.	.	none	TRIM49B,NS,NS,-1,1	TRIM49B	27	1	NM_001206626	exon1	c.T239C	p.V80A	GAAAAGTCAGTCT	.	scavenged	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71654175	71654175	+	Missense_Mutation	SNP	G	G	A	rs1804020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	125	0	1	0	G|0.710;A|0.290	0.290	strong	ZNF638,tonsil,carcinoma,0,1	ZNF638	179	1	NM_014497	exon24	c.G5176A	p.V1726M	TCTCAGGTGCCCG	.	PASS	Atlas-SNP
ZNF510	22869	hgsc.bcm.edu	37	9	99522508	99522508	+	Missense_Mutation	SNP	C	C	T	rs61731162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	67	116	0	0.62037	0	C|0.973;T|0.027	0.027	strong	.	ZNF510	59	.	NM_014930	exon6	c.G604A	p.G202S	CGCAACCTATTTT	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56483852	56483852	+	Silent	SNP	T	T	G	rs2230863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	103	212	0	0.502439	0	T|0.957;G|0.043	0.043	strong	.	DST	1427	.	NM_001723	exon23	c.A4980C	p.V1660V	TTCACTTACCAAA	.	PASS	Atlas-SNP
LIPM	340654	hgsc.bcm.edu	37	10	90575251	90575251	+	Silent	SNP	T	T	C	rs61737049	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	46	98	0	0.4	0	T|0.985;C|0.015	0.015	strong	.	LIPM	17	.	NM_001128215	exon6	c.T849C	p.N283N	CAACAATATGAAC	.	PASS	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	37	X	65427124	65427124	+	Silent	SNP	A	A	G	rs809363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	124	0	1	0	A|0.687;0|0.002	.	strong	.	HEPH	224	.	NM_138737	exon14	c.A2541G	p.T847T	TGGTACATTCAGG	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7951878	7951878	+	Missense_Mutation	SNP	A	A	G	rs7225107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	30	49	0	0.416667	0	A|0.907;G|0.093	0.093	strong	ALOX15B,NS,carcinoma,-2,2	ALOX15B	66	2	NM_001141	exon14	c.A2026G	p.I676V	GTCTCCATCTAAA	.	PASS	Atlas-SNP
KIAA1024	23251	hgsc.bcm.edu	37	15	79749447	79749447	+	Missense_Mutation	SNP	G	G	T	rs11634652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	99	0	0.439024	0	G|0.866;T|0.134	0.134	strong	.	KIAA1024	146	.	NM_015206	exon2	c.G958T	p.V320F	TCCCCGGTTCCTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284576	152284576	+	Missense_Mutation	SNP	C	C	A	rs143382793	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	745	145	591	1	0.194631	0.00169205	C|0.993;A|0.007	0.007	strong	.	FLG	900	.	NM_002016	exon3	c.G2786T	p.G929V	CCCTGGCCTGCCT	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	27	63	0	0.519231	0	G|0.696;A|0.304	0.304	strong	TECPR1,NS,carcinoma,0,2	TECPR1	77	2	NM_015395	exon5	c.C420T	p.Y140Y	GATGGCGTACGTC	.	PASS	Atlas-SNP
TINF2	26277	hgsc.bcm.edu	37	14	24709351	24709351	+	Silent	SNP	C	C	T	rs10141326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	64	125	0	0.520325	0	C|0.944;T|0.056	0.056	strong	.	TINF2	61	.	NM_001099274	exon8	c.G1140A	p.P380P	CAGAGACGGAGGA	.	PASS	Atlas-SNP
FASLG	356	hgsc.bcm.edu	37	1	172628521	172628521	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	2	164	0	0.0116959	0	.	.	none	FASLG,colon,carcinoma,0,2	FASLG	44	2	NM_000639	exon1	c.G180A	p.P60P	GCCGCCGCCACCA	.	scavenged	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155486535	155486535	+	Missense_Mutation	SNP	A	A	G	rs62621836	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	59	96	0	0.517544	0	A|0.979;G|0.021	0.021	strong	.	TIAM2	161	.	NM_012454	exon8	c.A2353G	p.I785V	CCTTCTATAACTC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74287204	74287204	+	Missense_Mutation	SNP	C	C	G	rs2279052	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	51	107	0	0.5	0	C|0.613;G|0.387	0.387	strong	.	QRICH2	143	.	NM_032134	exon4	c.G3106C	p.E1036Q	TGAGCTCTCCCAT	.	PASS	Atlas-SNP
ECM2	1842	hgsc.bcm.edu	37	9	95267938	95267938	+	Silent	SNP	T	T	C	rs35161698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	62	117	0	0.626263	0	T|0.978;C|0.022	0.022	strong	.	ECM2	147	.	NM_001393	exon7	c.A1341G	p.G447G	ATTGTTTCCTTCC	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151127074	151127074	+	Missense_Mutation	SNP	G	G	A	rs78970280	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	32	81	0	0.450704	0	G|0.993;A|0.007	0.007	strong	MED12L,colon,carcinoma,-1,1	MED12L	271	1	NM_053002	exon38	c.G5759A	p.R1920Q	AAGCACGGCCCTC	.	PASS	Atlas-SNP
MINPP1	9562	hgsc.bcm.edu	37	10	89312046	89312046	+	Silent	SNP	T	T	C	rs2233169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	61	160	0	0.445255	0	T|0.975;C|0.025	0.025	strong	.	MINPP1	22	.	NM_004897	exon5	c.T1275C	p.A425A	AAATGCTAAGACT	.	PASS	Atlas-SNP
COL17A1	1308	hgsc.bcm.edu	37	10	105824332	105824332	+	Silent	SNP	C	C	T	rs149012179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	79	141	0	0.50641	0	C|0.993;T|0.007	0.007	strong	.	COL17A1	149	.	NM_000494	exon10	c.G630A	p.T210T	CAGGATCGTTGCA	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	155059	155059	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	3	54	0	0.0422535	0	.	.	none	PLEKHG4B_ENST00000283426,NS,carcinoma,-2,2	PLEKHG4B	167	2	NM_052909	exon6	c.G994A	p.D332N	GACCTCGACGGCT	.	scavenged	Atlas-SNP
KREMEN2	79412	hgsc.bcm.edu	37	16	3017854	3017854	+	Missense_Mutation	SNP	G	G	C	rs11866302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	45	130	0	0.387931	0	G|0.891;C|0.109	0.109	strong	.	KREMEN2	13	.	NM_172229	exon9	c.G1222C	p.A408P	CTGGGGGCTTCCA	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16262404	16262404	+	Silent	SNP	C	C	T	rs61749277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	49	100	0	0.453704	0	C|0.902;G|0.000;T|0.098	0.098	strong	.	SPEN	374	.	NM_015001	exon11	c.C9669T	p.S3223S	AGCCAGCAAGGCC	.	PASS	Atlas-SNP
STOM	2040	hgsc.bcm.edu	37	9	124110368	124110368	+	Silent	SNP	C	C	T	rs115702601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	55	123	0	0.55	0	C|0.996;T|0.004	0.004	strong	.	STOM	15	.	NM_001270526	exon6	c.G585A	p.K195K	CACATCCTTAATT	.	PASS	Atlas-SNP
TAF5L	27097	hgsc.bcm.edu	37	1	229750089	229750089	+	Silent	SNP	T	T	C	rs144626601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	65	136	0	0.416667	0	T|0.997;C|0.003	0.003	strong	.	TAF5L	76	.	NM_001025247	exon2	c.A141G	p.T47T	ATTACCTGTTAGA	.	PASS	Atlas-SNP
ALG1L2	644974	hgsc.bcm.edu	37	3	129810973	129810973	+	Missense_Mutation	SNP	G	G	A	rs114865400	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	556	273	493	0	0.491007	0	G|0.968;A|0.032	0.032	strong	.	.	.	.	NM_001136152	exon3	c.G161A	p.R54Q	CAGAGCGGTCGGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179659912	179659912	+	Missense_Mutation	SNP	G	G	A	rs16866538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	52	81	0	0.58427	0	G|0.845;A|0.155	0.155	strong	TTN_ENST00000360870,NS,carcinoma,+1,16	TTN	18412	16	NM_001267550	exon7	c.C982T	p.R328C	TCTTACGCATGAG	.	PASS	Atlas-SNP
WNT2B	7482	hgsc.bcm.edu	37	1	113063125	113063125	+	Silent	SNP	A	A	G	rs910697	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	52	109	0	0.485981	0	A|0.500;C|0.000;G|0.499;T|0.001	0.499	strong	.	WNT2B	51	.	NM_024494	exon5	c.A1170G	p.Q390Q	GGACCAAACCTGA	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119445092	119445092	+	Missense_Mutation	SNP	T	T	A	rs9817771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	56	98	0	0.504505	0	T|0.984;A|0.016	0.016	strong	.	.	.	.	NM_033364	exon7	c.T757A	p.S253T	GAAGCCTCTCTCC	.	PASS	Atlas-SNP
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	57	123	0	0.463415	0	G|0.742;A|0.258	0.258	strong	.	DLG4	110	.	NM_001365	exon12	c.C1296T	p.I432I	CTGAGCGATGATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511937	195511937	+	Missense_Mutation	SNP	C	C	T	rs201509113	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	355	58	473	0	0.16338	0	C|0.953;T|0.047	0.047	strong	.	MUC4	1505	.	NM_018406	exon2	c.G6514A	p.G2172S	CGTGACCTGTGGA	.	PASS	Atlas-SNP
THEM5	284486	hgsc.bcm.edu	37	1	151825991	151825991	+	Silent	SNP	G	G	T	rs7556386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	98	0	1	0	G|0.330;T|0.670	0.670	strong	.	THEM5	41	.	NM_182578	exon1	c.C51A	p.G17G	AAGAAGGCCTCTG	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42729508	42729508	+	Silent	SNP	G	G	A	rs4924677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	137	224	1	0.503676	0.00446429	G|0.933;A|0.067	0.067	strong	.	ZFP106	117	.	NM_022473	exon10	c.C4599T	p.A1533A	ATTTACGGCAGCT	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	705795	705795	+	Silent	SNP	C	C	T	rs12599798	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	24	57	0	0.5	0	C|0.785;T|0.215	0.215	strong	.	WDR90	107	.	NM_145294	exon17	c.C1872T	p.S624S	CAGCAGCCTCAGC	.	PASS	Atlas-SNP
GKN2	200504	hgsc.bcm.edu	37	2	69172570	69172570	+	Missense_Mutation	SNP	G	G	A	rs73935451	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	85	138	0	0.559211	0	G|0.983;A|0.017	0.017	strong	.	GKN2	28	.	NM_182536	exon6	c.C485T	p.A162V	CCTCCAGCACCGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515257	195515257	+	Missense_Mutation	SNP	G	G	T	rs71187744	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	62	171	0	0.233962	0	G|0.500;A|0.500	.	alt	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C3194A	p.A1065E	GTGGATGCTGAGG	.	PASS	Atlas-SNP
SAMD13	148418	hgsc.bcm.edu	37	1	84791374	84791374	+	Silent	SNP	C	C	T	rs55638637	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	108	236	0	0.459574	0	C|0.962;T|0.038	0.038	strong	.	SAMD13	5	.	NM_001010971	exon3	c.C150T	p.V50V	GGATGTCGTCAAT	.	PASS	Atlas-SNP
SUMF1	285362	hgsc.bcm.edu	37	3	4403837	4403837	+	Silent	SNP	A	A	G	rs2633852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	93	0	1	0	A|0.307;G|0.693	0.693	strong	.	SUMF1	23	.	NM_182760	exon9	c.T1116C	p.T372T	GTCCATAGTGGGC	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377086	49377086	+	Missense_Mutation	SNP	T	T	C	rs611251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	31	77	0	0.553571	0	T|0.735;G|0.004	.	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.T596C	p.V199A	AAGCTGTAAAGAA	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	37	14	101005236	101005236	+	Silent	SNP	A	A	G	rs12892571	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	18	25	0	1	0	A|0.415;G|0.585	0.585	strong	.	BEGAIN	32	.	NM_020836	exon7	c.T852C	p.H284H	GGCCTCATGCTGG	.	PASS	Atlas-SNP
EVC2	132884	hgsc.bcm.edu	37	4	5624670	5624670	+	Missense_Mutation	SNP	T	T	C	rs730469	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	74	156	0	0.440476	0	T|0.515;C|0.485	0.485	strong	EVC2,colon,carcinoma,+2,1	EVC2	202	1	NM_147127	exon14	c.A2095G	p.T699A	CAACCGTTCGGAA	.	PASS	Atlas-SNP
CCDC107	203260	hgsc.bcm.edu	37	9	35660901	35660901	+	Missense_Mutation	SNP	C	C	T	rs2275420	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	81	0	1	0	C|0.831;T|0.169	0.169	strong	.	CCDC107	12	.	NM_174923	exon5	c.C569T	p.S190F	AAGTCTCTGAAAC	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31122500	31122500	+	Missense_Mutation	SNP	G	G	A	rs130065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	43	89	0	0.518072	0	G|0.836;A|0.164	0.164	strong	.	CCHCR1	68	.	NM_001105564	exon4	c.C574T	p.R192W	CCAGCCGCCGCAG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128341904	128341904	+	Silent	SNP	G	G	A	rs61743462	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	53	92	0	0.445378	0	G|0.993;A|0.007	0.007	strong	.	MYO7B	359	.	NM_001080527	exon13	c.G1551A	p.P517P	CTTCCCGCAGGTG	.	PASS	Atlas-SNP
APH1B	83464	hgsc.bcm.edu	37	15	63597857	63597857	+	Missense_Mutation	SNP	T	T	G	rs1047552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	76	0	0.489583	0	G|0.065;T|0.935	0.065	strong	APH1B,NS,carcinoma,0,1	APH1B	27	1	NM_031301	exon6	c.T651G	p.F217L	AGCATTTATAATC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20837033	20837033	+	Missense_Mutation	SNP	T	T	C	rs2104978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	81	148	0	0.409091	0	T|0.957;C|0.043	0.043	strong	.	TEP1	224	.	NM_007110	exon54	c.A7685G	p.H2562R	AGCACATGGAGGG	.	PASS	Atlas-SNP
PTPN3	5774	hgsc.bcm.edu	37	9	112219474	112219474	+	Missense_Mutation	SNP	C	C	G	rs3793524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	91	123	0	0.705426	0	C|0.619;G|0.380	0.380	strong	.	PTPN3	106	.	NM_001145368	exon4	c.G268C	p.A90P	TGATGGCTTTGCT	.	PASS	Atlas-SNP
SAMD15	161394	hgsc.bcm.edu	37	14	77843920	77843920	+	Silent	SNP	A	A	G	rs61729313	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	54	97	0	0.529412	0	A|0.932;G|0.068	0.068	strong	.	SAMD15	60	.	NM_001010860	exon1	c.A159G	p.Q53Q	TTACCAAGAGCCA	.	PASS	Atlas-SNP
MED7	9443	hgsc.bcm.edu	37	5	156565839	156565839	+	Missense_Mutation	SNP	C	C	T	rs151231455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	319	149	348	1	0.467085	0.00287356	C|0.991;T|0.009	0.009	strong	.	MED7	18	.	NM_001100816	exon2	c.G604A	p.E202K	GATGTTCATTCTG	.	PASS	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168180081	168180081	+	Missense_Mutation	SNP	C	C	T	rs10036727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	70	154	0	0.44586	0	C|0.423;N|0.000	.	strong	.	SLIT3	224	.	NM_001271946	exon18	c.G1852A	p.G618S	CACAGCCGATCAA	.	PASS	Atlas-SNP
THTPA	79178	hgsc.bcm.edu	37	14	24026174	24026174	+	Missense_Mutation	SNP	G	G	T	rs141465409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	115	201	0	0.534884	0	G|0.999;T|0.001	0.001	strong	.	THTPA	11	.	NM_001256321	exon2	c.G208T	p.A70S	GGAGCAGCAGGTG	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117079687	117079687	+	Silent	SNP	G	G	A	rs148329047	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	92	393	0	0.373984	0	G|0.991;A|0.009	0.009	strong	.	PCSK7	59	.	NM_004716	exon13	c.C1617T	p.R539R	GCTGCCGCGCCGT	.	PASS	Atlas-SNP
PRSS41	360226	hgsc.bcm.edu	37	16	2849542	2849542	+	Silent	SNP	C	C	T	rs6500613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	35	77	0	0.4375	0	C|0.978;T|0.022	0.022	strong	.	.	.	.	NM_001135086	exon3	c.C552T	p.T184T	GGTGACCGGCTGG	.	PASS	Atlas-SNP
ASB15	142685	hgsc.bcm.edu	37	7	123269280	123269280	+	Missense_Mutation	SNP	T	T	C	rs73718442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	66	129	0	0.511628	0	T|0.992;C|0.008	0.008	strong	.	ASB15	94	.	NM_080928	exon8	c.T1232C	p.M411T	ATTTTATGCATGT	.	PASS	Atlas-SNP
CLRN3	119467	hgsc.bcm.edu	37	10	129676520	129676520	+	Missense_Mutation	SNP	T	T	C	rs34656572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	69	141	0	0.507353	0	T|0.989;C|0.011	0.011	strong	.	CLRN3	27	.	NM_152311	exon3	c.A574G	p.I192V	TGACTATATTTAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11654	11654	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	7	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.A895G	p.T299A	GTAGTAACAGCCA	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5352731	5352731	+	Silent	SNP	G	G	A	rs114222264	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	8	20	0	0.347826	0	G|0.964;A|0.036	0.036	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7791T	p.T2597T	GCCCCCGGTGCCG	.	PASS	Atlas-SNP
PPFIA1	8500	hgsc.bcm.edu	37	11	70185325	70185325	+	Silent	SNP	C	C	T	rs1061328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	199	190	0	0.995	0	C|0.776;T|0.224	0.224	strong	.	PPFIA1	114	.	NM_177423	exon14	c.C1620T	p.D540D	GGCAGACGGCCAC	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3848013	3848013	+	Silent	SNP	A	A	C	rs1800911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	117	0	1	0	A|0.610;C|0.390	0.390	strong	.	ATP2A3	148	.	NM_174956	exon10	c.T1272G	p.A424A	GTCCAGAGCCGAG	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43154064	43154064	+	Silent	SNP	C	C	T	rs79828871	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	58	118	0	0.414286	0	C|0.967;T|0.033	0.033	strong	.	CUL9	248	.	NM_015089	exon4	c.C1122T	p.G374G	TAGTGGCTATGGA	.	PASS	Atlas-SNP
THADA	63892	hgsc.bcm.edu	37	2	43518843	43518843	+	Missense_Mutation	SNP	A	A	G	rs17030648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	118	204	1	0.553991	0.00490196	A|0.958;G|0.042	0.042	strong	.	THADA	131	.	NM_001083953	exon34	c.T5002C	p.C1668R	CCACACATGTCTG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145006866	145006866	+	Silent	SNP	G	G	A	rs185978075	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	39	0	0.482143	0	G|0.994;A|0.006	0.006	strong	.	PLEC	1144	.	NM_201380	exon15	c.C2163T	p.P721P	GGTGGCGGGGGAG	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24802245	24802245	+	Missense_Mutation	SNP	T	T	G	rs112027699	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	45	0	0.48	0	T|0.999;G|0.001	0.001	strong	.	TNRC6A	171	.	NM_014494	exon6	c.T2282G	p.F761C	AGACTTTTAACTC	.	PASS	Atlas-SNP
COLEC12	81035	hgsc.bcm.edu	37	18	334742	334742	+	Missense_Mutation	SNP	C	C	T	rs2305027	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	53	103	0	0.360544	0	C|0.591;T|0.409	0.409	strong	.	COLEC12	121	.	NM_130386	exon6	c.G1816A	p.G606S	ACTTACCATTGTC	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26700344	26700344	+	Silent	SNP	G	G	C	rs150900623	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	39	75	0	0.433333	0	G|0.994;C|0.006	0.006	strong	.	SLC5A12	134	.	NM_178498	exon13	c.C1494G	p.T498T	GTACCAGGTATCA	.	PASS	Atlas-SNP
UPF1	5976	hgsc.bcm.edu	37	19	18958562	18958562	+	Silent	SNP	A	A	T	rs73526913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	70	146	0	0.466667	0	A|0.991;T|0.009	0.009	strong	.	UPF1	88	.	NM_002911	exon3	c.A381T	p.G127G	CTGTGGAATACAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511214	195511214	+	Missense_Mutation	SNP	G	G	C	rs202190300		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	11	747	0	0.0404412	0	G|0.999;C|0.001	0.001	weak	MUC4_ENST00000463781,NS,carcinoma,+2,3	MUC4	1505	3	NM_018406	exon2	c.C7237G	p.H2413D	TGGCGTGACCTGT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168100280	168100280	+	Missense_Mutation	SNP	G	G	A	rs201184820	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	83	199	0	0.592857	0	.	.	weak	XIRP2,larynx,carcinoma,+1,2	XIRP2	914	2	NM_152381	exon9	c.G2378A	p.R793Q	TTGTCCGAGGAAT	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386301	7386301	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	5	147	0	0.0285714	0	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	NM_001102614	exon2	c.A998C	p.E333A	AGAGGGAAGGGAA	.	scavenged	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56507489	56507489	+	Missense_Mutation	SNP	A	A	G	rs1024196	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	72	153	0	0.45	0	A|0.848;G|0.152	0.152	strong	.	DST	1427	.	NM_001723	exon1	c.T98C	p.L33S	TGAACCAAGAGAA	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818403	55818403	+	Missense_Mutation	SNP	T	T	C	rs35070799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	80	147	0	0.512821	0	T|0.945;C|0.055	0.055	strong	.	FBXO34	61	.	NM_017943	exon2	c.T1295C	p.V432A	ATGCTGTTGATTG	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276876	71276876	+	Silent	SNP	A	A	G	rs12788123	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	24	162	20	0.135593	0.123457	A|0.998;G|0.002	0.002	weak	KRTAP5-10,NS,carcinoma,0,1	KRTAP5-10	37	1	NM_001012710	exon1	c.A243G	p.K81K	CTCCAAAGGGGGC	.	scavenged	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34105084	34105084	+	Silent	SNP	A	A	G	rs16958093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	35	68	0	0.454545	0	A|0.955;G|0.045	0.045	strong	.	RYR3	760	.	NM_001036	exon73	c.A10278G	p.K3426K	TGTAAAATGGCAA	.	PASS	Atlas-SNP
PSG4	5672	hgsc.bcm.edu	37	19	43699336	43699336	+	Missense_Mutation	SNP	T	T	C	rs1058718	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	81	0	1	0	T|0.323;C|0.677	0.677	strong	.	PSG4	129	.	NM_002780	exon4	c.T799G	p.Y267D	AGTTCTTACTCTT	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27692835	27692835	+	Silent	SNP	G	G	A	rs12923861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	18	28	0	0.529412	0	G|0.863;A|0.137	0.137	strong	.	KIAA0556	348	.	NM_015202	exon8	c.G924A	p.Q308Q	AGACCAGGAGAGG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs56319010		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	136	0	1	0	.	.	weak	.	MICA	21	.	NM_001177519	exon4	c.C663T	p.I221I	CAACATCACCGTG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373114	5373114	+	Missense_Mutation	SNP	G	G	A	rs5006888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	246	241	0	0.991935	0	G|0.408;A|0.592	0.592	strong	.	OR51B6	53	.	NM_001004750	exon1	c.G377A	p.S126N	TCCGCAGCCCCTT	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	432	21	370	7	0.0486111	0.0189189	A|0.990;T|0.010	0.010	strong	LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	NM_006847	exon11	c.A1101T	p.R367S	CTCCAGACCTAGG	.	scavenged	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549492	158549492	+	Nonsense_Mutation	SNP	C	C	T	rs863362	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	66	134	0	0.471429	0	C|0.488;N|0.000	.	strong	.	OR10X1	96	.	NM_001004477	exon1	c.G198A	p.W66X	GTCCACCCAAGTT	.	PASS	Atlas-SNP
C15orf40	123207	hgsc.bcm.edu	37	15	83680313	83680313	+	Missense_Mutation	SNP	T	T	G	rs114478510	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	9	37	0	0.3	0	T|0.992;G|0.008	0.008	strong	.	C15orf40	18	.	NM_001160116	exon1	c.A47C	p.N16T	CGAGTATTGGGTG	.	PASS	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	37	3	38052725	38052725	+	Missense_Mutation	SNP	C	C	T	rs933135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	20	62	0	0.338983	0	C|0.958;A|0.000	.	strong	.	PLCD1	87	.	NM_001130964	exon5	c.G833A	p.R278H	TCGTAGCGCTCAA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	85	0	1	0	T|0.817;C|0.183	0.183	strong	.	MDN1	478	.	NM_014611	exon14	c.A1978G	p.I660V	GCTCGATGAGAAC	.	PASS	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	37	19	50099422	50099422	+	Silent	SNP	C	C	T	rs73058052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	38	88	0	0.404255	0	C|0.876;T|0.124	0.124	strong	.	PRR12	157	.	NM_020719	exon4	c.C1830T	p.A610A	TGCAGCCGGAGCA	.	PASS	Atlas-SNP
WDR78	79819	hgsc.bcm.edu	37	1	67327986	67327986	+	Splice_Site	SNP	C	C	G	rs144890566		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	93	196	0	0.522472	0	C|1.000;G|0.000	0.000	weak	.	WDR78	102	.	NM_024763	exon8	c.941-1G>C	.	TTATGCCTAGATA	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24922407	24922407	+	Missense_Mutation	SNP	C	C	T	rs79339610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	41	99	0	0.383178	0	C|0.996;T|0.004	0.004	strong	C15orf2,colon,carcinoma,0,1	.	.	1	NM_018958	exon1	c.C1393T	p.L465F	CTGGCTCTTCCTG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184298663	184298663	+	Silent	SNP	G	G	A	rs11719912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	59	119	0	0.44697	0	G|0.909;A|0.091	0.091	strong	.	EPHB3	114	.	NM_004443	exon13	c.G2535A	p.Q845Q	CAACCAGGATGTG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511746	4511746	+	Missense_Mutation	SNP	A	A	T	rs62115192	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	433	52	261	0	0.120092	0	A|0.333;T|0.667	0.667	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T2184A	p.N728K	GGCCACATTCGCA	.	PASS	Atlas-SNP
HDX	139324	hgsc.bcm.edu	37	X	83591879	83591879	+	Missense_Mutation	SNP	T	T	C	rs77791258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	26	66	0	0.38806	0	T|0.950;C|0.050	0.050	strong	.	HDX	124	.	NM_144657	exon7	c.A1670G	p.N557S	ACTTCATTGGGCT	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373972	27373972	+	Silent	SNP	T	T	C	rs2234900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	30	79	0	0.309278	0	T|0.727;C|0.273	0.273	strong	.	IL4R	70	.	NM_000418	exon11	c.T1299C	p.L433L	CCTTCTTCCACCT	.	PASS	Atlas-SNP
WNK4	65266	hgsc.bcm.edu	37	17	40947320	40947320	+	Missense_Mutation	SNP	C	C	T	rs2290041	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	51	151	0	0.459459	0	C|0.927;T|0.073	0.073	strong	.	WNK4	182	.	NM_032387	exon14	c.C2881T	p.P961S	CCCCTCCCTAGCC	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31599594	31599594	+	Silent	SNP	A	A	G	rs10947220	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	18	37	0	0.473684	0	A|0.949;G|0.050;T|0.000	0.050	strong	PRRC2A,NS,neuroblastoma,0,1	PRRC2A	152	1	NM_004638	exon16	c.A3144G	p.G1048G	GCGGGGAGCCCGA	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50954850	50954850	+	Silent	SNP	G	G	A	rs75974530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	66	114	0	0.52381	0	G|0.976;A|0.024	0.024	strong	.	OGDHL	149	.	NM_018245	exon10	c.C1242T	p.S414S	CAGGTCGCTCAGG	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	93	195	0	0.455882	0	C|0.386;A|0.614	0.614	strong	SYNE2,NS,carcinoma,0,1	SYNE2	577	1	NM_182914	exon84	c.C15556A	p.L5186M	AACTGGCTGGAAG	.	PASS	Atlas-SNP
PTPRN	5798	hgsc.bcm.edu	37	2	220164886	220164886	+	Missense_Mutation	SNP	A	A	C	rs35314717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	53	73	0	0.595506	0	A|0.966;C|0.034	0.034	strong	.	PTPRN	138	.	NM_002846	exon9	c.T1257G	p.S419R	GACTTCACTGGAG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505204	228505204	+	Missense_Mutation	SNP	G	G	A	rs4653942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	196	208	0	0.989899	0	G|0.671;A|0.329	0.329	strong	.	OBSCN	2142	.	NM_001271223	exon63	c.G16472A	p.R5491H	TGGCTCGCAGCAG	.	PASS	Atlas-SNP
FKTN	2218	hgsc.bcm.edu	37	9	108366734	108366734	+	Missense_Mutation	SNP	G	G	A	rs34787999	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	27	66	0	0.509434	0	G|0.755;A|0.245	0.245	strong	.	FKTN	47	.	NM_006731	exon5	c.G608A	p.R203Q	CCTTCCGAAAGTT	.	PASS	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	37	3	10420087	10420087	+	Silent	SNP	T	T	C	rs751122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	20	45	0	0.454545	0	T|0.596;C|0.404	0.404	strong	.	ATP2B2	304	.	NM_001001331	exon10	c.A1050G	p.Q350Q	GTCCTGTTGTTTG	.	PASS	Atlas-SNP
OC90	729330	hgsc.bcm.edu	37	8	133044172	133044172	+	Silent	SNP	G	G	A	rs6989686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	65	130	0	0.451389	0	G|0.994;A|0.006	0.006	strong	.	OC90	163	.	NM_001080399	exon12	c.C987T	p.Y329Y	TCCACAGTAACAG	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50718941	50718941	+	Silent	SNP	C	C	T	rs73891209	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	11	22	0	0.37931	0	C|0.976;G|0.000;T|0.024	0.024	strong	.	PLXNB2	172	.	NM_012401	exon25	c.G4152A	p.K1384K	GGGGTTCTTGGCC	.	PASS	Atlas-SNP
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	11	26	0	0.407407	0	A|0.741;G|0.259	0.259	strong	TRIM55,NS,carcinoma,0,1	TRIM55	91	1	NM_184086	exon8	c.A1028G	p.K343R	GAGAAAAAGAAGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100675367	100675367	+	Missense_Mutation	SNP	A	A	G	rs116801454	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	46	99	0	0.429907	0	A|0.987;G|0.013	0.013	strong	.	MUC17	804	.	NM_001040105	exon3	c.A670G	p.S224G	CCTGCCAGCACCA	.	PASS	Atlas-SNP
CCDC11	220136	hgsc.bcm.edu	37	18	47788535	47788535	+	Missense_Mutation	SNP	G	G	A	rs138060809	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	57	98	0	0.537736	0	G|0.999;A|0.001	0.001	strong	.	CCDC11	59	.	NM_145020	exon2	c.C124T	p.R42C	GGCTGCGTCGGAT	.	PASS	Atlas-SNP
FAM118A	55007	hgsc.bcm.edu	37	22	45723807	45723807	+	Missense_Mutation	SNP	G	G	C	rs11556482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	86	168	0	0.551282	0	G|0.539;C|0.461	0.461	strong	.	FAM118A	32	.	NM_017911	exon4	c.G385C	p.V129L	AGTCCTGTGGTGC	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558159	48558159	+	Silent	SNP	G	G	A	rs2307280	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	66	121	0	0.507692	0	G|0.926;A|0.074	0.074	strong	.	PLA2G4C	76	.	NM_001159322	exon15	c.C1435T	p.L479L	TGAACAGGGGAAA	.	PASS	Atlas-SNP
GPR108	56927	hgsc.bcm.edu	37	19	6735929	6735929	+	Missense_Mutation	SNP	C	C	T	rs11539588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	63	0	0.477612	0	C|0.952;T|0.048	0.048	strong	.	GPR108	35	.	NM_001080452	exon3	c.G281A	p.R94H	TAGGAGCGAACTC	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	133	278	0	0.494424	0	G|0.827;A|0.173	0.173	strong	.	PIGG	86	.	NM_001127178	exon10	c.G2095A	p.V699I	CTCTCTGTCCTGG	.	PASS	Atlas-SNP
MRPS9	64965	hgsc.bcm.edu	37	2	105665808	105665808	+	Silent	SNP	C	C	T	rs11538197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	96	69	0	0.989691	0	C|0.797;T|0.203	0.203	strong	.	MRPS9	32	.	NM_182640	exon2	c.C315T	p.D105D	TATTGACGTAAGT	.	PASS	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63433785	63433785	+	Silent	SNP	G	G	A	rs4775629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	78	209	0	0.450867	0	G|0.904;A|0.096	0.096	strong	LACTB,NS,carcinoma,0,1	LACTB	29	1	NM_032857	exon6	c.G1425A	p.S475S	TGGTTCGTGTAGA	.	PASS	Atlas-SNP
SLC22A12	116085	hgsc.bcm.edu	37	11	64367862	64367862	+	Silent	SNP	T	T	C	rs7932775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	88	0	1	0	T|0.629;C|0.371	0.371	strong	.	SLC22A12	68	.	NM_144585	exon8	c.T1309C	p.L437L	TCAGCCTTGGCCG	.	PASS	Atlas-SNP
LGR5	8549	hgsc.bcm.edu	37	12	71977787	71977787	+	Missense_Mutation	SNP	T	T	C	rs17109924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	177	162	0	0.988827	0	T|0.922;C|0.078	0.078	strong	LGR5,bladder,carcinoma,-1,1	LGR5	103	1	NM_003667	exon18	c.T1997C	p.V666A	TCTCTGTGAAATA	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671786	25671786	+	Missense_Mutation	SNP	G	G	A	rs113301206	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	5	95	0	0.0454545	0	G|0.938;A|0.062	0.062	strong	PABPC3,brain,glioma,0,1	PABPC3	129	1	NM_030979	exon1	c.G1450A	p.V484M	CAGACAGTGGGTC	.	scavenged	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73759254	73759254	+	Missense_Mutation	SNP	C	C	A	rs1632245	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	42	98	0	0.42	0	A|0.037;C|0.963	0.037	strong	C2CD3_ENST00000334126,NS,carcinoma,+2,2	C2CD3	288	2	NM_015531	exon28	c.G5491T	p.G1831W	ACCTCCCAGGAGA	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622115	121622115	+	Missense_Mutation	SNP	C	C	T	rs28360459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	11	37	0	0.392857	0	C|0.965;T|0.035	0.035	strong	.	P2RX7	53	.	NM_002562	exon13	c.C1298T	p.A433V	GACCTGCGATGGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179435887	179435887	+	Missense_Mutation	SNP	A	A	G	rs744427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	53	0	0.528571	0	A|0.984;G|0.016	0.016	strong	.	TTN	18412	.	NM_001267550	exon326	c.T74972C	p.I24991T	TTGCCAATGCCCA	.	PASS	Atlas-SNP
TGFBR3	7049	hgsc.bcm.edu	37	1	92177938	92177938	+	Silent	SNP	A	A	G	rs1805113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	76	160	0	0.5	0	A|0.655;G|0.345	0.345	strong	.	TGFBR3	103	.	NM_003243	exon13	c.T2028C	p.F676F	GATAGGAAAGTGC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634373	32634373	+	Silent	SNP	C	C	T	rs9274522	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	36	0	1	0	C|0.670;T|0.330	0.330	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.G12A	p.K4K	AGCCTTCTTCCAA	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	12477	12477	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	8	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.T141C	p.S47S	TATCAGTCTCTTC	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247655275	247655275	+	Silent	SNP	T	T	C	rs12141850	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	85	209	0	0.445026	0	T|0.648;C|0.352	0.352	strong	.	OR2W5	97	.	NM_001004698	exon1	c.T846C	p.H282H	TCGTCATTCCCAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1267917	1267917	+	Silent	SNP	T	T	C	rs3021163	bycluster;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	377	141	395	1	0.374005	0.00253165	C|1.000;|0.000	1.000	weak	MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	NM_002458	exon31	c.T9807C	p.S3269S	CTCCTCTACTCCA	.	PASS	Atlas-SNP
WWOX	51741	hgsc.bcm.edu	37	16	78148935	78148935	+	Missense_Mutation	SNP	C	C	T	rs144601717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	100	153	0	0.526316	0	C|0.985;T|0.015	0.015	strong	.	WWOX	98	.	NM_130791	exon4	c.C293T	p.P98L	ATAATCCGACCAA	.	PASS	Atlas-SNP
CATSPER3	347732	hgsc.bcm.edu	37	5	134343661	134343661	+	Silent	SNP	C	C	T	rs10044000	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	120	188	0	0.56872	0	C|0.678;T|0.322	0.322	strong	CATSPER3,NS,carcinoma,0,1	CATSPER3	38	1	NM_178019	exon4	c.C507T	p.A169A	CACCGCCGTGGGG	.	PASS	Atlas-SNP
NMRK2	27231	hgsc.bcm.edu	37	19	3942110	3942110	+	Missense_Mutation	SNP	G	G	A	rs16992131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	38	64	0	0.469136	0	G|0.977;A|0.023	0.023	strong	.	.	.	.	NM_170678	exon8	c.G532A	p.E178K	CGAGAGGAGCTCT	.	PASS	Atlas-SNP
ITGA2B	3674	hgsc.bcm.edu	37	17	42457120	42457120	+	Silent	SNP	C	C	T	rs5912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	81	0	0.52	0	C|0.982;T|0.018	0.018	strong	ITGA2B,colon,carcinoma,-1,1	ITGA2B	88	1	NM_000419	exon18	c.G1815A	p.P605P	CGTGGGCGGTAGG	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261717	39261717	+	Missense_Mutation	SNP	G	G	A	rs149483591	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	60	129	2	0.5	0.0155039	G|0.956;A|0.044	0.044	strong	KRTAP4-9,NS,carcinoma,+1,1	KRTAP4-9	110	1	NM_001146041	exon1	c.G77A	p.R26H	GCTGCCGCCCCAG	.	scavenged	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007272	6007272	+	Missense_Mutation	SNP	A	A	G	rs4237768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	67	158	0	0.478571	0	A|0.165;G|0.835	0.835	strong	.	OR52L1	100	.	NM_001005173	exon1	c.T889C	p.W297R	GATACCATGTGGC	.	PASS	Atlas-SNP
ZHX1	11244	hgsc.bcm.edu	37	8	124265676	124265676	+	Silent	SNP	C	C	T	rs34145851	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	149	325	0	0.4791	0	C|0.986;T|0.014	0.014	strong	ZHX1,NS,carcinoma,-2,1	ZHX1	89	1	NM_007222	exon3	c.G2511A	p.E837E	ATCTTCCTCCTCA	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52351377	52351377	+	Silent	SNP	T	T	C	rs1139484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	74	0	0.547945	0	C|0.107;G|0.000;T|0.893	0.107	strong	.	ITGA2	211	.	NM_002203	exon8	c.T789C	p.A263A	ATATGCTTATTCA	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124135481	124135481	+	Silent	SNP	C	C	T	rs2466701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	268	272	0	1	0	C|0.521;T|0.479	0.479	strong	.	.	.	.	NM_001005198	exon1	c.C759T	p.Y253Y	CTCTTACATCTTC	.	PASS	Atlas-SNP
MED28	80306	hgsc.bcm.edu	37	4	17616349	17616349	+	Silent	SNP	G	G	A	rs146036794	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	72	101	0	0.461538	0	G|0.996;A|0.004	0.004	strong	.	MED28	16	.	NM_025205	exon1	c.G72A	p.P24P	CCTTCCGGGCCAA	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	37	4	25806319	25806319	+	Silent	SNP	C	C	T	rs34954596	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	130	283	0	0.481481	0	C|0.978;T|0.022	0.022	strong	.	SEL1L3	62	.	NM_015187	exon10	c.G1620A	p.K540K	TACAGCCTTCTCA	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	279	268	0	0.996429	0	G|0.785;T|0.215	0.215	strong	KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	NM_198687	exon1	c.G853T	p.G285C	CCTGTCGGCTCTG	.	PASS	Atlas-SNP
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105924699	105924699	+	Silent	SNP	G	G	A	rs115690647	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	50	76	0	0.568182	0	G|0.990;A|0.010	0.010	strong	.	TGFBRAP1	70	.	NM_004257	exon2	c.C60T	p.G20G	CTTGTCGCCCATC	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36349736	36349736	+	Silent	SNP	G	G	C	rs34006827	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	100	252	1	0.478469	0.00396825	G|0.963;C|0.037	0.037	strong	.	KIRREL2	170	.	NM_199180	exon4	c.G492C	p.G164G	AGATGGGGTCCTG	.	PASS	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	37	11	71718413	71718413	+	Missense_Mutation	SNP	C	C	T	rs149588226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	28	79	0	0.329412	0	C|0.995;T|0.005	0.005	strong	.	NUMA1	142	.	NM_006185	exon21	c.G5285A	p.R1762H	GGCAGGCGCTGGG	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5863013	5863013	+	Missense_Mutation	SNP	T	T	C	rs4362173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	94	154	0	0.537143	0	T|0.606;C|0.394	0.394	strong	.	OR52E6	70	.	NM_001005167	exon1	c.A115G	p.I39V	GTGCAATAAGATA	.	PASS	Atlas-SNP
EVPLL	645027	hgsc.bcm.edu	37	17	18284263	18284263	+	Silent	SNP	C	C	T	rs116412205	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	100	266	0	0.413223	0	C|0.993;T|0.007	0.007	strong	.	EVPLL	10	.	NM_001145127	exon2	c.C12T	p.S4S	AGCCAGCGCCGAC	.	PASS	Atlas-SNP
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69094472	69094472	+	Silent	SNP	A	A	T	rs34044450	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	114	234	0	0.452381	0	A|0.990;T|0.010	0.010	strong	TMPRSS11B,NS,carcinoma,0,1	TMPRSS11B	66	1	NM_182502	exon9	c.T1077A	p.A359A	TGCATCAGCTTCT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149512267	149512267	+	Silent	SNP	C	C	T	rs142728666	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	33	81	0	0.44	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_198455	exon75	c.C10587T	p.C3529C	AGACTGCGGGGGT	.	PASS	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169842746	169842746	+	Silent	SNP	T	T	C	rs7563233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	123	1	1	0.00813008	T|0.885;C|0.115	0.115	strong	.	ABCB11	136	.	NM_003742	exon10	c.A957G	p.G319G	CACTATTCCTTTT	.	PASS	Atlas-SNP
ITPR1	3708	hgsc.bcm.edu	37	3	4856234	4856234	+	Silent	SNP	G	G	A	rs901854	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	43	102	0	0.462366	0	G|0.382;A|0.618	0.618	strong	.	ITPR1	659	.	NM_001168272	exon57	c.G7644A	p.K2548K	CAGGAAGCCGTCC	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32912299	32912299	+	Silent	SNP	T	T	C	rs543304	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	45	41	0	1	0	C|0.187;N|0.000;T|0.813	0.187	strong	.	BRCA2	812	.	NM_000059	exon11	c.T3807C	p.V1269V	TTCTGTTGTTTCA	.	PASS	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	7013874	7013874	+	Silent	SNP	C	C	T	rs35006356	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	76	0	0.522388	0	C|0.993;T|0.007	0.007	strong	.	KDM4C	186	.	NM_001146696	exon14	c.C2121T	p.L707L	GCCCCTCATACCA	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777513	52777513	+	Missense_Mutation	SNP	T	T	C	rs2245203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	123	152	0	0.991935	0	T|0.684;C|0.316	0.316	strong	.	KRT84	61	.	NM_033045	exon2	c.A616G	p.I206V	TCCTGATACATTT	.	PASS	Atlas-SNP
LEKR1	389170	hgsc.bcm.edu	37	3	156763279	156763279	+	Silent	SNP	C	C	T	rs73873779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	121	90	0	1	0	C|0.852;T|0.148	0.148	strong	.	LEKR1	66	.	NM_001004316	exon13	c.C1819T	p.L607L	GGCAGCCTAACCT	.	PASS	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	132	133	0	0.985075	0	G|0.585;A|0.415	0.415	strong	.	OR6K3	101	.	NM_001005327	exon1	c.C743T	p.P248L	AATATCGGGAAGA	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54420799	54420799	+	Silent	SNP	A	A	C	rs382402	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	29	84	0	0.432836	0	A|0.851;C|0.149	0.149	strong	CDC20B,NS,carcinoma,0,1	CDC20B	61	1	NM_001170402	exon9	c.T1047G	p.V349V	TGTTCCAACATGA	.	PASS	Atlas-SNP
C16orf82	162083	hgsc.bcm.edu	37	16	27078545	27078545	+	Missense_Mutation	SNP	C	C	T	rs185409807	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	27	60	0	0.409091	0	C|0.982;T|0.018	0.018	strong	.	.	.	.	NM_001145545	exon1	c.C229T	p.P77S	CAGCACCCGAGGC	.	PASS	Atlas-SNP
IGJ	3512	hgsc.bcm.edu	37	4	71522999	71522999	+	Silent	SNP	C	C	T	rs75928327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	46	0	0.431373	0	C|0.990;T|0.010	0.010	strong	.	IGJ	13	.	NM_144646	exon3	c.G198A	p.L66L	GTTGTTCAGAGGA	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109347314	109347314	+	Missense_Mutation	SNP	C	C	G	rs144278795	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	142	250	0	0.47973	0	C|0.996;G|0.004	0.004	strong	.	RANBP2	488	.	NM_006267	exon3	c.C225G	p.N75K	AGAAAACACAGAC	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	304	157	278	0	0.516447	0	A|0.634;G|0.366	0.366	strong	NRP1,NS,carcinoma,0,1	NRP1	126	1	NM_003873	exon17	c.T2595C	p.S865S	CAGGGCACTCATG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	134	0	1	0	A|0.700;G|0.300	0.300	strong	.	MICA	21	.	NM_001177519	exon4	c.A685G	p.S229G	GCTTCCAGCTTCT	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152496526	152496526	+	Missense_Mutation	SNP	A	A	G	rs6713162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	114	0	1	0	A|0.570;G|0.430	0.430	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_004543	exon62	c.T8734C	p.S2912P	CAATGGACACCCA	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	382646	382646	+	Silent	SNP	C	C	T	rs116523732	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	62	96	0	0.525424	0	C|0.991;T|0.009	0.009	strong	.	DOCK8	401	.	NM_203447	exon22	c.C2739T	p.S913S	ACACTCCGCAGCA	.	PASS	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	95	0	1	0	C|0.506;G|0.494	0.494	strong	.	.	.	.	NM_001271428	exon10	c.G1034C	p.S345T	CTGCTACTTTTCT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191052	152191052	+	Missense_Mutation	SNP	G	G	T	rs115232928	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	122	224	0	0.462121	0	G|0.985;T|0.015	0.015	strong	.	HRNR	403	.	NM_001009931	exon3	c.C3053A	p.S1018Y	TGCCCGGAACCAG	.	PASS	Atlas-SNP
TRIM4	89122	hgsc.bcm.edu	37	7	99500911	99500911	+	Silent	SNP	A	A	G	rs2247761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	110	0	1	0	A|0.383;G|0.617	0.617	strong	.	TRIM4	33	.	NM_033017	exon6	c.T849C	p.S283S	TTCAAGAGAATAG	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585286	43585286	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	357	15	314	0	0.0420168	0	.	.	none	PSG2,colon,carcinoma,-2,4	PSG2	84	4	NM_031246	exon2	c.C177T	p.P59P	ATTCTGGGGCAAA	.	scavenged	Atlas-SNP
CXCL1	2919	hgsc.bcm.edu	37	4	74735244	74735244	+	Silent	SNP	A	A	G	rs2071425	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	15	23	0	1	0	A|0.668;G|0.332	0.332	strong	.	CXCL1	6	.	NM_001511	exon1	c.A57G	p.A19A	AGTGGCACTGCTG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970718	45970718	+	Silent	SNP	C	C	T	rs233238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	108	182	0	0.471616	0	C|0.742;T|0.258	0.258	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G624A	p.P208P	GCAGCACGGAGAG	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44561069	44561069	+	Silent	SNP	G	G	T	rs139088020	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	41	50	0	0.585714	0	G|0.998;T|0.002	0.002	strong	.	TCEB3B	141	.	NM_016427	exon1	c.C567A	p.P189P	CTTCCCGGGCGCA	.	PASS	Atlas-SNP
PDZD3	79849	hgsc.bcm.edu	37	11	119059404	119059404	+	Missense_Mutation	SNP	G	G	A	rs1815811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	144	1	1	0.00694444	G|0.395;A|0.605	0.605	strong	.	PDZD3	42	.	NM_001168468	exon9	c.G1115A	p.R372Q	CGCCCCGGGGCAG	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240981362	240981362	+	Silent	SNP	T	T	C	rs115420937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	57	144	0	0.428571	0	T|0.992;C|0.008	0.008	strong	.	PRR21	53	.	NM_001080835	exon1	c.A1038G	p.L346L	GAGGCGTAGATGA	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49070329	49070329	+	Missense_Mutation	SNP	C	C	T	rs34308720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	55	116	0	0.470085	0	C|0.993;T|0.007	0.007	strong	.	CACNA1F	218	.	NM_005183	exon31	c.G3775A	p.A1259T	TAAGAGCGTCAAA	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	31496431	31496431	+	Missense_Mutation	SNP	T	T	A	rs41305353	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	95	231	0	0.458937	0	T|0.792;A|0.208	0.208	strong	.	DMD	2127	.	NM_004006	exon59	c.A8729T	p.E2910V	TTGACCTCCTCAG	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31092629	31092629	+	Missense_Mutation	SNP	G	G	A	rs370035952		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	83	141	0	0.576389	0	.	.	weak	.	ZNF646	133	.	NM_014699	exon2	c.G4984A	p.G1662R	AGGGGAGGACAAG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	27	66	0	0.397059	0	G|0.810;A|0.190	0.190	strong	MYOM1,NS,carcinoma,0,2	MYOM1	192	2	NM_003803	exon35	c.C4662T	p.A1554A	AGCATAGGCCTCA	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021539	132021539	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	352	4	336	0	0.0113636	0	.	.	none	ENSG00000188219,NS,carcinoma,+2,2	.	.	2	NM_001083538	exon15	c.G2511A	p.Q837Q	CATCCAGGCCGTG	.	scavenged	Atlas-SNP
PCYOX1	51449	hgsc.bcm.edu	37	2	70485332	70485332	+	Silent	SNP	G	G	A	rs114523411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	40	137	0	0.36036	0	G|0.995;A|0.005	0.005	strong	.	PCYOX1	34	.	NM_016297	exon1	c.G36A	p.L12L	CTCGCTGCTGGGG	.	PASS	Atlas-SNP
GKN2	200504	hgsc.bcm.edu	37	2	69173570	69173570	+	Missense_Mutation	SNP	C	C	T	rs1128272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	73	66	0	1	0	C|0.754;T|0.246	0.246	strong	.	GKN2	28	.	NM_182536	exon5	c.G338A	p.S113N	TATTTGCTGGAGA	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132193225	132193225	+	Silent	SNP	G	G	A	rs78248128	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	92	110	0	0.582278	0	G|0.966;A|0.034	0.034	strong	.	PLXNA4	873	.	NM_001105543	exon2	c.C228T	p.S76S	CAGGTCGCTGGAG	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149245754	149245754	+	Silent	SNP	A	A	G	rs17110644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	43	74	0	0.494253	0	A|0.946;G|0.054	0.054	strong	.	PDE6A	98	.	NM_000440	exon20	c.T2337C	p.F779F	GCAAACAAAGTCA	.	PASS	Atlas-SNP
MKLN1	4289	hgsc.bcm.edu	37	7	131128450	131128450	+	Silent	SNP	T	T	C	rs10224156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	89	134	0	0.566879	0	T|0.948;C|0.052	0.052	strong	.	MKLN1	67	.	NM_013255	exon11	c.T1384C	p.L462L	TGCATGTTATTCC	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008497	11008497	+	Silent	SNP	G	G	C	rs1281017	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	80	159	0	0.506329	0	G|0.745;C|0.255	0.255	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C1695G	p.G565G	TGACAAGCCTCTC	.	PASS	Atlas-SNP
TMEM132D	121256	hgsc.bcm.edu	37	12	129559557	129559557	+	Silent	SNP	C	C	T	rs10773594	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	13	32	0	0.333333	0	C|0.337;T|0.663	0.663	strong	TMEM132D,bladder,carcinoma,-2,2	TMEM132D	299	2	NM_133448	exon9	c.G2163A	p.T721T	CAAGGGCGTGACT	.	PASS	Atlas-SNP
HDAC4	9759	hgsc.bcm.edu	37	2	240111556	240111556	+	Silent	SNP	G	G	A	rs6740794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	54	83	0	0.469565	0	G|0.938;A|0.062	0.062	strong	HDAC4,colon,carcinoma,0,1	HDAC4	127	1	NM_006037	exon4	c.C312T	p.H104H	CGCCTCGTGCTGC	.	PASS	Atlas-SNP
XKR5	389610	hgsc.bcm.edu	37	8	6690276	6690276	+	Missense_Mutation	SNP	T	T	C	rs2741098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	107	97	0	1	0	T|0.360;C|0.640	0.640	strong	.	XKR5	20	.	NM_207411	exon2	c.A205G	p.M69V	GCATCATCAAGGA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547096	132547096	+	Silent	SNP	G	G	A	rs74479394	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	17	133	0	0.132812	0	.	.	weak	EP400,colon,carcinoma,0,3	EP400	370	3	NM_015409	exon47	c.G8184A	p.Q2728Q	ACAACAGCAGCAG	.	PASS	Atlas-SNP
SNRPA1	6627	hgsc.bcm.edu	37	15	101835306	101835306	+	Silent	SNP	G	G	C	rs61738984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	21	36	0	0.446809	0	G|0.906;C|0.094	0.094	strong	.	SNRPA1	11	.	NM_003090	exon1	c.C78G	p.L26L	ACCCCGGAGGTCC	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6012658	6012658	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	6	181	2	0.0240964	0.0110497	.	.	none	RANBP6,bladder,carcinoma,0,7	RANBP6	127	7	NM_012416	exon1	c.A2950C	p.I984L	TCCCTATTGCTGA	.	scavenged	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50874851	50874851	+	Silent	SNP	G	G	A	rs78837601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	342	166	314	0	0.48538	0	G|0.976;A|0.024	0.024	strong	.	PPP6R2	71	.	NM_001242899	exon14	c.G1575A	p.T525T	GCTGACGGAGACG	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	37	15	52553259	52553259	+	Missense_Mutation	SNP	C	C	G	rs200784696	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	56	0	0.439394	0	.	.	weak	.	MYO5C	162	.	NM_018728	exon10	c.G1113C	p.Q371H	CAGCCACTGAGCA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107745029	107745029	+	Silent	SNP	A	A	G	rs2074748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	56	167	0	0.455285	0	A|0.944;G|0.056	0.056	strong	.	LAMB4	253	.	NM_007356	exon9	c.T906C	p.D302D	CGGACCATCTGTA	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101778272	101778272	+	Missense_Mutation	SNP	A	A	C	rs35250850	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	28	101	0	0.241379	0	A|0.927;C|0.073	0.073	strong	.	COL15A1	211	.	NM_001855	exon11	c.A1518C	p.E506D	TGATGAAGAAGAC	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168377054	168377054	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	52	309	0	0.1571	0	.	.	none	.	.	.	.	NM_001129895	exon1	c.C279A	p.S93S	GTGGGGGGAGGAG	.	PASS	Atlas-SNP
LPL	4023	hgsc.bcm.edu	37	8	19818436	19818436	+	Silent	SNP	C	C	A	rs316	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	23	72	0	0.323944	0	C|0.846;A|0.154	0.154	strong	.	LPL	78	.	NM_000237	exon8	c.C1164A	p.T388T	TAAGACCTACTCC	.	PASS	Atlas-SNP
KRT71	112802	hgsc.bcm.edu	37	12	52946424	52946424	+	Silent	SNP	G	G	A	rs61729863	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	87	225	0	0.418269	0	G|0.970;A|0.030	0.030	strong	.	KRT71	70	.	NM_033448	exon1	c.C438T	p.D146D	CACCTTGTCGATG	.	PASS	Atlas-SNP
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692346	31692346	+	Missense_Mutation	SNP	C	C	T	rs115381362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	65	111	0	0.460993	0	C|0.993;T|0.007	0.007	strong	.	KRTAP26-1	58	.	NM_203405	exon1	c.G8A	p.C3Y	TTGGGGCAAGACA	.	PASS	Atlas-SNP
CCDC173	129881	hgsc.bcm.edu	37	2	170537661	170537661	+	Silent	SNP	A	A	G	rs145389999	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	108	203	1	0.534653	0.00492611	A|0.993;G|0.007	0.007	strong	.	.	.	.	NM_001085447	exon2	c.T150C	p.I50I	GTGTGGAATTATG	.	PASS	Atlas-SNP
CHRDL2	25884	hgsc.bcm.edu	37	11	74415606	74415606	+	Missense_Mutation	SNP	T	T	C	rs59876990	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	102	223	0	0.445415	0	T|0.978;C|0.022	0.022	strong	.	CHRDL2	47	.	NM_015424	exon7	c.A676G	p.I226V	GAGGGATGAAGCT	.	PASS	Atlas-SNP
ATP6AP2	10159	hgsc.bcm.edu	37	X	40460040	40460040	+	Silent	SNP	T	T	C	rs7691	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	226	231	0	0.995595	0	0|0.015;C|0.145	0.145	strong	.	ATP6AP2	45	.	NM_005765	exon8	c.T765C	p.Y255Y	TCTTTATGGTGGG	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39228514	39228514	+	Missense_Mutation	SNP	G	G	A	rs61736154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	73	149	0	0.462025	0	G|0.977;A|0.023	0.023	strong	.	XIRP1	173	.	NM_001198621	exon2	c.C2423T	p.S808L	GTGCCCGAGAGCA	.	PASS	Atlas-SNP
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	91	135	0	0.554878	0	C|0.881;T|0.119	0.119	strong	CREB3L3,NS,carcinoma,+1,2	CREB3L3	53	2	NM_001271997	exon2	c.C42T	p.A14A	TGCTGCCTGCTCC	.	PASS	Atlas-SNP
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763029	140763029	+	Missense_Mutation	SNP	A	A	G	rs2072315	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	176	214	0	0.99435	0	A|0.473;G|0.527	0.527	strong	.	PCDHGA7	130	.	NM_032087	exon1	c.A563G	p.E188G	ACGATGAAACTAA	.	PASS	Atlas-SNP
C10orf62	414157	hgsc.bcm.edu	37	10	99350128	99350128	+	Silent	SNP	A	A	G	rs7093643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	29	46	1	0.568627	0.0217391	A|0.704;G|0.296	0.296	strong	C10orf62,colon,carcinoma,0,1	C10orf62	14	1	NM_001009997	exon1	c.A474G	p.L158L	TCACCTAGAGTCC	.	scavenged	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106156983	106156983	+	Silent	SNP	G	G	A	rs35695427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	71	132	0	0.522059	0	G|0.982;A|0.018	0.018	strong	TET2_ENST00000305737,bladder,carcinoma,+2,2	TET2	1762	2	NM_001127208	exon3	c.G1884A	p.E628E	GCTGGAGCACAAG	.	PASS	Atlas-SNP
CCDC142	84865	hgsc.bcm.edu	37	2	74708454	74708454	+	Missense_Mutation	SNP	A	A	C	rs142978072	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	56	175	0	0.386207	0	A|0.997;C|0.003	0.003	strong	.	CCDC142	40	.	NM_032779	exon3	c.T1154G	p.L385R	GTGGGAAGGCTGC	.	PASS	Atlas-SNP
TMPRSS9	360200	hgsc.bcm.edu	37	19	2413788	2413788	+	Missense_Mutation	SNP	G	G	A	rs147023760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	46	107	0	0.464646	0	G|0.983;A|0.017	0.017	strong	.	TMPRSS9	79	.	NM_182973	exon9	c.G1243A	p.A415T	GCGGAAGCCCGGC	.	PASS	Atlas-SNP
MYH7	4625	hgsc.bcm.edu	37	14	23892888	23892888	+	Silent	SNP	A	A	G	rs7157716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	144	309	2	0.469055	0.00647249	A|0.583;G|0.416	0.416	strong	MYH7,NS,carcinoma,0,1	MYH7	349	1	NM_000257	exon24	c.T2967C	p.I989I	CTTGGCAATGATC	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910562	29910562	+	Silent	SNP	A	A	C	rs1059418	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	15	66	0	0.205479	0	A|0.837;C|0.159;T|0.004	0.159	strong	.	HLA-A	89	.	NM_001242758	exon2	c.A102C	p.T34T	CTTCACATCCGTG	.	PASS	Atlas-SNP
INSRR	3645	hgsc.bcm.edu	37	1	156814884	156814884	+	Silent	SNP	C	C	T	rs149474857	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	56	83	0	0.486957	0	C|0.991;T|0.009	0.009	strong	.	INSRR	309	.	NM_014215	exon12	c.G2421A	p.A807A	GGTGCGCGCAAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513590	195513590	+	Missense_Mutation	SNP	C	C	T	rs74192533	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	488	9	567	4	0.0184426	0.00705467	CGGTGACAG|0.500;TGGTGACAA|0.500	.	alt	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G4861A	p.D1621N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
ZNF157	7712	hgsc.bcm.edu	37	X	47272480	47272480	+	Silent	SNP	G	G	A	rs61736399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	27	93	0	0.333333	0	G|0.990;A|0.010	0.010	strong	.	ZNF157	46	.	NM_003446	exon4	c.G1008A	p.G336G	ATGTGGGAAATTC	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305800	39305800	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	16	132	0	0.146789	0	.	.	none	KRTAP4-5,NS,carcinoma,0,4	KRTAP4-5	34	4	NM_033188	exon1	c.A220T	p.S74C	AGCAGCTGGATTC	.	PASS	Atlas-SNP
TOM1L2	146691	hgsc.bcm.edu	37	17	17786042	17786042	+	Missense_Mutation	SNP	G	G	T	rs146710625	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	166	0	0.442708	0	G|0.999;T|0.001	0.001	strong	.	TOM1L2	54	.	NM_001082968	exon6	c.C637A	p.P213T	TGATGGGGCCAGT	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	128795081	128795081	+	Silent	SNP	G	G	A	rs79043452	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	79	130	0	0.496855	0	G|0.997;A|0.003	0.003	strong	.	DOCK1	188	.	NM_001380	exon7	c.G543A	p.T181T	TAGCACGATTAGT	.	PASS	Atlas-SNP
CCDC8	83987	hgsc.bcm.edu	37	19	46915182	46915182	+	Missense_Mutation	SNP	C	C	T	rs11880658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	53	111	0	0.5	0	C|0.962;T|0.038	0.038	strong	.	CCDC8	56	.	NM_032040	exon1	c.G886A	p.G296R	CTCCCCCCTGATC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2957005	2957005	+	Silent	SNP	T	T	C	rs3735124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	21	59	0	0.477273	0	T|0.633;C|0.367	0.367	strong	.	CARD11	339	.	NM_032415	exon20	c.A2622G	p.P874P	TTCTTCTGGCTGC	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	28	51	0	0.451613	0	T|0.747;C|0.253	0.253	strong	.	KLHL33	37	.	NM_001109997	exon3	c.A1034G	p.E345G	TTGAGCTCAGGGT	.	PASS	Atlas-SNP
SAA1	6288	hgsc.bcm.edu	37	11	18290866	18290866	+	Silent	SNP	T	T	C	rs71469385	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	22	138	14	0.170543	0.101449	C|1.000;|0.000	1.000	weak	SAA1,NS,carcinoma,0,1	SAA1	14	1	NM_199161	exon3	c.T216C	p.A72A	CTGGGCTGCAGAA	.	scavenged	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449409	35449409	+	Silent	SNP	G	G	A	rs2651081	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	99	0	1	0	G|0.659;A|0.341	0.341	strong	FLJ38451,NS,carcinoma,0,1	ZNF792	46	1	NM_175872	exon4	c.C1350T	p.H450H	ACACCCGTGAGGC	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234546245	234546245	+	Silent	SNP	C	C	T	rs1141264	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	89	225	0	0.478495	0	C|0.658;T|0.342	0.342	strong	.	TARBP1	111	.	NM_005646	exon23	c.G3738A	p.T1246T	TAAAAACGTACAA	.	PASS	Atlas-SNP
RAD9A	5883	hgsc.bcm.edu	37	11	67160961	67160961	+	Missense_Mutation	SNP	A	A	G	rs2066496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	115	1	1	0.00869565	A|0.819;G|0.181	0.181	strong	.	RAD9A	15	.	NM_001243224	exon1	c.A1G	p.M1V	TATCCCATGCAGT	.	PASS	Atlas-SNP
KY	339855	hgsc.bcm.edu	37	3	134322814	134322814	+	Silent	SNP	G	G	C	rs2293294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	52	73	0	0.577778	0	G|0.694;C|0.306	0.306	strong	KY_ENST00000423778,NS,carcinoma,0,1	KY	92	1	NM_178554	exon11	c.C1593G	p.G531G	AAACTTGCCTGCA	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39874092	39874092	+	Silent	SNP	C	C	T	rs35248254	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	57	128	0	0.456	0	C|0.985;T|0.015	0.015	strong	.	THBS1	106	.	NM_003246	exon2	c.C34T	p.L12L	CTGTTCCTGATGC	.	PASS	Atlas-SNP
SCG2	7857	hgsc.bcm.edu	37	2	224462714	224462714	+	Silent	SNP	G	G	A	rs721233	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	44	86	0	0.556962	0	G|0.932;A|0.068	0.068	strong	.	SCG2	99	.	NM_003469	exon2	c.C1287T	p.D429D	GAGCCCGTCTGGT	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909638	123909638	+	Missense_Mutation	SNP	G	G	A	rs148218442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	109	408	2	0.475983	0.00490196	G|0.992;A|0.008	0.008	strong	OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	NM_001004463	exon1	c.C71T	p.P24L	AAGAGGGGGGCGT	.	scavenged	Atlas-SNP
ALAS2	212	hgsc.bcm.edu	37	X	55035751	55035751	+	Silent	SNP	C	C	T	rs6612251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	130	217	0	0.507812	0	C|0.974;0|0.006	.	strong	.	ALAS2	163	.	NM_000032	exon11	c.G1626A	p.A542A	CCCCACCGCAGTC	.	PASS	Atlas-SNP
TTLL12	23170	hgsc.bcm.edu	37	22	43568512	43568512	+	Missense_Mutation	SNP	C	C	T	rs34074034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	82	170	0	0.460674	0	C|0.803;G|0.000;T|0.197	0.197	strong	.	TTLL12	50	.	NM_015140	exon10	c.G1390A	p.V464M	TTCCCACGTCTTC	.	PASS	Atlas-SNP
RET	5979	hgsc.bcm.edu	37	10	43615094	43615094	+	Silent	SNP	C	C	T	rs1800862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	61	113	0	0.491935	0	C|0.960;T|0.040	0.040	strong	.	RET	916	.	NM_020630	exon14	c.C2508T	p.S836S	CTCCAGCTCCCTG	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73150984	73150984	+	Missense_Mutation	SNP	C	C	T	rs6560142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	166	155	1	0.994012	0.00645161	C|0.396;T|0.604	0.604	strong	.	TRPM3	700	.	NM_001007471	exon25	c.G5009A	p.R1670Q	GGATTTCGCAGGC	.	PASS	Atlas-SNP
CCDC7	221016	hgsc.bcm.edu	37	10	32832249	32832249	+	Nonsense_Mutation	SNP	C	C	T	rs201935164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	3	176	0	0.0140845	0	C|0.999;T|0.001	0.001	weak	CCDC7,colon,carcinoma,-1,1	CCDC7	47	1	NM_145023	exon13	c.C1015T	p.R339X	AATAATCGAACAA	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78853916	78853916	+	Missense_Mutation	SNP	G	G	C	rs17062264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	128	120	0	0.992248	0	G|0.882;C|0.118	0.118	strong	.	PCSK5	329	.	NM_001190482	exon23	c.G2908C	p.G970R	GAGTGTGGAGATA	.	PASS	Atlas-SNP
ABCC10	89845	hgsc.bcm.edu	37	6	43411700	43411700	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	91	0	0.542169	0	.	.	none	.	ABCC10	118	.	NM_001198934	exon11	c.C2446T	p.Q816X	CTGGTACAAGCTG	.	PASS	Atlas-SNP
SBSPON	157869	hgsc.bcm.edu	37	8	74005179	74005179	+	Silent	SNP	T	T	G	rs114228241	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	23	55	0	0.370968	0	T|0.913;G|0.087	0.087	strong	.	.	.	.	NM_153225	exon1	c.A124C	p.R42R	CCAGCCTCCAGCC	.	PASS	Atlas-SNP
FMO3	2328	hgsc.bcm.edu	37	1	171076888	171076888	+	Missense_Mutation	SNP	G	G	C	rs12072582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	73	176	0	0.386243	0	G|0.983;C|0.017	0.017	strong	.	FMO3	73	.	NM_006894	exon4	c.G394C	p.D132H	GAAAGGGATGGTA	.	PASS	Atlas-SNP
IDS	3423	hgsc.bcm.edu	37	X	148579705	148579705	+	Missense_Mutation	SNP	G	G	A	rs61736892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	110	240	0	0.470085	0	G|0.982;A|0.018	0.018	strong	.	IDS	46	.	NM_006123	exon5	c.C641T	p.T214M	GCTGACGTTTTCA	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2728559	2728559	+	Missense_Mutation	SNP	A	A	G	rs9961682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	36	65	0	0.62069	0	A|0.969;G|0.031	0.031	strong	.	SMCHD1	88	.	NM_015295	exon23	c.A2878G	p.I960V	GACAACATAACAG	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	379598	379598	+	Silent	SNP	A	A	G	rs1134699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	6	0	1	0	A|0.483;G|0.517	0.517	strong	B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	NM_178537	exon15	c.A2385G	p.E795E	TCCCGAACCCGCT	.	scavenged	Atlas-SNP
CLEC4C	170482	hgsc.bcm.edu	37	12	7894056	7894056	+	Missense_Mutation	SNP	G	G	A	rs73056605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	74	143	0	0.513889	0	G|0.766;A|0.234	0.234	strong	CLEC4C,NS,carcinoma,+2,2	CLEC4C	44	2	NM_130441	exon4	c.C196T	p.P66S	GGCTTGGATGATA	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	81	225	0	0.421875	0	T|0.810;C|0.190	0.190	strong	.	CDRT1	83	.	NM_006382	exon6	c.A1132G	p.N378D	ACAGGTTGTACTC	.	PASS	Atlas-SNP
PDE6B	5158	hgsc.bcm.edu	37	4	660340	660340	+	Silent	SNP	G	G	A	rs61739716	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	34	79	0	0.4	0	G|0.990;A|0.010	0.010	strong	.	PDE6B	80	.	NM_001145291	exon20	c.G2289A	p.K763K	GAACAAGGCGGCC	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6468331	6468331	+	Missense_Mutation	SNP	T	T	C	rs62107586	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	121	216	0	0.502075	0	A|0.000;C|0.295;G|0.000;T|0.705	0.295	strong	.	DENND1C	93	.	NM_024898	exon22	c.A1705G	p.M569V	CTCCCATGCTAAG	.	PASS	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	176915087	176915087	+	Missense_Mutation	SNP	C	C	T	rs138686233	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	49	94	0	0.597561	0	C|0.998;T|0.002	0.002	strong	ASTN1,NS,carcinoma,0,1	ASTN1	314	1	NM_004319	exon13	c.G2224A	p.G742R	CCTGTCCGGCAGC	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	144	0	1	0	A|0.549;G|0.451	0.451	strong	.	TRIM45	55	.	NM_025188	exon5	c.T1487C	p.M496T	CTCACCATCACAG	.	PASS	Atlas-SNP
NRK	203447	hgsc.bcm.edu	37	X	105168689	105168689	+	Missense_Mutation	SNP	C	C	A	rs16984889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	163	254	0	0.610487	0	0|0.008;A|0.143	0.143	strong	.	NRK	321	.	NM_198465	exon19	c.C2978A	p.A993E	TCAGGGCAAGCTA	.	PASS	Atlas-SNP
CXorf30	645090	hgsc.bcm.edu	37	X	36371719	36371719	+	Missense_Mutation	SNP	T	T	A	rs41309695	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	86	141	0	0.511905	0	T|0.835;A|0.165	0.165	strong	.	CXorf30	76	.	NM_001098843	exon15	c.T1112A	p.F371Y	TCGGATTTAGTCT	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865615	118865615	+	Missense_Mutation	SNP	G	G	C	rs9859242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	48	78	0	0.428571	0	G|0.977;C|0.023	0.023	strong	.	C3orf30	64	.	NM_152539	exon1	c.G579C	p.Q193H	CGAGCAGATGGAC	.	PASS	Atlas-SNP
INHA	3623	hgsc.bcm.edu	37	2	220439700	220439700	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	2	91	1	0.0224719	0.010989	.	.	none	INHA,right_upper_lobe,carcinoma,-1,1	INHA	30	1	NM_002191	exon2	c.G553T	p.A185S	ACCTCTGCTCTCT	.	scavenged	Atlas-SNP
ZNF200	7752	hgsc.bcm.edu	37	16	3282468	3282468	+	Missense_Mutation	SNP	G	G	A	rs9302870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	68	98	0	0.53125	0	G|0.914;A|0.086	0.086	strong	.	ZNF200	36	.	NM_003454	exon4	c.C419T	p.T140M	TCTGACGTGAGTT	.	PASS	Atlas-SNP
CLTA	1211	hgsc.bcm.edu	37	9	36197564	36197564	+	Silent	SNP	A	A	G	rs138682143	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	109	178	0	0.57672	0	A|0.998;G|0.002	0.002	strong	.	CLTA	18	.	NM_001184761	exon2	c.A234G	p.V78V	TGGAGTAATGAAT	.	PASS	Atlas-SNP
ZNF28	7576	hgsc.bcm.edu	37	19	53304448	53304448	+	Missense_Mutation	SNP	C	C	T	rs143289804	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	109	0	0.469388	0	C|0.998;T|0.002	0.002	strong	.	ZNF28	191	.	NM_006969	exon4	c.G650A	p.C217Y	TCAATACATTGGA	.	PASS	Atlas-SNP
OR10R2	343406	hgsc.bcm.edu	37	1	158450314	158450314	+	Missense_Mutation	SNP	A	A	G	rs6679056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	110	216	2	0.482456	0.00925926	A|0.467;G|0.533	0.533	strong	OR10R2,colon,carcinoma,+1,1	OR10R2	81	1	NM_001004472	exon1	c.A647G	p.E216G	TTAACGAATTTGT	.	scavenged	Atlas-SNP
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118187528	118187528	+	Missense_Mutation	SNP	C	C	T	rs10885929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	73	203	0	0.45625	0	C|0.961;T|0.039	0.039	strong	.	PNLIPRP3	101	.	NM_001011709	exon1	c.C4T	p.L2F	TAGATGCTTGGAA	.	PASS	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55183716	55183716	+	Silent	SNP	T	T	C	rs1050515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	121	126	0	0.991803	0	C|0.565;G|0.000;T|0.435	0.565	strong	.	AKAP1	73	.	NM_001242902	exon3	c.T891C	p.D297D	CCAGGATAGAGGT	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20443943	20443943	+	Missense_Mutation	SNP	A	A	G	rs45516109	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	177	149	0	0.994382	0	.	.	weak	.	OR4K15	82	.	NM_001005486	exon1	c.A266G	p.N89S	TTGCAAACCTGTC	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38907222	38907222	+	Silent	SNP	A	A	G	rs17501308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	96	206	1	0.561404	0.00485437	A|0.990;G|0.010	0.010	strong	.	FAM114A1	42	.	NM_138389	exon5	c.A516G	p.G172G	TGAAGGAGCCCAA	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55817708	55817708	+	Silent	SNP	T	T	C	rs10144418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	85	178	1	0.464481	0.00561798	T|0.655;C|0.345	0.345	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T600C	p.Y200Y	AGTCTATGCTGGG	.	scavenged	Atlas-SNP
NDUFAF2	91942	hgsc.bcm.edu	37	5	60448734	60448734	+	Silent	SNP	T	T	C	rs77878573	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	71	147	0	0.496504	0	T|0.981;C|0.019	0.019	strong	.	NDUFAF2	10	.	NM_174889	exon4	c.T462C	p.F154F	AACCTTTCAGCCA	.	PASS	Atlas-SNP
AGPAT2	10555	hgsc.bcm.edu	37	9	139571560	139571560	+	Silent	SNP	G	G	A	rs73668354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	85	120	0	0.732759	0	G|0.982;A|0.018	0.018	strong	AGPAT2,NS,carcinoma,0,1	AGPAT2	17	1	NM_001012727	exon3	c.C345T	p.C115C	CTGCACGCAGCGC	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	37	16	71318577	71318577	+	Missense_Mutation	SNP	T	T	C	rs3803704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	60	122	0	0.491803	0	T|0.735;C|0.265	0.265	strong	FTSJD1,NS,carcinoma,0,1	FTSJD1	70	1	NM_018348	exon3	c.A1247G	p.N416S	CAATTATTTCTGG	.	PASS	Atlas-SNP
SLC13A2	9058	hgsc.bcm.edu	37	17	26824156	26824156	+	Missense_Mutation	SNP	A	A	G	rs11567842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	298	275	1	1	0.00363636	A|0.560;G|0.440	0.440	strong	SLC13A2,NS,carcinoma,0,1	SLC13A2	125	1	NM_001145975	exon12	c.A1795G	p.I599V	GTCCTGATCATCG	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234529519	234529519	+	Silent	SNP	C	C	T	rs1802871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	68	191	0	0.441558	0	C|0.797;T|0.203	0.203	strong	TARBP1,caecum,carcinoma,0,1	TARBP1	111	1	NM_005646	exon27	c.G4308A	p.P1436P	GTTCCACGGGATA	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39908215	39908215	+	Silent	SNP	G	G	A	rs142309421		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	55	93	0	0.561224	0	G|1.000;A|0.000	0.000	weak	.	PLEKHG2	329	.	NM_022835	exon8	c.G765A	p.A255A	CTGGGCGGAGGGC	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	37	14	101005215	101005215	+	Silent	SNP	T	T	C	rs12893951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	20	39	0	0.909091	0	T|0.388;C|0.612	0.612	strong	.	BEGAIN	32	.	NM_020836	exon7	c.A873G	p.A291A	TGAGCCTGCGTAG	.	PASS	Atlas-SNP
SNX18	112574	hgsc.bcm.edu	37	5	53815560	53815560	+	Missense_Mutation	SNP	A	A	C	rs13162502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	42	126	0	0.365217	0	A|0.866;C|0.134	0.134	strong	.	SNX18	102	.	NM_052870	exon1	c.A1778C	p.K593T	AGTGTAAGTTGGA	.	PASS	Atlas-SNP
CASC1	55259	hgsc.bcm.edu	37	12	25311489	25311489	+	Missense_Mutation	SNP	G	G	T	rs10842496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	66	0	0.421687	0	G|0.728;T|0.272	0.272	strong	.	CASC1	146	.	NM_001082972	exon4	c.C289A	p.R97S	TCAAACGGGCTTC	.	PASS	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43654194	43654194	+	Silent	SNP	A	A	G	rs35718664	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	57	107	0	0.564356	0	A|0.955;G|0.045	0.045	strong	.	CSGALNACT2	67	.	NM_018590	exon3	c.A693G	p.T231T	GGGCACACAGTAT	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4351534	4351534	+	Missense_Mutation	SNP	G	G	C	rs61740736	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	43	95	0	0.417476	0	G|0.989;C|0.011	0.011	strong	.	SPNS3	52	.	NM_182538	exon6	c.G706C	p.G236R	ACACAGGGGGAGG	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	28	132	0	0.282828	0	A|0.646;T|0.354	0.354	strong	KRTAP4-5,colon,carcinoma,0,3	KRTAP4-5	34	3	NM_033188	exon1	c.T235A	p.C79S	AGCAGCAGGGGCG	.	PASS	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80364341	80364341	+	Silent	SNP	C	C	T	rs34315006	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	25	41	0	0.431034	0	C|0.997;T|0.003	0.003	strong	.	.	.	.	NM_175902	exon5	c.G441A	p.L147L	TGAGTGCAAGTCC	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077755	19077755	+	Silent	SNP	A	A	C	rs11024969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	45	91	0	0.454545	0	A|0.900;C|0.100	0.100	strong	MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	NM_054030	exon2	c.T195G	p.S65S	GTAGACAGAGAAG	.	PASS	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97877478	97877478	+	Missense_Mutation	SNP	G	G	A	rs10194525	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	503	172	417	0	0.341948	0	G|0.500;A|0.500	0.500	strong	ANKRD36_ENST00000420699,NS,carcinoma,0,2	ANKRD36	170	2	NM_001164315	exon58	c.G3469A	p.V1157M	GGGACAGGTAATT	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299188	125299188	+	Silent	SNP	T	T	G	rs12014937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	107	0	1	0	T|0.485;G|0.515	0.515	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.A720C	p.P240P	ATATACTGGGAGA	.	PASS	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21909548	21909548	+	Silent	SNP	A	A	G	rs371600049	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	27	43	0	0.75	0	.	.	weak	.	ZNF100	62	.	NM_173531	exon5	c.T1566C	p.F522F	CTGGTTAAAGTCT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	79	0	0.459459	0	A|0.702;G|0.298	0.298	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T197C	p.F66S	AGCCTGAAGAGGA	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790471	4790471	+	Missense_Mutation	SNP	G	G	A	rs1030723	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	63	132	0	0.443662	0	G|0.798;A|0.202	0.202	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C677T	p.S226F	AGGACAGAGTGAA	.	PASS	Atlas-SNP
ADRB1	153	hgsc.bcm.edu	37	10	115804206	115804206	+	Silent	SNP	G	G	T	rs7921133	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	52	118	0	0.448276	0	G|0.963;T|0.037	0.037	strong	.	ADRB1	16	.	NM_000684	exon1	c.G315T	p.L105L	CGACCTGGTCATG	.	PASS	Atlas-SNP
SFRP4	6424	hgsc.bcm.edu	37	7	37947103	37947103	+	Missense_Mutation	SNP	C	C	T	rs1802074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	349	305	0	1	0	C|0.744;T|0.256	0.256	strong	.	SFRP4	66	.	NM_003014	exon6	c.G1019A	p.R340K	TTTGTTCTCTTCT	.	PASS	Atlas-SNP
RBP1	5947	hgsc.bcm.edu	37	3	139258508	139258508	+	Missense_Mutation	SNP	G	G	A	rs2071386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	5	7	0	0.454545	0	G|0.850;A|0.150	0.150	strong	.	RBP1	39	.	NM_002899	exon1	c.C53T	p.P18L	CTCTGCGGGGCGG	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17513414	17513414	+	Silent	SNP	G	G	A	rs12224	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	102	229	0	0.474419	0	G|0.920;A|0.080	0.080	strong	.	MTUS1	144	.	NM_001001924	exon9	c.C3066T	p.Y1022Y	TTCAATGTAAGTG	.	PASS	Atlas-SNP
PSTK	118672	hgsc.bcm.edu	37	10	124742858	124742858	+	Silent	SNP	G	G	A	rs45498396	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	58	114	0	0.563107	0	G|0.842;A|0.158	0.158	strong	.	PSTK	34	.	NM_153336	exon3	c.G579A	p.R193R	CCAGAGGCCACAG	.	PASS	Atlas-SNP
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329779	24329779	+	Missense_Mutation	SNP	C	C	G	rs189357682	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	130	198	0	0.588235	0	C|0.927;G|0.073	0.073	strong	.	.	.	.	NM_001136233	exon1	c.G1654C	p.G552R	GGCGCCCGGCAGC	.	PASS	Atlas-SNP
AHR	196	hgsc.bcm.edu	37	7	17379110	17379110	+	Missense_Mutation	SNP	G	G	A	rs2066853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	37	0	1	0	G|0.757;A|0.243	0.243	strong	.	AHR	89	.	NM_001621	exon10	c.G1661A	p.R554K	ACATCAGACACAT	.	PASS	Atlas-SNP
SLC7A5	8140	hgsc.bcm.edu	37	16	87902684	87902684	+	Silent	SNP	G	G	T	rs17853938	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	62	111	0	0.563636	0	G|0.835;T|0.165	0.165	strong	.	SLC7A5	28	.	NM_003486	exon1	c.C345A	p.G115G	GTAGTCGCCGCCC	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	37	19	41198210	41198210	+	Silent	SNP	A	A	G	rs17851001	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	38	86	0	0.404255	0	A|0.986;G|0.014	0.014	strong	.	ADCK4	92	.	NM_024876	exon15	c.T1365C	p.Y455Y	AAAGTCATAAGGG	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50746166	50746166	+	Silent	SNP	G	G	C	rs368983791		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	400	8	376	2	0.02	0.00531915	.	.	weak	FAM186A_ENST00000327337,NS,carcinoma,0,3	FAM186A	181	3	NM_001145475	exon4	c.C4449G	p.L1483L	AGGGATGAGAGGG	.	scavenged	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48807367	48807367	+	Silent	SNP	C	C	A	rs28582401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	85	0	1	0	C|0.817;A|0.183	0.183	strong	.	CCDC114	100	.	NM_144577	exon7	c.G585T	p.L195L	CTCCCGCAGCAAG	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87229948	87229948	+	Silent	SNP	T	T	A	rs4621787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	34	56	0	0.507463	0	A|0.126;G|0.000;T|0.873	0.126	strong	.	SLC7A13	97	.	NM_138817	exon3	c.A930T	p.S310S	TCTCGATGATTTA	.	PASS	Atlas-SNP
CD300E	342510	hgsc.bcm.edu	37	17	72613589	72613589	+	Missense_Mutation	SNP	T	T	G	rs581157	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	81	0	1	0	T|0.531;G|0.469	0.469	strong	.	CD300E	70	.	NM_181449	exon2	c.A56C	p.K19T	GGGCCCTTCAGAG	.	PASS	Atlas-SNP
MAP3K9	4293	hgsc.bcm.edu	37	14	71202692	71202692	+	Silent	SNP	T	T	C	rs78155813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	44	85	0	0.54321	0	T|0.989;C|0.011	0.011	strong	.	MAP3K9	109	.	NM_033141	exon9	c.A1899G	p.P633P	GAAATGTGGAGAT	.	PASS	Atlas-SNP
RLBP1	6017	hgsc.bcm.edu	37	15	89762198	89762198	+	Missense_Mutation	SNP	T	T	G	rs146844731	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	38	76	0	0.603175	0	T|0.998;G|0.002	0.002	strong	RLBP1,NS,carcinoma,-2,1	RLBP1	34	1	NM_000326	exon3	c.A9C	p.E3D	TACCCCTTCTGAC	.	PASS	Atlas-SNP
GPRASP2	114928	hgsc.bcm.edu	37	X	101970877	101970877	+	Silent	SNP	T	T	C	rs113906002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	38	104	0	0.336283	0	T|0.986;C|0.014	0.014	strong	.	GPRASP2	89	.	NM_138437	exon4	c.T1080C	p.T360T	TAATACTGCCTTG	.	PASS	Atlas-SNP
SLC2A1	6513	hgsc.bcm.edu	37	1	43396414	43396414	+	Silent	SNP	G	G	A	rs11537641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	30	53	0	0.535714	0	G|0.840;A|0.160	0.160	strong	.	SLC2A1	36	.	NM_006516	exon4	c.C399T	p.C133C	CAGGCCGCAGTAC	.	PASS	Atlas-SNP
DENND2A	27147	hgsc.bcm.edu	37	7	140221878	140221878	+	Silent	SNP	G	G	A	rs61737088	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	29	42	0	0.508772	0	G|0.993;A|0.007	0.007	strong	.	DENND2A	132	.	NM_015689	exon16	c.C2688T	p.N896N	CACCTCGTTCAAG	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67809160	67809160	+	Missense_Mutation	SNP	C	C	G	rs35595089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	59	146	0	0.495798	0	C|0.993;G|0.007	0.007	strong	.	MCMDC2	84	.	NM_173518	exon12	c.C1592G	p.A531G	ATGCGGCTTCTAG	.	PASS	Atlas-SNP
MRPL22	29093	hgsc.bcm.edu	37	5	154346259	154346259	+	Silent	SNP	A	A	G	rs14922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	71	152	0	0.482993	0	T|0.168;G|0.092	0.092	strong	.	MRPL22	18	.	NM_014180	exon7	c.A423G	p.S141S	CACCTCAGGACGA	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16918459	16918459	+	Missense_Mutation	SNP	C	C	T	rs78570914	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	125	0	0.439024	0	C|0.997;T|0.003	0.003	strong	NWD1_ENST00000524140,NS,carcinoma,-1,3	NWD1	303	3	NM_001007525	exon18	c.C3799T	p.R1267C	GAGCAGCGCAAGC	.	PASS	Atlas-SNP
EPHB6	2051	hgsc.bcm.edu	37	7	142562011	142562011	+	Silent	SNP	C	C	T	rs8177141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	60	99	0	0.566038	0	C|0.970;T|0.030	0.030	strong	EPHB6,right_lower_lobe,carcinoma,-2,1	EPHB6	168	1	NM_004445	exon7	c.C453T	p.R151R	CAAACGCTGGACC	.	PASS	Atlas-SNP
LONRF2	164832	hgsc.bcm.edu	37	2	100911980	100911980	+	Silent	SNP	C	C	T	rs116227203	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	41	80	0	0.455556	0	C|0.986;T|0.014	0.014	strong	.	LONRF2	62	.	NM_198461	exon8	c.G1512A	p.L504L	TTCGGCCAGAACA	.	PASS	Atlas-SNP
C9orf171	389799	hgsc.bcm.edu	37	9	135418389	135418389	+	Silent	SNP	G	G	A	rs61308567	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	88	0	1	0	G|0.948;A|0.052	0.052	strong	.	C9orf171	53	.	NM_207417	exon6	c.G795A	p.P265P	CAAGCCGCCCGTG	.	PASS	Atlas-SNP
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27886820	27886820	+	Silent	SNP	G	G	T	rs58106741	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	66	0	0.45614	0	G|0.940;T|0.060	0.060	strong	.	SLC4A1AP	63	.	NM_018158	exon1	c.G201T	p.S67S	GGCGTCGCAAGAC	.	PASS	Atlas-SNP
AGO3	192669	hgsc.bcm.edu	37	1	36521340	36521340	+	Silent	SNP	C	C	T	rs61743816	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	43	122	0	0.477778	0	C|0.992;T|0.008	0.008	strong	.	.	.	.	NM_024852	exon19	c.C2577T	p.F859F	GTACTTCGCTTAA	.	PASS	Atlas-SNP
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	36	93	0	0.423529	0	C|0.654;T|0.346	0.346	strong	MRAP2,NS,carcinoma,0,1	MRAP2	40	1	NM_138409	exon4	c.C603T	p.H201H	CTCACACAAAGAC	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744195	54744195	+	Missense_Mutation	SNP	G	G	A	rs1132604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	43	324	0	0.142857	0	G|0.954;A|0.046	0.046	strong	LILRA6,colon,carcinoma,+1,1	LILRA6	75	1	NM_024318	exon6	c.C1213T	p.H405Y	GCAGGTGGGGGTT	.	scavenged	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184765072	184765072	+	Missense_Mutation	SNP	A	A	G	rs28927681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	32	74	0	0.492308	0	G|0.177;A|0.823	0.177	strong	FAM129A,NS,carcinoma,-1,2	FAM129A	98	2	NM_052966	exon14	c.T1826C	p.L609P	CTACCCAGAACTC	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228118867	228118867	+	Missense_Mutation	SNP	G	G	A	rs80109666	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	61	125	0	0.451852	0	G|0.956;A|0.044	0.044	strong	.	COL4A3	293	.	NM_000091	exon14	c.G805A	p.E269K	ATGGGCGAGCCTG	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158533224	158533224	+	Silent	SNP	A	A	G	rs12081915	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	96	0	1	0	A|0.441;G|0.558	0.558	strong	OR6P1,NS,carcinoma,-1,1	OR6P1	47	1	NM_001160325	exon1	c.T171C	p.R57R	CATGGGACGATGA	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24524958	24524958	+	Missense_Mutation	SNP	C	C	T	rs7603997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	28	73	0	0.405797	0	C|0.652;N|0.000	.	strong	.	ITSN2	224	.	NM_147152	exon10	c.G871A	p.V291I	CATCAACGTCAGC	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	37	2	241713646	241713646	+	Silent	SNP	A	A	G	rs1063353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	105	153	0	0.512195	0	A|0.528;G|0.472	0.472	strong	.	KIF1A	152	.	NM_001244008	exon12	c.T991C	p.L331L	GACTCAAGGCTGC	.	PASS	Atlas-SNP
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201951	32201951	+	Silent	SNP	A	A	G	rs9982775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	103	208	0	0.497585	0	A|0.490;G|0.510	0.510	strong	.	.	.	.	NM_181606	exon2	c.T66C	p.H22H	GGTCCCATGGAAG	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	77010661	77010661	+	Silent	SNP	T	T	C	rs17152629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	15	43	0	0.405405	0	T|0.965;C|0.035	0.035	strong	.	PION	74	.	NM_017439	exon8	c.A537G	p.Q179Q	ACGAAATTGTTCA	.	PASS	Atlas-SNP
FYB	2533	hgsc.bcm.edu	37	5	39202911	39202911	+	Missense_Mutation	SNP	G	G	A	rs1642515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	57	121	0	0.475	0	G|0.959;A|0.041	0.041	strong	.	FYB	354	.	NM_001243093	exon2	c.C182T	p.P61L	TTGCTGGGTCCTG	.	PASS	Atlas-SNP
FXYD3	5349	hgsc.bcm.edu	37	19	35612168	35612168	+	Missense_Mutation	SNP	T	T	A	rs1688016	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	248	182	0	0.992	0	T|0.672;A|0.328	0.328	strong	.	FXYD3	15	.	NM_001136010	exon5	c.T116A	p.L39H	GCCCCCTTTCCCC	.	PASS	Atlas-SNP
MMP21	118856	hgsc.bcm.edu	37	10	127456150	127456150	+	Missense_Mutation	SNP	G	G	A	rs28381319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	64	135	0	0.507937	0	G|0.956;A|0.044	0.044	strong	.	MMP21	46	.	NM_147191	exon6	c.C1361T	p.A454V	TAAAACGCCGTGT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12187210	12187210	+	Silent	SNP	A	A	G	rs6511764	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	33	54	1	0.55	0.0185185	A|0.772;G|0.228	0.228	strong	ZNF844,right_upper_lobe,carcinoma,0,2	ZNF844	69	2	NM_001136501	exon4	c.A1275G	p.V425V	CAGTGTAGTAAAG	.	scavenged	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801104	140801104	+	Missense_Mutation	SNP	T	T	C	rs11167744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	56	99	0	0.478632	0	T|0.896;C|0.104	0.104	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.T310C	p.F104L	TCCTGTTTTTTAA	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94320237	94320237	+	Silent	SNP	T	T	C	rs7110167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	21	61	0	0.362069	0	T|0.476;C|0.524	0.524	strong	PIWIL4,NS,carcinoma,+2,1	PIWIL4	70	1	NM_152431	exon7	c.T738C	p.F246F	TGGGTTTGCCATT	.	PASS	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39847153	39847153	+	Missense_Mutation	SNP	C	C	A	rs150676991	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	110	216	0	0.44	0	C|0.998;A|0.002	0.002	strong	.	DAAM2	101	.	NM_015345	exon14	c.C1745A	p.P582H	CCCTCCCTCAGGA	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64519053	64519053	+	Silent	SNP	C	C	T	rs35960129	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	56	85	0	0.491228	0	C|0.990;T|0.010	0.010	strong	.	SYNE2	577	.	NM_182914	exon48	c.C8422T	p.L2808L	AATACCCTAGAGG	.	PASS	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70078393	70078393	+	Nonsense_Mutation	SNP	C	C	T	rs138593124	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	151	312	0	0.449405	0	C|0.993;T|0.007	0.007	strong	.	UGT2B11	92	.	NM_001073	exon2	c.G768A	p.W256X	CATAAGCCATATG	.	PASS	Atlas-SNP
TBX3	6926	hgsc.bcm.edu	37	12	115118722	115118722	+	Silent	SNP	G	G	A	rs35069811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	118	231	0	0.460938	0	G|0.979;A|0.021	0.021	strong	.	TBX3	106	.	NM_005996	exon2	c.C619T	p.L207L	GTTTCAGTTTGTG	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108384857	108384857	+	Silent	SNP	T	T	C	rs116565594	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	55	136	0	0.474138	0	T|0.987;C|0.013	0.013	strong	.	EXPH5	193	.	NM_015065	exon6	c.A1377G	p.R459R	GAAAGATCTGGTA	.	PASS	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73627539	73627539	+	Missense_Mutation	SNP	T	T	C	rs820196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	73	173	0	0.489933	0	T|0.746;C|0.254	0.254	strong	.	RECQL5	77	.	NM_004259	exon9	c.A1439G	p.D480G	CTGAAGTCCCCGT	.	PASS	Atlas-SNP
FASTKD1	79675	hgsc.bcm.edu	37	2	170428198	170428198	+	Silent	SNP	G	G	A	rs113959605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	45	157	0	0.424528	0	G|0.993;A|0.007	0.007	strong	.	FASTKD1	86	.	NM_024622	exon2	c.C342T	p.D114D	GGTATCGTCATTC	.	PASS	Atlas-SNP
LCN1	3933	hgsc.bcm.edu	37	9	138413373	138413373	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	11	202	0	0.0514019	0	.	.	none	LCN1,NS,carcinoma,0,3	LCN1	21	3	NM_001252617	exon1	c.T30C	p.L10L	CAGCCTTGGCCTC	.	scavenged	Atlas-SNP
RPL5	6125	hgsc.bcm.edu	37	1	93299193	93299193	+	Silent	SNP	G	G	A	rs58263806	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	25	67	0	0.357143	0	G|0.977;A|0.023	0.023	strong	.	RPL5	38	.	NM_000969	exon3	c.G165A	p.V55V	TCGTGTGACAAAC	.	PASS	Atlas-SNP
CDK5R1	8851	hgsc.bcm.edu	37	17	30815208	30815208	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	20	107	0	0.152672	0	.	.	none	.	CDK5R1	30	.	NM_003885	exon2	c.G570A	p.W190X	GGGCTGGCAGGAC	.	PASS	Atlas-SNP
SKA1	220134	hgsc.bcm.edu	37	18	47918536	47918536	+	Silent	SNP	C	C	T	rs16951872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	49	89	0	0.505155	0	C|0.925;T|0.075	0.075	strong	.	SKA1	21	.	NM_001039535	exon7	c.C687T	p.H229H	GTTTCACGTGTTA	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887546	9887546	+	Missense_Mutation	SNP	G	G	A	rs2240906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	56	123	0	0.466667	0	G|0.562;A|0.438	0.438	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.G1070A	p.G357D	AGAAGGGTGACAT	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	142	218	0	0.501767	0	C|0.840;G|0.160	0.160	strong	.	HLA-C	92	.	NM_002117	exon2	c.G270C	p.K90N	CTTGTACTTCTGT	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124352728	124352728	+	Silent	SNP	G	G	A	rs652863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	47	79	0	0.573171	0	G|0.917;A|0.083	0.083	strong	TRAD,NS,carcinoma,+1,2	KALRN	556	2	NM_001024660	exon36	c.G5493A	p.P1831P	TGAGCCGGATGAA	.	PASS	Atlas-SNP
CLYBL	171425	hgsc.bcm.edu	37	13	100425097	100425097	+	Missense_Mutation	SNP	G	G	T	rs17577293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	43	120	0	0.488636	0	G|0.982;T|0.018	0.018	strong	.	CLYBL	48	.	NM_206808	exon2	c.G82T	p.D28Y	GCAGCTGATATCC	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61542863	61542863	+	Silent	SNP	G	G	A	rs11907248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	93	148	0	0.508197	0	G|0.924;A|0.076	0.076	strong	.	DIDO1	321	.	NM_080797	exon3	c.C102T	p.I34I	CTTGGCGATAGTG	.	PASS	Atlas-SNP
SERPINB8	5271	hgsc.bcm.edu	37	18	61654297	61654297	+	Missense_Mutation	SNP	A	A	G	rs3169983	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	65	118	0	0.474453	0	A|0.851;G|0.149	0.149	strong	.	SERPINB8	42	.	NM_198833	exon7	c.A910G	p.T304A	ATGTCAACTGAGA	.	PASS	Atlas-SNP
CYTH4	27128	hgsc.bcm.edu	37	22	37693632	37693632	+	Silent	SNP	C	C	T	rs73887105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	48	123	0	0.516129	0	C|0.992;T|0.008	0.008	strong	.	CYTH4	51	.	NM_013385	exon5	c.C262T	p.L88L	CACAAGCTGCTGA	.	PASS	Atlas-SNP
FH	2271	hgsc.bcm.edu	37	1	241676972	241676972	+	Silent	SNP	G	G	A	rs10926501	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	141	282	0	0.516484	0	G|0.975;A|0.025	0.025	strong	FH,NS,carcinoma,0,2	FH	64	2	NM_000143	exon3	c.C309T	p.A103A	TTCAGCGGCCGCT	.	PASS	Atlas-SNP
PANK4	55229	hgsc.bcm.edu	37	1	2441358	2441358	+	Missense_Mutation	SNP	T	T	C	rs2494620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	102	187	0	0.512563	0	T|0.615;C|0.385	0.385	strong	PANK4,NS,lymphoid_neoplasm,0,2	PANK4	64	2	NM_018216	exon18	c.A2051G	p.Q684R	TCTTCCTGGAGCG	.	PASS	Atlas-SNP
CCDC94	55702	hgsc.bcm.edu	37	19	4251069	4251069	+	Silent	SNP	T	T	C	rs1045750	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	155	147	1	1	0.00680272	T|0.563;C|0.437	0.437	strong	CCDC94,NS,carcinoma,0,1	CCDC94	28	1	NM_018074	exon3	c.T171C	p.N57N	ATTCAATGCTCGG	.	PASS	Atlas-SNP
PHAX	51808	hgsc.bcm.edu	37	5	125944131	125944131	+	Silent	SNP	G	G	C	rs61747690	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	46	122	0	0.489362	0	G|0.963;C|0.037	0.037	strong	.	PHAX	20	.	NM_032177	exon3	c.G786C	p.L262L	ACTTCTGATGGAA	.	PASS	Atlas-SNP
CCDC69	26112	hgsc.bcm.edu	37	5	150567017	150567017	+	Missense_Mutation	SNP	A	A	G	rs61745454	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	22	27	0	0.458333	0	A|0.960;G|0.040	0.040	strong	.	CCDC69	30	.	NM_015621	exon5	c.T323C	p.L108P	GCCCGGAGGACTG	.	PASS	Atlas-SNP
PRSS12	8492	hgsc.bcm.edu	37	4	119237348	119237348	+	Silent	SNP	T	T	C	rs2292597	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	107	0	1	0	T|0.467;C|0.533	0.533	strong	PRSS12,NS,carcinoma,0,1	PRSS12	71	1	NM_003619	exon6	c.A1281G	p.Q427Q	TCCCAATTGTCGA	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	37	6	97580539	97580539	+	Silent	SNP	A	A	G	rs13208956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	28	54	0	0.5	0	A|0.967;G|0.033	0.033	strong	KLHL32,neck,malignant_melanoma,+2,1	KLHL32	85	1	NM_052904	exon10	c.A1617G	p.E539E	AAATGAATCTGGA	.	PASS	Atlas-SNP
SLC17A3	10786	hgsc.bcm.edu	37	6	25849620	25849620	+	Silent	SNP	A	A	G	rs942379	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	62	0	1	0	A|0.326;G|0.674	0.674	strong	.	SLC17A3	95	.	NM_001098486	exon11	c.T1344C	p.S448S	AAATCCACTGACA	.	PASS	Atlas-SNP
VAV2	7410	hgsc.bcm.edu	37	9	136633606	136633606	+	Silent	SNP	G	G	A	rs9722384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	68	69	0	0.715789	0	G|0.895;A|0.105	0.105	strong	.	VAV2	165	.	NM_001134398	exon29	c.C2547T	p.I849I	TCCGCCGATGCGG	.	PASS	Atlas-SNP
DCLK1	9201	hgsc.bcm.edu	37	13	36385031	36385031	+	Silent	SNP	G	G	T	rs2322807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	62	133	0	0.521008	0	G|0.713;T|0.287	0.287	strong	.	DCLK1	350	.	NM_004734	exon12	c.C1629A	p.P543P	GTACAGGGGGCCG	.	PASS	Atlas-SNP
DNAH12	201625	hgsc.bcm.edu	37	3	57469151	57469151	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	79	169	0	0.509677	0	.	.	none	.	DNAH12	182	.	NM_178504	exon13	c.A1602G	p.V534V	TTTTTCTACATAA	.	PASS	Atlas-SNP
PHRF1	57661	hgsc.bcm.edu	37	11	609577	609577	+	Missense_Mutation	SNP	C	C	T	rs7123948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	46	77	0	0.541176	0	C|0.902;T|0.098	0.098	strong	.	PHRF1	188	.	NM_020901	exon14	c.C4118T	p.A1373V	CCTCTGCGAGTGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552092	32552092	+	Missense_Mutation	SNP	A	A	T	rs16822516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	22	31	0	0.338462	0	A|0.778;T|0.222	0.222	strong	.	HLA-DRB1	41	.	NM_002124	exon2	c.T164A	p.F55Y	TCCAGGAACCGCA	.	PASS	Atlas-SNP
NUMBL	9253	hgsc.bcm.edu	37	19	41190455	41190455	+	Missense_Mutation	SNP	G	G	T	rs143941883	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	58	145	0	0.394558	0	G|0.987;T|0.013	0.013	strong	.	NUMBL	49	.	NM_004756	exon3	c.C116A	p.A39E	GTGCCCGCCCCGT	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12410362	12410362	+	Silent	SNP	C	C	T	rs1072557	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	100	152	0	0.588235	0	T|0.098;G|0.321;C|0.497;A|0.083	0.098	strong	VWDE_ENST00000275358,colon,carcinoma,0,1	VWDE	123	1	NM_001135924	exon11	c.G1716A	p.P572P	ATTTTCCGGATTT	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135368590	135368590	+	Missense_Mutation	SNP	T	T	C	rs3737031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	85	164	0	0.47486	0	T|0.856;C|0.144	0.144	strong	SYCE1_ENST00000343131,NS,carcinoma,0,1	SYCE1	81	1	NM_001143764	exon13	c.A962G	p.H321R	GCTTGGTGTGCAG	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	517622	517622	+	Silent	SNP	C	C	T	rs13150531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	64	117	0	0.481203	0	C|0.779;T|0.221	0.221	strong	.	PIGG	86	.	NM_001127178	exon9	c.C1989T	p.A663A	ACTGGCCTGCTGC	.	PASS	Atlas-SNP
CETP	1071	hgsc.bcm.edu	37	16	57017279	57017279	+	Missense_Mutation	SNP	G	G	A	rs2228667	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	107	0	0.515789	0	A|0.002;G|0.998	0.002	strong	CETP,NS,carcinoma,-1,1	CETP	50	1	NM_000078	exon15	c.G1363A	p.V455M	AAAGGCGTGAGCC	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3599220	3599220	+	Missense_Mutation	SNP	C	C	T	rs373104014		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	43	103	0	0.434343	0	.	.	weak	.	NLRC3	103	.	NM_178844	exon14	c.G2525A	p.R842Q	TTTTCTCGAAGGC	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78896529	78896529	+	Silent	SNP	C	C	T	rs2271603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	32	58	0	0.484848	0	C|0.748;T|0.252	0.252	strong	RPTOR,NS,carcinoma,0,1	RPTOR	122	1	NM_020761	exon22	c.C2526T	p.T842T	GGCCACCGTGAAC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78937974	78937974	+	Missense_Mutation	SNP	C	C	T	rs3001772	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	54	56	0	0.72	0	C|0.517;T|0.483	0.483	strong	.	PCSK5	329	.	NM_001190482	exon31	c.C4028T	p.T1343M	AGTGCACGCCTGA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169529826	169529826	+	Silent	SNP	C	C	A	rs6022	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	194	147	0	0.994872	0	C|0.638;A|0.362	0.362	strong	.	F5	301	.	NM_000130	exon4	c.G552T	p.S184S	CAGCCCCGAGTTG	.	PASS	Atlas-SNP
SPINT4	391253	hgsc.bcm.edu	37	20	44351095	44351095	+	Missense_Mutation	SNP	C	C	A	rs16990631	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	99	197	0	0.515625	0	C|0.963;A|0.037	0.037	strong	.	SPINT4	17	.	NM_178455	exon1	c.C89A	p.A30E	AAATTGCGGAGAA	.	PASS	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24797333	24797333	+	Missense_Mutation	SNP	G	G	C	rs1220545	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	50	60	0	0.632911	0	G|0.997;C|0.003	0.003	strong	.	SPATA13	92	.	NM_001166271	exon2	c.G266C	p.R89P	CCGAGCGGCCCCA	.	PASS	Atlas-SNP
DDI1	414301	hgsc.bcm.edu	37	11	103908517	103908517	+	Missense_Mutation	SNP	G	G	A	rs116423827	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	41	105	0	0.350427	0	G|0.995;A|0.005	0.005	strong	.	DDI1	222	.	NM_001001711	exon1	c.G967A	p.D323N	CTTGAGGATCAAC	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192330	102192330	+	Silent	SNP	T	T	C	rs61745025	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	278	341	0	0.996416	0	T|0.823;C|0.177	0.177	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.T84C	p.S28S	CAAGAGTGAGATC	.	PASS	Atlas-SNP
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	41	70	0	0.554054	0	A|0.868;T|0.132	0.132	strong	.	.	.	.	NM_017986	exon5	c.T1263A	p.L421L	GGCACCAAGCAGG	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160468278	160468278	+	Silent	SNP	A	A	G	rs998075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	72	0	1	0	A|0.458;G|0.542	0.542	strong	.	IGF2R	251	.	NM_000876	exon16	c.A2139G	p.T713T	CGGCACACCCTAT	.	PASS	Atlas-SNP
RPS24	6229	hgsc.bcm.edu	37	10	79814747	79814747	+	Silent	SNP	C	C	T	rs76653255	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	55	134	0	0.509259	0	C|0.947;T|0.053	0.053	strong	.	RPS24	23	.	NM_001142285	exon5	c.C849T	p.C283C	TTCCTGCCTCTCT	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135613947	135613947	+	Missense_Mutation	SNP	C	C	T	rs35003767	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	83	0	0.47561	0	C|0.971;T|0.029	0.029	strong	.	ZFAT	265	.	NM_020863	exon6	c.G2015A	p.R672K	AGACACCTGCTGG	.	PASS	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	75	172	0	0.471698	0	T|0.725;C|0.275	0.275	strong	PLCD1_ENST00000463876,NS,carcinoma,0,2	PLCD1	87	2	NM_001130964	exon6	c.A966G	p.P322P	GCTAAGTGGCTGG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46496854	46496854	+	Missense_Mutation	SNP	G	G	A	rs60938611	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	68	132	0	0.482269	0	G|0.949;A|0.051	0.051	strong	.	LTF	98	.	NM_002343	exon5	c.C578T	p.A193V	GTCCCCGCACACA	.	PASS	Atlas-SNP
FAM9B	171483	hgsc.bcm.edu	37	X	8997440	8997440	+	Missense_Mutation	SNP	G	G	A	rs141078293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	75	166	0	0.394737	0	G|0.993;A|0.007	0.007	strong	.	FAM9B	32	.	NM_205849	exon5	c.C301T	p.H101Y	GAGAATGTATATA	.	PASS	Atlas-SNP
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257381	114257381	+	Missense_Mutation	SNP	T	T	G	rs13428956	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	82	148	0	0.471264	0	T|0.973;G|0.027	0.027	strong	.	FOXD4L1	48	.	NM_012184	exon1	c.T548G	p.L183R	GGAGCCTGGACCC	.	PASS	Atlas-SNP
HAP1	9001	hgsc.bcm.edu	37	17	39884065	39884065	+	Missense_Mutation	SNP	C	C	A	rs35612698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	29	52	0	0.446154	0	C|0.692;A|0.308	0.308	strong	.	HAP1	48	.	NM_177977	exon8	c.G1224T	p.L408F	CTTCTGCAACTTT	.	PASS	Atlas-SNP
ATAD2	29028	hgsc.bcm.edu	37	8	124357302	124357302	+	Missense_Mutation	SNP	C	C	T	rs78548009	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	44	61	0	0.578947	0	C|0.999;T|0.001	0.001	strong	ATAD2,NS,carcinoma,0,1	ATAD2	160	1	NM_014109	exon19	c.G2540A	p.R847H	GCTTCACGAATCA	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	37	3	182994744	182994744	+	Missense_Mutation	SNP	C	C	T	rs61731401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	47	131	0	0.451923	0	C|0.975;T|0.025	0.025	strong	MCF2L2,brain,glioma,0,1	MCF2L2	164	1	NM_015078	exon15	c.G1778A	p.S593N	TCTTCACTCTGAA	.	PASS	Atlas-SNP
HSD17B12	51144	hgsc.bcm.edu	37	11	43876698	43876698	+	Missense_Mutation	SNP	C	C	T	rs11555762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	62	128	0	0.469697	0	C|0.665;T|0.335	0.335	strong	.	HSD17B12	25	.	NM_016142	exon11	c.C839T	p.S280L	AGGGCTCGATAAT	.	PASS	Atlas-SNP
TSSK6	83983	hgsc.bcm.edu	37	19	19626087	19626087	+	Silent	SNP	C	C	T	rs150432013	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	38	50	0	0.527778	0	C|0.996;T|0.004	0.004	strong	.	TSSK6	32	.	NM_032037	exon1	c.G150A	p.P50P	GAAGTCCGGGGGC	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	37	2	135988236	135988236	+	Nonsense_Mutation	SNP	G	G	A	rs200823309	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	145	349	0	0.448916	0	G|1.000;A|0.000	0.000	strong	.	ZRANB3	109	.	NM_032143	exon13	c.C1801T	p.R601X	GAGTTCGGATTTG	.	PASS	Atlas-SNP
BIN3	55909	hgsc.bcm.edu	37	8	22481449	22481449	+	Silent	SNP	A	A	G	rs1871900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	91	83	0	0.98913	0	G|0.475;C|0.000;A|0.525	0.475	strong	.	BIN3	16	.	NM_018688	exon8	c.T594C	p.F198F	GGACTCAAAGCTG	.	PASS	Atlas-SNP
RASA2	5922	hgsc.bcm.edu	37	3	141327474	141327474	+	Silent	SNP	G	G	A	rs295323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	113	201	0	0.511312	0	G|0.523;A|0.477	0.477	strong	RASA2_ENST00000286364,NS,carcinoma,0,1	RASA2	169	1	NM_006506	exon21	c.G2160A	p.L720L	GTATCTGAACGGA	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	50	128	0	0.423729	0	C|0.884;T|0.116	0.116	strong	.	KIF5C	166	.	NM_004522	exon9	c.C750T	p.D250D	TCTTGACGAAGCT	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232942028	232942028	+	Missense_Mutation	SNP	A	A	G	rs61739198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	87	0	1	0	A|0.970;G|0.030	0.030	strong	.	.	.	.	NM_019090	exon1	c.A1259G	p.N420S	CTGGCAATGGGAG	.	PASS	Atlas-SNP
OR6N2	81442	hgsc.bcm.edu	37	1	158746847	158746847	+	Silent	SNP	A	A	G	rs16841094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	93	0	1	0	A|0.870;G|0.130	0.130	strong	.	OR6N2	78	.	NM_001005278	exon1	c.T579C	p.S193S	GTTAGCAGATGTG	.	PASS	Atlas-SNP
FAM136A	84908	hgsc.bcm.edu	37	2	70528092	70528092	+	Silent	SNP	G	G	A	rs72904358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	113	217	2	0.502222	0.00921659	G|0.921;A|0.079	0.079	strong	FAM136A,caecum,carcinoma,0,1	FAM136A	14	1	NM_032822	exon2	c.C108T	p.S36S	GCTGGCGCTGCAC	.	scavenged	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52478215	52478215	+	Silent	SNP	C	C	T	rs3743797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	60	84	1	0.638298	0.0119048	C|0.891;T|0.109	0.109	strong	TOX3_ENST00000407228,NS,carcinoma,0,3	TOX3	121	3	NM_001080430	exon6	c.G960A	p.A320A	GTATGCCGCCAGG	.	scavenged	Atlas-SNP
TESK1	7016	hgsc.bcm.edu	37	9	35608962	35608962	+	Silent	SNP	C	C	T	rs148341917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	59	0	0.520548	0	C|0.994;T|0.006	0.006	strong	.	TESK1	46	.	NM_006285	exon10	c.C1104T	p.P368P	ATCACCCCCCAAC	.	PASS	Atlas-SNP
FIBCD1	84929	hgsc.bcm.edu	37	9	133787225	133787225	+	Silent	SNP	A	A	G	rs6597650	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	51	99	0	0.392308	0	A|0.442;G|0.558	0.558	strong	.	FIBCD1	34	.	NM_001145106	exon6	c.T900C	p.D300D	GTACGCATCCCAG	.	PASS	Atlas-SNP
SLC28A2	9153	hgsc.bcm.edu	37	15	45556163	45556163	+	Silent	SNP	T	T	C	rs8023604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	82	189	0	0.463277	0	T|0.841;C|0.159	0.159	strong	.	SLC28A2	64	.	NM_004212	exon6	c.T531C	p.F177F	CCCCTTTGCAGGA	.	PASS	Atlas-SNP
C8orf74	203076	hgsc.bcm.edu	37	8	10555263	10555263	+	Missense_Mutation	SNP	C	C	G	rs147047803	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	44	79	0	0.453608	0	C|0.997;G|0.003	0.003	strong	.	C8orf74	28	.	NM_001040032	exon3	c.C396G	p.D132E	CCAGGACCAGCAG	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448389	4448389	+	Missense_Mutation	SNP	G	G	T	rs72830101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	62	122	0	0.504065	0	G|0.995;T|0.005	0.005	strong	.	MYBBP1A	69	.	NM_014520	exon17	c.C2242A	p.R748S	CGTCGCGCTCCTC	.	PASS	Atlas-SNP
ASB16	92591	hgsc.bcm.edu	37	17	42254165	42254165	+	Missense_Mutation	SNP	A	A	G	rs146134954	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	19	67	0	0.316667	0	A|0.987;G|0.013	0.013	strong	.	ASB16	34	.	NM_080863	exon3	c.A629G	p.Q210R	AGAGCCAGGAGAC	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166758389	166758389	+	Missense_Mutation	SNP	C	C	T	rs76726265	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	80	178	0	0.441989	0	C|0.998;T|0.002	0.002	strong	TTC21B,NS,carcinoma,-1,1	TTC21B	130	1	NM_024753	exon20	c.G2600A	p.R867H	TGAACACGTTTTA	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85780131	85780131	+	Silent	SNP	G	G	A	rs2592551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	140	245	0	0.459016	0	G|0.693;A|0.307	0.307	strong	GGCX,NS,carcinoma,0,1	GGCX	44	1	NM_000821	exon9	c.C1218T	p.R406R	GTGGGAGCGGGAG	.	PASS	Atlas-SNP
ZNF519	162655	hgsc.bcm.edu	37	18	14106039	14106039	+	Missense_Mutation	SNP	T	T	C	rs62086326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	17	48	0	0.386364	0	T|0.799;C|0.201	0.201	strong	.	ZNF519	53	.	NM_145287	exon3	c.A500G	p.N167S	CTAATATTTGAGT	.	PASS	Atlas-SNP
SLC35D1	23169	hgsc.bcm.edu	37	1	67518534	67518534	+	Missense_Mutation	SNP	C	C	T	rs10157422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	80	1	1	0.0125	C|0.884;T|0.116	0.116	strong	SLC35D1,NS,carcinoma,+2,1	SLC35D1	22	1	NM_015139	exon3	c.G244A	p.A82T	CTGTGGCCACCAT	.	scavenged	Atlas-SNP
MYOZ3	91977	hgsc.bcm.edu	37	5	150056296	150056296	+	Silent	SNP	C	C	T	rs57761602	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	48	0	0.466667	0	C|0.902;T|0.098	0.098	strong	MYOZ3,colon,carcinoma,0,1	MYOZ3	21	1	NM_001122853	exon7	c.C615T	p.L205L	ACCCCTCGTGGGG	.	PASS	Atlas-SNP
SLC35C1	55343	hgsc.bcm.edu	37	11	45827783	45827783	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	4	63	0	0.0519481	0	.	.	none	.	SLC35C1	23	.	NM_018389	exon1	c.A431G	p.N144S	TCTACAATGTGGG	.	PASS	Atlas-SNP
AGXT2L1	64850	hgsc.bcm.edu	37	4	109674116	109674116	+	Missense_Mutation	SNP	A	A	G	rs1377210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	47	119	0	0.484536	0	A|0.791;G|0.209	0.209	strong	.	AGXT2L1	67	.	NM_031279	exon6	c.T553C	p.S185P	TGGCTGAGTCTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508382	195508382	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	354	69	417	0	0.194915	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C10069T	p.H3357Y	TGGCGTGACCTGT	.	PASS	Atlas-SNP
LRTOMT	220074	hgsc.bcm.edu	37	11	71806515	71806515	+	Silent	SNP	A	A	G	rs150245488	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	81	160	0	0.543624	0	A|0.995;G|0.005	0.005	strong	.	LRTOMT	20	.	NM_145309	exon6	c.A528G	p.K176K	CTGGAAACGCATG	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	134	0	1	0	T|0.549;C|0.451	0.451	strong	.	GPATCH1	79	.	NM_018025	exon2	c.T162C	p.S54S	CTTTAGTGGAGGT	.	PASS	Atlas-SNP
H6PD	9563	hgsc.bcm.edu	37	1	9324670	9324670	+	Silent	SNP	A	A	G	rs9434743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	65	143	0	0.414013	0	A|0.603;G|0.397	0.397	strong	.	H6PD	71	.	NM_004285	exon5	c.A2118G	p.S706S	ACAGTCACCCACT	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13055915	13055915	+	Missense_Mutation	SNP	A	A	C	rs11080623	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	50	125	0	0.46729	0	A|0.980;C|0.020	0.020	strong	.	CEP192	340	.	NM_032142	exon19	c.A3326C	p.Q1109P	TTATCCAGAATAA	.	PASS	Atlas-SNP
TARS2	80222	hgsc.bcm.edu	37	1	150470182	150470182	+	Silent	SNP	A	A	G	rs115388015	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	28	67	0	0.466667	0	A|0.981;G|0.019	0.019	strong	.	TARS2	91	.	NM_025150	exon10	c.A1197G	p.T399T	TATCACAGATACA	.	PASS	Atlas-SNP
MMS22L	253714	hgsc.bcm.edu	37	6	97613163	97613163	+	Silent	SNP	T	T	C	rs1209290	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	105	103	0	0.990566	0	T|0.475;C|0.525	0.525	strong	.	MMS22L	102	.	NM_198468	exon21	c.A3180G	p.P1060P	TATTGGTGGAATA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513468	195513468	+	Missense_Mutation	SNP	G	G	C	rs76596008	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	627	8	601	2	0.0127592	0.00332779	A|0.004;C|0.007;G|0.989	0.007	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C4983G	p.H1661Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
NEU2	4759	hgsc.bcm.edu	37	2	233899148	233899148	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	48	98	0	0.461538	0	.	.	none	.	NEU2	42	.	NM_005383	exon2	c.T524C	p.V175A	GCCTGGTGGTGCC	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39141120	39141120	+	Missense_Mutation	SNP	C	C	A	rs28705715	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	193	227	0	0.989744	0	C|0.914;A|0.086	0.086	strong	.	ADAM32	70	.	NM_145004	exon24	c.C2334A	p.D778E	ACAGGACAGTACC	.	PASS	Atlas-SNP
FPGT	8790	hgsc.bcm.edu	37	1	74670277	74670277	+	Silent	SNP	G	G	A	rs139749795	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	78	185	0	0.46988	0	G|0.996;A|0.004	0.004	strong	FPGT,NS,carcinoma,0,1	FPGT	77	1	NM_003838	exon4	c.G546A	p.R182R	TATTAGGTTTGAC	.	PASS	Atlas-SNP
SMC2	10592	hgsc.bcm.edu	37	9	106888978	106888978	+	Silent	SNP	C	C	T	rs6479217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	8	43	0	0.195122	0	C|0.935;T|0.065	0.065	strong	.	SMC2	127	.	NM_006444	exon19	c.C2508T	p.Y836Y	ATCTTACAAACAA	.	PASS	Atlas-SNP
FZD1	8321	hgsc.bcm.edu	37	7	90895944	90895944	+	Silent	SNP	C	C	T	rs2232161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	70	0	0.473684	0	C|0.983;T|0.017	0.017	strong	FZD1,NS,carcinoma,0,2	FZD1	64	2	NM_003505	exon1	c.C1749T	p.H583H	CCCTCACCTCCAG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27279185	27279185	+	Silent	SNP	A	A	T	rs16897553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	51	81	0	0.542553	0	A|0.953;T|0.047	0.047	strong	.	POM121L2	61	.	NM_033482	exon1	c.T765A	p.A255A	GCCAATAGCATTC	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5085245	5085245	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	18	154	0	0.18	0	.	.	none	.	ZNF594	89	.	NM_032530	exon2	c.C2307T	p.T769T	CTGGAAGGTCCTA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238283605	238283605	+	Silent	SNP	G	G	A	rs12622093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	63	0	0.490196	0	G|0.795;A|0.205	0.205	strong	COL6A3_ENST00000392004,NS,carcinoma,0,2	COL6A3	608	2	NM_004369	exon8	c.C3129T	p.G1043G	AGGGAAGCCGCTC	.	PASS	Atlas-SNP
ENTHD2	146705	hgsc.bcm.edu	37	17	79202956	79202956	+	Silent	SNP	T	T	C	rs2048057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	51	93	0	0.53125	0	A|0.000;C|0.395;T|0.605	0.395	strong	C17orf56,colon,carcinoma,0,1	.	.	1	NM_144679	exon12	c.A1350G	p.P450P	GCCCCCTGGGATC	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970993	45970993	+	Missense_Mutation	SNP	C	C	G	rs233239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	320	144	261	0	0.45	0	C|0.702;G|0.298	0.298	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G349C	p.A117P	AAGAAGCCCCACA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506258	195506258	+	Missense_Mutation	SNP	G	G	T	rs11929196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	270	154	0	0.967742	0	G|0.963;T|0.037	0.037	strong	.	MUC4	1505	.	NM_018406	exon2	c.C12193A	p.L4065I	CATGAAGAGGGGT	.	PASS	Atlas-SNP
FCGRT	2217	hgsc.bcm.edu	37	19	50017724	50017724	+	Silent	SNP	C	C	T	rs2878342	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	55	0	0.439394	0	C|0.846;T|0.154	0.154	strong	FCGRT,NS,carcinoma,0,1	FCGRT	23	1	NM_001136019	exon4	c.C582T	p.R194R	GGGCCGCGGAAAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513743	195513743	+	Missense_Mutation	SNP	G	G	T	rs59668135	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	148	278	0	0.544118	0	G|0.944;T|0.055	0.055	strong	.	MUC4	1505	.	NM_018406	exon2	c.C4708A	p.P1570T	TGACAGGAAGAGG	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504745	227504745	+	Silent	SNP	A	A	G	rs144296174	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	84	129	0	0.502994	0	A|1.000;G|0.000	0.000	strong	.	CDC42BPA	528	.	NM_003607	exon1	c.T139C	p.L47L	TTCTCAATGGAGA	.	PASS	Atlas-SNP
GUCA1C	9626	hgsc.bcm.edu	37	3	108639384	108639384	+	Missense_Mutation	SNP	T	T	C	rs6804162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	302	323	0	1	0	T|0.647;C|0.353	0.353	strong	.	GUCA1C	39	.	NM_005459	exon2	c.A253G	p.M85V	CTTGCATGATTAG	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61513649	61513649	+	Missense_Mutation	SNP	G	G	T	rs6011441	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	126	0	1	0	A|0.000;G|0.803;T|0.197	0.197	strong	DIDO1,NS,carcinoma,+1,1	DIDO1	321	1	NM_001193369	exon16	c.C3659A	p.P1220Q	TCTTCCGGTTGAA	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145007409	145007409	+	Silent	SNP	G	G	A	rs115081018	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	62	118	0	0.521008	0	G|0.988;A|0.012	0.012	strong	.	PLEC	1144	.	NM_201380	exon13	c.C1785T	p.T595T	CTTGAGGGTCTGC	.	PASS	Atlas-SNP
HMMR	3161	hgsc.bcm.edu	37	5	162910165	162910165	+	Missense_Mutation	SNP	G	G	C	rs2230362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	48	104	0	0.403361	0	G|0.990;C|0.010	0.010	strong	.	HMMR	64	.	NM_001142556	exon14	c.G1672C	p.D558H	CTGGAAGATGAAG	.	PASS	Atlas-SNP
CPNE2	221184	hgsc.bcm.edu	37	16	57144689	57144689	+	Missense_Mutation	SNP	C	C	T	rs141954860	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	66	114	0	0.536585	0	C|0.999;T|0.001	0.001	strong	.	CPNE2	48	.	NM_152727	exon2	c.C35T	p.A12V	CAGCAGCGGGGGC	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11583192	11583192	+	Missense_Mutation	SNP	C	C	T	rs8070501	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	50	90	0	0.50505	0	C|0.988;T|0.012	0.012	strong	DNAH9,rectum,carcinoma,0,1	DNAH9	695	1	NM_001372	exon18	c.C3472T	p.R1158W	AAAGAACGGCAGA	.	PASS	Atlas-SNP
SLCO1C1	53919	hgsc.bcm.edu	37	12	20864356	20864356	+	Silent	SNP	C	C	T	rs7963279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	62	186	0	0.492063	0	C|0.727;T|0.273	0.273	strong	.	SLCO1C1	216	.	NM_017435	exon5	c.C441T	p.S147S	CAATTCCACTCTC	.	PASS	Atlas-SNP
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	62	130	0	0.439716	0	C|0.897;T|0.103	0.103	strong	.	ZNF69	27	.	NM_021915	exon1	c.C39T	p.P13P	GGACCCCGGGACA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234113	8234113	+	Silent	SNP	G	G	A	rs2921005	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	45	99	0	0.46875	0	G|0.918;A|0.082	0.082	strong	.	.	.	.	NM_001080826	exon2	c.C1806T	p.V602V	GATAGCGACACCG	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179310262	179310262	+	Silent	SNP	C	C	T	rs11576517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	109	218	1	0.47807	0.00458716	C|0.773;T|0.227	0.227	strong	SOAT1,NS,carcinoma,0,1	SOAT1	53	1	NM_003101	exon7	c.C597T	p.P199P	AGTTCCCTATTTT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539175	110539175	+	Missense_Mutation	SNP	T	T	A	rs141977750	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	105	162	0	0.514706	0	T|0.993;A|0.007	0.007	strong	.	PKHD1L1	522	.	NM_177531	exon77	c.T12647A	p.I4216N	TAGTAATTAGCTG	.	PASS	Atlas-SNP
PIGR	5284	hgsc.bcm.edu	37	1	207110888	207110888	+	Silent	SNP	G	G	A	rs291097	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	59	120	0	0.440298	0	G|0.779;A|0.221	0.221	strong	PIGR,NS,carcinoma,0,1	PIGR	98	1	NM_002644	exon4	c.C597T	p.G199G	TAACTGGCCAGTA	.	PASS	Atlas-SNP
XPO4	64328	hgsc.bcm.edu	37	13	21374333	21374333	+	Silent	SNP	A	A	G	rs9579954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	89	164	0	0.508571	0	A|0.912;G|0.088	0.088	strong	.	XPO4	153	.	NM_022459	exon15	c.T2109C	p.T703T	CTGCACAGTGTCA	.	PASS	Atlas-SNP
FZD5	7855	hgsc.bcm.edu	37	2	208632817	208632817	+	Missense_Mutation	SNP	G	G	A	rs35994626	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	40	62	0	0.5	0	G|0.953;A|0.047	0.047	strong	.	FZD5	22	.	NM_003468	exon2	c.C647T	p.P216L	CAGTTGGGCACCT	.	PASS	Atlas-SNP
CEACAM6	4680	hgsc.bcm.edu	37	19	42260697	42260697	+	Missense_Mutation	SNP	G	G	A	rs61736638	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	429	205	446	1	0.477855	0.00224215	G|0.974;A|0.026	0.026	strong	.	CEACAM6	52	.	NM_002483	exon2	c.G254A	p.G85E	TAATAGGAACTCA	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226034913	226034913	+	Missense_Mutation	SNP	G	G	A	rs58852301	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	104	0	0.469388	0	G|0.956;A|0.044	0.044	strong	TMEM63A,colon,carcinoma,+1,1	TMEM63A	75	1	NM_014698	exon24	c.C2252T	p.P751L	ACGTAGGGCTGTC	.	PASS	Atlas-SNP
RECQL	5965	hgsc.bcm.edu	37	12	21623969	21623969	+	Silent	SNP	A	A	G	rs6500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	66	150	0	0.461538	0	A|0.888;G|0.112	0.112	strong	.	RECQL	45	.	NM_032941	exon15	c.T1731C	p.N577N	CAGAAGATTAGCT	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139273402	139273402	+	Silent	SNP	C	C	T	rs3812567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	257	236	0	0.996124	0	C|0.201;T|0.799	0.799	strong	.	SNAPC4	82	.	NM_003086	exon21	c.G2877A	p.A959A	GGCTGCCGCGGGG	.	PASS	Atlas-SNP
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	29	83	0	0.491525	0	C|0.849;T|0.151	0.151	strong	.	HPS3	104	.	NM_032383	exon14	c.C2526T	p.H842H	GGTTCACGTCGTA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919624	12919624	+	Missense_Mutation	SNP	C	C	G	rs80027487	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	153	343	1	0.469325	0.00291545	C|0.896;G|0.104	0.104	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.C364G	p.L122V	TGGGCCCTGTCCT	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159654720	159654720	+	Missense_Mutation	SNP	G	G	C	rs115529940	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	9	37	0	0.2	0	G|0.986;C|0.014	0.014	strong	.	FNDC1	250	.	NM_032532	exon11	c.G3176C	p.S1059T	CGGCGAGCTCCAG	.	PASS	Atlas-SNP
USP17L2	377630	hgsc.bcm.edu	37	8	11995004	11995004	+	Silent	SNP	C	C	T	rs186311075	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	27	95	0	0.206107	0	C|0.992;T|0.008	0.008	strong	.	USP17L2	47	.	NM_201402	exon1	c.G1266A	p.E422E	CAAGCGCTCGTCC	.	PASS	Atlas-SNP
RPP38	10557	hgsc.bcm.edu	37	10	15145855	15145855	+	Missense_Mutation	SNP	C	C	G	rs15772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	71	0	1	0	C|0.612;G|0.388	0.388	strong	.	RPP38	26	.	NM_001265601	exon2	c.C542G	p.A181G	CCTTGGCGTTCAA	.	PASS	Atlas-SNP
C19orf44	84167	hgsc.bcm.edu	37	19	16612011	16612011	+	Silent	SNP	T	T	C	rs728117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	41	65	0	0.577465	0	T|0.663;C|0.337	0.337	strong	.	C19orf44	47	.	NM_032207	exon2	c.T408C	p.S136S	CCTCTCTGGGGGT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	58	332	0	0.16763	0	.	.	weak	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.C2055T	p.N685N	CAGCAACAGCAGT	.	PASS	Atlas-SNP
VDR	7421	hgsc.bcm.edu	37	12	48272895	48272895	+	Missense_Mutation	SNP	A	A	G	rs2228570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	33	0	1	0	T|0.044;G|0.570;C|0.097;A|0.288	0.570	strong	.	VDR	47	.	NM_001017536	exon3	c.T152C	p.M51T	GCCTCCATCCCTG	.	PASS	Atlas-SNP
CNGA4	1262	hgsc.bcm.edu	37	11	6262909	6262909	+	Missense_Mutation	SNP	G	G	A	rs61745230	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	78	128	0	0.4875	0	G|0.966;A|0.034	0.034	strong	.	CNGA4	96	.	NM_001037329	exon5	c.G1166A	p.R389Q	TCATCCGAGAGGG	.	PASS	Atlas-SNP
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	35	46	0	0.686275	0	T|0.714;G|0.286	0.286	strong	.	CCL24	11	.	NM_002991	exon2	c.A85C	p.I29L	AGGGGATGACCAC	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641255	55641255	+	Nonsense_Mutation	SNP	C	C	T	rs4522268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	83	232	0	0.378995	0	C|0.743;N|0.000	.	strong	OR6C74,colon,carcinoma,0,6	OR6C74	52	6	NM_001005490	exon1	c.C184T	p.R62X	TTCCTCCGAAATT	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18766123	18766123	+	Missense_Mutation	SNP	C	C	T	rs61742608	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	17	12	0	0.85	0	C|0.899;T|0.101	0.101	strong	.	NT5C1B	72	.	NM_001199087	exon5	c.G611A	p.R204Q	AGCGACCGGGGCA	.	PASS	Atlas-SNP
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692277	31692277	+	Missense_Mutation	SNP	G	G	T	rs3804007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	107	188	0	0.514423	0	G|0.909;T|0.091	0.091	strong	.	KRTAP26-1	58	.	NM_203405	exon1	c.C77A	p.S26Y	TCGATGGAGGTGA	.	PASS	Atlas-SNP
CELA2B	51032	hgsc.bcm.edu	37	1	15809876	15809876	+	Silent	SNP	G	G	A	rs77217853		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	62	121	0	0.433566	0	G|0.250;A|0.750	0.750	weak	.	CELA2B	37	.	NM_015849	exon5	c.G474A	p.T158T	CGTCACGGGCTGG	.	PASS	Atlas-SNP
ATOH1	474	hgsc.bcm.edu	37	4	94750650	94750650	+	Silent	SNP	C	C	T	rs34543561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	98	139	0	0.510417	0	C|0.992;T|0.008	0.008	strong	ATOH1,NS,carcinoma,+2,1	ATOH1	40	1	NM_005172	exon1	c.C573T	p.N191N	CAACAACGACAAG	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197093361	197093361	+	Missense_Mutation	SNP	G	G	A	rs16841081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	138	327	0	0.485915	0	G|0.952;A|0.048	0.048	strong	.	ASPM	444	.	NM_001206846	exon13	c.C3269T	p.S1090F	TCATCAGAATGGC	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	927	15	816	4	0.0161812	0.00490196	.	.	none	POTEC,NS,carcinoma,-1,5	POTEC	129	5	NM_001137671	exon1	c.G492T	p.T164T	CATGTCCGTGTCC	.	scavenged	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952238	14952238	+	Missense_Mutation	SNP	A	A	G	rs12972670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	91	129	0	0.554878	0	A|0.860;G|0.140	0.140	strong	OR7A10,colon,carcinoma,0,1	OR7A10	33	1	NM_001005190	exon1	c.T452C	p.M151T	ACACTCATGATCC	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077904	19077904	+	Missense_Mutation	SNP	T	T	G	rs11024970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	53	94	0	0.449153	0	T|0.899;G|0.101	0.101	strong	.	MRGPRX2	42	.	NM_054030	exon2	c.A46C	p.N16H	TTCCATTCACTGT	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238267717	238267717	+	Silent	SNP	C	C	T	rs2646254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	98	216	0	0.441441	0	C|0.720;T|0.280	0.280	strong	.	COL6A3	608	.	NM_004369	exon20	c.G6369A	p.L2123L	ACCAGGCAATCCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277239	152277239	+	Missense_Mutation	SNP	G	G	A	rs111486002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	385	185	443	1	0.480519	0.00225734	G|0.986;A|0.014	0.014	strong	.	FLG	900	.	NM_002016	exon3	c.C10123T	p.R3375W	CTGACCGGTCACG	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46859701	46859701	+	Silent	SNP	C	C	T	rs140328042	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	27	61	0	0.465517	0	C|0.997;T|0.003	0.003	strong	.	CELSR1	242	.	NM_014246	exon2	c.G4086A	p.T1362T	GATCTCCGTCTCG	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105260518	105260518	+	Silent	SNP	G	G	A	rs579565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	93	0	0.506024	0	G|0.759;A|0.241	0.241	strong	.	ALCAM	71	.	NM_001627	exon8	c.G900A	p.L300L	CACACTGACGGAT	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25027745	25027745	+	Missense_Mutation	SNP	T	T	C	rs1130943	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	95	169	0	0.497382	0	T|0.949;C|0.051	0.051	strong	PARP4,NS,carcinoma,+2,1	PARP4	142	1	NM_006437	exon23	c.A2806G	p.M936V	CTGCCATGGTATT	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6904137	6904137	+	Missense_Mutation	SNP	C	C	T	rs370094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	58	136	0	0.513274	0	C|0.602;T|0.398	0.398	strong	.	EMR1	153	.	NM_001256253	exon8	c.C893T	p.A298V	GCATTGCAGGCTT	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197248	39197248	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	2	160	1	0.0107527	0.00625	.	.	none	KRTAP1-1,NS,carcinoma,0,1	KRTAP1-1	23	1	NM_030967	exon1	c.C402T	p.C134C	CACCACGCAGCAG	.	scavenged	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39226163	39226163	+	Silent	SNP	G	G	A	rs141009431	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	100	0	0.401869	0	G|0.998;A|0.002	0.002	strong	.	CAPN12	43	.	NM_144691	exon13	c.C1605T	p.S535S	GTCTGCGCTGATC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45017301	45017301	+	Missense_Mutation	SNP	T	T	C	rs34921521	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	37	67	0	0.45679	0	T|0.986;C|0.014	0.014	strong	CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	NM_001102600	exon7	c.A1357G	p.I453V	TCCCGATGACAAT	.	PASS	Atlas-SNP
HSPA4	3308	hgsc.bcm.edu	37	5	132437531	132437531	+	Silent	SNP	C	C	T	rs1131809	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	79	198	0	0.403061	0	C|0.802;T|0.198	0.198	strong	.	HSPA4	68	.	NM_002154	exon17	c.C2118T	p.I706I	ACAGATCCAACAG	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16932490	16932490	+	Missense_Mutation	SNP	G	G	T	rs1801238	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	68	0	0.466667	0	G|0.977;T|0.023	0.023	strong	.	CUBN	515	.	NM_001081	exon55	c.C8635A	p.L2879I	TGGCTAGCAGGGC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28389880	28389880	+	Silent	SNP	G	G	A	rs1133496	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	73	129	0	0.503448	0	G|0.916;A|0.084	0.084	strong	.	HERC2	501	.	NM_004667	exon72	c.C11079T	p.S3693S	CCCATCGCTGATG	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1484455	1484455	+	Missense_Mutation	SNP	T	T	C	rs61743495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	57	98	0	0.606383	0	T|0.943;C|0.057	0.057	strong	.	CCDC154	27	.	NM_001143980	exon17	c.A1958G	p.Q653R	TGCTCCTGGCTGT	.	PASS	Atlas-SNP
NTRK3	4916	hgsc.bcm.edu	37	15	88576215	88576215	+	Silent	SNP	G	G	A	rs2229909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	47	98	0	0.484536	0	G|0.962;A|0.038	0.038	strong	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	3	NM_001012338	exon14	c.C1458T	p.H486H	GATGCCGTGGTTG	.	PASS	Atlas-SNP
CAMKK1	84254	hgsc.bcm.edu	37	17	3786456	3786456	+	Silent	SNP	C	C	T	rs737362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	18	43	0	0.428571	0	C|0.934;T|0.066	0.066	strong	.	CAMKK1	70	.	NM_032294	exon6	c.G528A	p.P176P	CCCTCTCGGGGGA	.	PASS	Atlas-SNP
KCTD19	146212	hgsc.bcm.edu	37	16	67325711	67325711	+	Missense_Mutation	SNP	C	C	T	rs16957289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	37	79	0	0.440476	0	C|0.929;T|0.071	0.071	strong	KCTD19,brain,glioma,0,1	KCTD19	82	1	NM_001100915	exon13	c.G2248A	p.E750K	TGGCCTCGGGCAG	.	PASS	Atlas-SNP
AKAP10	11216	hgsc.bcm.edu	37	17	19835185	19835185	+	Missense_Mutation	SNP	G	G	C	rs141355495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	36	55	0	0.5625	0	G|0.999;C|0.001	0.001	strong	.	AKAP10	47	.	NM_007202	exon10	c.C1574G	p.T525S	GGAGCAGTCAGCG	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	76	100	0	0.628099	0	C|0.859;T|0.141	0.141	strong	.	AKAP6	308	.	NM_004274	exon4	c.C1010T	p.A337V	ATGCTGCTCAACC	.	PASS	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	37	11	128994781	128994781	+	Silent	SNP	G	G	A	rs114955890	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	34	42	0	0.576271	0	G|0.998;A|0.002	0.002	strong	.	ARHGAP32	307	.	NM_001142685	exon3	c.C234T	p.G78G	ATCTGCGCCTCTT	.	PASS	Atlas-SNP
QRFP	347148	hgsc.bcm.edu	37	9	133769169	133769169	+	Silent	SNP	G	G	A	rs3847193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	171	0	1	0	G|0.629;A|0.371	0.371	strong	.	QRFP	14	.	NM_198180	exon1	c.C57T	p.F19F	TAGAGGGAAGCAG	.	PASS	Atlas-SNP
ELK3	2004	hgsc.bcm.edu	37	12	96641344	96641344	+	Silent	SNP	G	G	A	rs115218295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	32	55	0	0.542373	0	G|0.990;A|0.010	0.010	strong	.	ELK3	36	.	NM_005230	exon3	c.G834A	p.S278S	GTCATCGGGCTCC	.	PASS	Atlas-SNP
KRTAP21-2	337978	hgsc.bcm.edu	37	21	32119495	32119495	+	Missense_Mutation	SNP	C	C	G	rs12053674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	103	192	0	0.427386	0	C|0.840;G|0.160	0.160	strong	.	KRTAP21-2	16	.	NM_181617	exon1	c.G26C	p.C9S	CCACAGCAGTTTC	.	PASS	Atlas-SNP
COG7	91949	hgsc.bcm.edu	37	16	23409440	23409440	+	Missense_Mutation	SNP	G	G	A	rs16940094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	87	125	0	0.58	0	G|0.931;A|0.069	0.069	strong	.	COG7	62	.	NM_153603	exon14	c.C1814T	p.T605M	CCAGCCGTATTCC	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72500863	72500863	+	Silent	SNP	C	C	G	rs10999500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	56	128	0	0.444444	0	C|0.339;G|0.661	0.661	strong	.	ADAMTS14	148	.	NM_139155	exon12	c.C1878G	p.S626S	CAACTCCTACTAT	.	PASS	Atlas-SNP
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471888	39471888	+	Silent	SNP	C	C	T	rs34354631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	44	44	0	0.956522	0	C|0.866;T|0.134	0.134	strong	.	KRTAP17-1	14	.	NM_031964	exon1	c.G15A	p.P5P	GTCCCCCGGGCAG	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29797921	29797921	+	Missense_Mutation	SNP	C	C	T	rs616114	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	106	160	0	0.566845	0	C|0.631;T|0.368	0.368	strong	.	MEP1B	54	.	NM_005925	exon14	c.C2084T	p.P695L	TGACTCCGCAAAA	.	PASS	Atlas-SNP
TTLL11	158135	hgsc.bcm.edu	37	9	124855220	124855220	+	Missense_Mutation	SNP	G	G	A	rs61742325	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	5	0	1	0	G|0.955;A|0.045	0.045	strong	.	TTLL11	67	.	NM_001139442	exon1	c.C478T	p.P160S	CACTGGGCTGCGC	.	PASS	Atlas-SNP
UCK2	7371	hgsc.bcm.edu	37	1	165859482	165859482	+	Silent	SNP	T	T	C	rs145654595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	118	207	0	0.485597	0	T|1.000;C|0.000	0.000	weak	.	UCK2	31	.	NM_012474	exon2	c.T141C	p.N47N	GCAGAATGAGGTG	.	PASS	Atlas-SNP
CRYBG3	131544	hgsc.bcm.edu	37	3	97607290	97607290	+	Silent	SNP	G	G	A	rs13065340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	59	141	0	0.483607	0	G|0.786;A|0.214	0.214	strong	CRYBG3,NS,carcinoma,0,1	CRYBG3	86	1	NM_153605	exon9	c.G7395A	p.P2465P	ACATCCGCTTCAA	.	PASS	Atlas-SNP
NLGN2	57555	hgsc.bcm.edu	37	17	7318396	7318396	+	Silent	SNP	C	C	T	rs2241233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	48	105	0	0.436364	0	C|0.234;T|0.766	0.766	strong	.	NLGN2	61	.	NM_020795	exon5	c.C966T	p.S322S	GGACAGCGCTGAA	.	PASS	Atlas-SNP
GRK5	2869	hgsc.bcm.edu	37	10	121086097	121086097	+	Missense_Mutation	SNP	A	A	T	rs2230345	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	23	52	0	0.433962	0	A|0.905;T|0.095	0.095	strong	.	GRK5	58	.	NM_005308	exon2	c.A122T	p.Q41L	TTAGCCAGTGTGA	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79974885	79974885	+	Missense_Mutation	SNP	C	C	T	rs35121792	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	23	62	0	0.410714	0	C|0.999;T|0.001	0.001	strong	.	MSH3	129	.	NM_002439	exon8	c.C1313T	p.A438V	CAGAGGCGCTCAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179447787	179447787	+	Missense_Mutation	SNP	G	G	T	rs62618736	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	122	182	0	0.535088	0	G|0.985;T|0.015	0.015	strong	.	TTN	18412	.	NM_001267550	exon313	c.C65743A	p.Q21915K	TCCGCTGCATGGC	.	PASS	Atlas-SNP
SLC5A11	115584	hgsc.bcm.edu	37	16	24888593	24888593	+	Silent	SNP	A	A	G	rs8052587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	115	173	0	0.481172	0	A|0.850;G|0.150	0.150	strong	.	SLC5A11	97	.	NM_052944	exon7	c.A492G	p.A164A	GTATGCAGGTGCC	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77082390	77082390	+	Missense_Mutation	SNP	G	G	A	rs11871357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	33	105	0	0.434211	0	G|0.965;A|0.035	0.035	strong	ENGASE,NS,carcinoma,-1,1	ENGASE	55	1	NM_001042573	exon14	c.G2191A	p.E731K	CAGGCCGAGTGGG	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031643	32031643	+	Missense_Mutation	SNP	A	A	G	rs13065048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	329	134	392	0	0.407295	0	A|0.615;G|0.385	0.385	strong	.	ZNF860	96	.	NM_001137674	exon2	c.A1072G	p.T358A	CACCTCACACAAC	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1618306	1618306	+	Missense_Mutation	SNP	C	C	T	rs8050974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	59	98	0	0.472	0	C|0.964;T|0.036	0.036	strong	.	IFT140	128	.	NM_014714	exon15	c.G1682A	p.S561N	GCCAGGCTCCTGC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1044712	1044712	+	Missense_Mutation	SNP	A	A	G	rs3764647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	32	96	0	0.355556	0	A|0.886;G|0.114	0.114	strong	.	ABCA7	174	.	NM_019112	exon11	c.A1184G	p.H395R	TGGGGCACCTGGT	.	PASS	Atlas-SNP
TOP3A	7156	hgsc.bcm.edu	37	17	18217958	18217958	+	Silent	SNP	C	C	T	rs2230153	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	89	107	0	0.508571	0	C|0.948;T|0.052	0.052	strong	.	TOP3A	85	.	NM_004618	exon1	c.G135A	p.A45A	CTTGGCCGCGTCG	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56096731	56096731	+	Silent	SNP	A	A	G	rs2274075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	63	171	0	0.396226	0	A|0.925;G|0.075	0.075	strong	KTN1_ENST00000416613,NS,carcinoma,+1,1	KTN1	147	1	NM_004986	exon7	c.A1137G	p.R379R	AGATCGAATTGGA	.	PASS	Atlas-SNP
DOK3	79930	hgsc.bcm.edu	37	5	176936822	176936822	+	Missense_Mutation	SNP	G	G	A	rs371788222		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	144	253	1	0.464516	0.00395257	.	.	weak	DOK3,NS,carcinoma,-1,1	DOK3	41	1	NM_024872	exon1	c.C32T	p.A11V	GCACGCGCGTCTG	.	PASS	Atlas-SNP
ITLN1	55600	hgsc.bcm.edu	37	1	160854620	160854620	+	Silent	SNP	T	T	C	rs35779394	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	47	110	0	0.47	0	T|0.921;C|0.079	0.079	strong	.	ITLN1	45	.	NM_017625	exon2	c.A48G	p.G16G	ACTCCATCCTCTG	.	PASS	Atlas-SNP
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28120898	28120898	+	Silent	SNP	G	G	A	rs17774663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	99	139	0	0.540984	0	G|0.765;A|0.235	0.235	strong	ZNF192,NS,carcinoma,+1,1	.	.	1	NM_006298	exon6	c.G840A	p.Q280Q	AATCCAGCCACAT	.	PASS	Atlas-SNP
APLP1	333	hgsc.bcm.edu	37	19	36370011	36370011	+	Silent	SNP	G	G	A	rs2227909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	41	45	0	1	0	G|0.886;A|0.114	0.114	strong	.	APLP1	77	.	NM_001024807	exon16	c.G1749A	p.V583V	GGCTGTGTCGGGT	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57101340	57101340	+	Missense_Mutation	SNP	T	T	C	rs7190199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	104	235	0	0.481481	0	T|0.912;C|0.088	0.088	strong	.	NLRC5	186	.	NM_032206	exon34	c.T4364C	p.V1455A	TTCTTGTCGGGCA	.	PASS	Atlas-SNP
AKAP11	11215	hgsc.bcm.edu	37	13	42876996	42876996	+	Missense_Mutation	SNP	G	G	A	rs114980445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	26	52	0	0.4	0	G|0.992;A|0.008	0.008	strong	.	AKAP11	146	.	NM_016248	exon8	c.G4114A	p.A1372T	AGGCTTGCCTACC	.	PASS	Atlas-SNP
MAP3K6	9064	hgsc.bcm.edu	37	1	27688633	27688633	+	Missense_Mutation	SNP	G	G	A	rs1138294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	146	232	0	0.481848	0	G|0.712;A|0.288	0.288	strong	.	MAP3K6	134	.	NM_004672	exon9	c.C1364T	p.T455I	ACCTGGGTGGGGT	.	PASS	Atlas-SNP
PPEF2	5470	hgsc.bcm.edu	37	4	76797551	76797551	+	Missense_Mutation	SNP	C	C	G	rs370312706	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	40	98	0	0.465116	0	.	.	alt	.	PPEF2	108	.	NM_006239	exon11	c.G1209C	p.Q403H	TGCTTGCTGCCGG	.	PASS	Atlas-SNP
STARD7	56910	hgsc.bcm.edu	37	2	96861159	96861159	+	Missense_Mutation	SNP	C	C	G	rs2276650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	84	218	0	0.380091	0	C|0.878;G|0.122	0.122	strong	STARD7,NS,carcinoma,0,1	STARD7	49	1	NM_020151	exon2	c.G419C	p.R140P	TCCCAACGTTGCT	.	PASS	Atlas-SNP
ARL11	115761	hgsc.bcm.edu	37	13	50205025	50205025	+	Missense_Mutation	SNP	T	T	C	rs3803185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	53	96	0	0.552083	0	T|0.660;C|0.340	0.340	strong	.	ARL11	26	.	NM_138450	exon2	c.T442C	p.C148R	GACCACTGCTGGG	.	PASS	Atlas-SNP
THADA	63892	hgsc.bcm.edu	37	2	43819139	43819139	+	Silent	SNP	A	A	G	rs17031095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	67	123	0	0.558333	0	A|0.886;G|0.114	0.114	strong	.	THADA	131	.	NM_001083953	exon3	c.T123C	p.H41H	CACACAATGTAAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	522	179	312	0	0.342912	0	A|0.761;G|0.239	0.239	strong	.	HLA-A	89	.	NM_001242758	exon5	c.A967G	p.T323A	GTGATCACTGGAG	.	PASS	Atlas-SNP
POFUT1	23509	hgsc.bcm.edu	37	20	30822455	30822455	+	Silent	SNP	C	C	T	rs7263390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	95	0	0.483516	0	C|0.973;T|0.027	0.027	strong	.	POFUT1	52	.	NM_015352	exon7	c.C1158T	p.D386D	GCGGGACGAGTTC	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	53907679	53907679	+	Silent	SNP	T	T	C	rs16966318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	81	121	0	0.554795	0	T|0.867;C|0.133	0.133	strong	.	WDR72	177	.	NM_182758	exon15	c.A2724G	p.L908L	TAAAAATAGTCTG	.	PASS	Atlas-SNP
RPS6KA1	6195	hgsc.bcm.edu	37	1	26887592	26887592	+	Silent	SNP	T	T	C	rs1064196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	128	0	1	0	T|0.604;C|0.396	0.396	strong	.	RPS6KA1	65	.	NM_001006665	exon15	c.T1425C	p.Y475Y	GCGGTATGGCCAG	.	PASS	Atlas-SNP
EXOSC9	5393	hgsc.bcm.edu	37	4	122737965	122737965	+	Missense_Mutation	SNP	G	G	C	rs1051881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	82	183	0	0.5125	0	G|0.885;C|0.115	0.115	strong	.	EXOSC9	51	.	NM_001034194	exon13	c.G1325C	p.S442T	CACCAAGTAAAAA	.	PASS	Atlas-SNP
INTS5	80789	hgsc.bcm.edu	37	11	62415285	62415285	+	Missense_Mutation	SNP	C	C	T	rs149821915	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	75	118	0	0.524476	0	C|1.000;T|0.000	0.000	strong	.	INTS5	81	.	NM_030628	exon2	c.G2267A	p.R756H	AAGCCACGGCCGA	.	PASS	Atlas-SNP
C9orf156	51531	hgsc.bcm.edu	37	9	100672338	100672338	+	Missense_Mutation	SNP	C	C	T	rs2282192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	62	86	0	0.652632	0	C|0.504;T|0.496	0.496	strong	C9orf156,NS,meningioma,0,1	C9orf156	35	1	NM_016481	exon4	c.G970A	p.V324M	GAACCACGCTGCG	.	PASS	Atlas-SNP
ANKRD28	23243	hgsc.bcm.edu	37	3	15807763	15807763	+	Silent	SNP	G	G	A	rs185386403	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	19	67	0	0.38	0	G|0.996;A|0.004	0.004	strong	.	ANKRD28	121	.	NM_015199	exon3	c.C168T	p.I56I	TTCAATGATTTCT	.	PASS	Atlas-SNP
PPEF2	5470	hgsc.bcm.edu	37	4	76811175	76811175	+	Missense_Mutation	SNP	G	G	T	rs28436183	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	126	241	0	0.468401	0	G|0.859;T|0.141	0.141	strong	.	PPEF2	108	.	NM_006239	exon5	c.C352A	p.R118S	AGAGGCGTGGCCC	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	73057755	73057755	+	Silent	SNP	G	G	C	rs10823720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	37	71	0	0.393617	0	G|0.964;C|0.036	0.036	strong	.	UNC5B	123	.	NM_170744	exon16	c.G2580C	p.L860L	CCCACTGTCCATC	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28722039	28722039	+	Silent	SNP	G	G	A	rs2577075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	96	238	0	0.424779	0	G|0.696;A|0.304	0.304	strong	.	DSC1	240	.	NM_004948	exon9	c.C1183T	p.L395L	CTTGTAGGATTTT	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39521726	39521726	+	Missense_Mutation	SNP	T	T	C	rs61741663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	111	220	0	0.482609	0	T|0.976;C|0.024	0.024	strong	KRT33B,NS,carcinoma,0,1	KRT33B	46	1	NM_002279	exon4	c.A668G	p.Q223R	AGGACCTGGTTCA	.	PASS	Atlas-SNP
TC2N	123036	hgsc.bcm.edu	37	14	92264736	92264736	+	Silent	SNP	A	A	G	rs147695092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	74	126	0	0.556391	0	A|1.000;G|0.000	0.000	weak	.	TC2N	49	.	NM_001128596	exon7	c.T645C	p.I215I	TAGAGTAATTGTA	.	PASS	Atlas-SNP
TCF21	6943	hgsc.bcm.edu	37	6	134210600	134210600	+	Missense_Mutation	SNP	G	G	T	rs56412384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	93	1	0.990654	0.0107527	G|0.944;T|0.056	0.056	strong	TCF21,NS,carcinoma,+1,1	TCF21	30	1	NM_003206	exon1	c.G65T	p.G22V	GTGACGGGTTGAA	.	scavenged	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs75081605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	718	299	753	1	0.416435	0.00132802	.	.	weak	OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	NM_001004482	exon1	c.G243C	p.T81T	CACTAGCGTGGAG	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56146357	56146357	+	Silent	SNP	G	G	A	rs11546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	63	138	0	0.4375	0	G|0.923;A|0.077	0.077	strong	.	KTN1	147	.	NM_001079521	exon43	c.G4023A	p.A1341A	TCAGGCGGTAAAC	.	PASS	Atlas-SNP
IFNL3	282617	hgsc.bcm.edu	37	19	39735535	39735535	+	Missense_Mutation	SNP	C	C	A	rs141536970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	322	171	321	1	0.531056	0.00311526	A|0.003;C|0.997	0.003	strong	.	.	.	.	NM_172139	exon1	c.G73T	p.A25S	GCCTGGCGACAGG	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6596360	6596360	+	Missense_Mutation	SNP	G	G	A	rs2301795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	61	120	0	0.508333	0	G|0.522;A|0.478	0.478	strong	.	MAN2B2	80	.	NM_015274	exon7	c.G958A	p.V320M	GTCTCGGTGCAGT	.	PASS	Atlas-SNP
ACSM4	341392	hgsc.bcm.edu	37	12	7477100	7477100	+	Missense_Mutation	SNP	G	G	A	rs61584783	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	76	174	0	0.484076	0	G|0.979;A|0.021	0.021	strong	.	ACSM4	98	.	NM_001080454	exon11	c.G1442A	p.R481H	GGTACCGTATTGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412260	105412260	+	Missense_Mutation	SNP	G	G	C	rs11160826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	393	382	391	0	0.97201	0	G|0.779;C|0.221	0.221	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C9528G	p.D3176E	GCTCAGGTCGGCC	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45606287	45606287	+	Missense_Mutation	SNP	C	C	T	rs10138997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	27	55	0	0.509434	0	C|0.815;T|0.185	0.185	strong	FANCM,NS,carcinoma,+1,1	FANCM	225	1	NM_020937	exon2	c.C524T	p.S175F	AAGCTTCCACCAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910660	29910660	+	Missense_Mutation	SNP	A	A	G	rs41559117	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	54	134	0	0.246575	0	A|0.977;C|0.002;G|0.021	0.021	strong	.	HLA-A	89	.	NM_001242758	exon2	c.A200G	p.Q67R	CGAGCCAGAGGAT	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69963355	69963355	+	Silent	SNP	G	G	A	rs1566452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	145	0	1	0	A|0.812;C|0.000	0.812	strong	.	WWP2	88	.	NM_001270454	exon12	c.G1239A	p.K413K	AGAGAAGAGACAG	.	PASS	Atlas-SNP
AGFG2	3268	hgsc.bcm.edu	37	7	100160264	100160264	+	Missense_Mutation	SNP	T	T	C	rs17855473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	54	79	0	0.490909	0	T|0.797;C|0.203	0.203	strong	AGFG2,NS,carcinoma,0,1	AGFG2	44	1	NM_006076	exon8	c.T1046C	p.M349T	TCACGATGGGCGG	.	PASS	Atlas-SNP
SPRR1A	6698	hgsc.bcm.edu	37	1	152957856	152957856	+	Missense_Mutation	SNP	C	C	G	rs143282605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	24	158	0	0.192	0	.	.	weak	.	SPRR1A	17	.	NM_001199828	exon2	c.C150G	p.H50Q	CTGCCACCCCAAA	.	PASS	Atlas-SNP
CES5A	221223	hgsc.bcm.edu	37	16	55880480	55880480	+	Missense_Mutation	SNP	A	A	C	rs11860456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	119	183	0	0.595	0	A|0.672;C|0.328	0.328	strong	.	CES5A	206	.	NM_001190158	exon14	c.T1698G	p.D566E	CCAAAAATCCACC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105405599	105405599	+	Missense_Mutation	SNP	G	G	C	rs3742935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	137	161	0	1	0	G|0.480;C|0.520	0.520	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,3	AHNAK2	719	3	NM_138420	exon7	c.C16189G	p.P5397A	GGGCAGGGAAGGA	.	PASS	Atlas-SNP
OR4X1	390113	hgsc.bcm.edu	37	11	48286256	48286256	+	Missense_Mutation	SNP	C	C	T	rs10838852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	119	259	0	0.463035	0	C|0.567;N|0.000	.	strong	.	OR4X1	75	.	NM_001004726	exon1	c.C844T	p.P282S	TTAAACCCTGTGA	.	PASS	Atlas-SNP
A2M	2	hgsc.bcm.edu	37	12	9251209	9251209	+	Silent	SNP	C	C	T	rs185750870	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	42	59	0	0.545455	0	C|0.998;T|0.002	0.002	strong	.	A2M	180	.	NM_000014	exon15	c.G1845A	p.A615A	CGAGGACGCCGAG	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	71	202	0	0.440994	0	G|0.679;A|0.321	0.321	strong	.	XRCC4	37	.	NM_022406	exon8	c.894-1G>A	.	TTTTCAGTTCTAG	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672253	238672253	+	Missense_Mutation	SNP	A	A	G	rs78053555		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	120	0	0.482517	0	.	.	weak	.	LRRFIP1	171	.	NM_001137552	exon11	c.A1897G	p.K633E	AAACAGAAAATTG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17025292	17025292	+	Missense_Mutation	SNP	G	G	A	rs706761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	142	153	0	0.993007	0	G|0.358;A|0.642	0.642	strong	.	CPAMD8	192	.	NM_015692	exon29	c.C3944T	p.T1315I	GGGACAGTGCCGT	.	PASS	Atlas-SNP
APOBEC3B	9582	hgsc.bcm.edu	37	22	39387531	39387531	+	Silent	SNP	C	C	T	rs200377379		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	43	251	0	0.209756	0	.	.	weak	APOBEC3B,colon,carcinoma,+2,2	APOBEC3B	32	2	NM_004900	exon6	c.C918T	p.R306R	ACTGCGCATCTTC	.	scavenged	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	T	G	rs200244531		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	377	4	362	2	0.0106101	0.00552486	.	.	weak	TPTE2_ENST00000400230,NS,carcinoma,0,1	TPTE2	225	1	NM_199254	exon5	c.A128C	p.E43A	AGTCGTTCTAACA	.	scavenged	Atlas-SNP
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	31	50	0	0.596154	0	G|0.649;A|0.351	0.351	strong	.	MURC	43	.	NM_001018116	exon2	c.G996A	p.R332R	AGGAAGGGAAATC	.	PASS	Atlas-SNP
CNGB3	54714	hgsc.bcm.edu	37	8	87588198	87588198	+	Missense_Mutation	SNP	T	T	C	rs3735972	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	172	317	1	0.532508	0.00315457	T|0.921;C|0.079	0.079	strong	CNGB3,NS,carcinoma,-1,1	CNGB3	176	1	NM_019098	exon18	c.A2264G	p.E755G	GTACATTCAGGTC	.	PASS	Atlas-SNP
MAP3K2	10746	hgsc.bcm.edu	37	2	128075319	128075319	+	Silent	SNP	C	C	T	rs11899533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	42	0	0.431373	0	C|0.981;T|0.019	0.019	strong	.	MAP3K2	78	.	NM_006609	exon13	c.G1212A	p.E404E	TTCACACTCAAGT	.	PASS	Atlas-SNP
TADA2A	6871	hgsc.bcm.edu	37	17	35830554	35830554	+	Missense_Mutation	SNP	A	A	C	rs142392695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	33	71	0	0.464789	0	A|0.996;C|0.004	0.004	strong	.	TADA2A	91	.	NM_001488	exon13	c.A946C	p.K316Q	CGCCTTAAACGCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408955	105408955	+	Missense_Mutation	SNP	A	A	G	rs2819422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	301	267	1	0.993399	0.00374532	A|0.462;G|0.538	0.538	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T12833C	p.V4278A	AGCCGCACACTGT	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	77	291	1	0.308	0.00343643	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	NM_001206609	exon2	c.C460G	p.P154A	CCGTGGGCACTGG	.	scavenged	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129824406	129824406	+	Missense_Mutation	SNP	A	A	G	rs73599293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	26	38	0	0.565217	0	A|0.980;G|0.020	0.020	strong	.	LAMA2	481	.	NM_000426	exon60	c.A8528G	p.N2843S	AAATCAATGATGG	.	PASS	Atlas-SNP
OR5B12	390191	hgsc.bcm.edu	37	11	58207203	58207203	+	Missense_Mutation	SNP	C	C	T	rs11229457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	78	0	0.508065	0	C|0.782;T|0.218	0.218	strong	.	OR5B12	80	.	NM_001004733	exon1	c.G422A	p.C141Y	GCCAGGCAAGCAC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179621353	179621353	+	Missense_Mutation	SNP	G	G	A	rs57389274	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	58	122	0	0.42963	0	G|0.982;A|0.018	0.018	strong	.	TTN	18412	.	NM_001267550	exon46	c.C10850T	p.S3617F	CTTTGAGATACAC	.	PASS	Atlas-SNP
MASP1	5648	hgsc.bcm.edu	37	3	186954324	186954324	+	Silent	SNP	G	G	A	rs3774268	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	56	95	0	0.427481	0	G|0.853;A|0.147	0.147	strong	.	MASP1	240	.	NM_139125	exon11	c.C1335T	p.S445S	GACCAGGCTTGGC	.	PASS	Atlas-SNP
LRRC36	55282	hgsc.bcm.edu	37	16	67418957	67418957	+	Missense_Mutation	SNP	A	A	G	rs16957415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	95	141	1	0.637584	0.0070922	A|0.907;G|0.093	0.093	strong	LRRC36,NS,carcinoma,-2,1	LRRC36	68	1	NM_018296	exon14	c.A2230G	p.S744G	ATACAGAGCGTCT	.	scavenged	Atlas-SNP
NUP153	9972	hgsc.bcm.edu	37	6	17675553	17675553	+	Silent	SNP	T	T	C	rs61748704	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	74	129	0	0.524823	0	T|0.978;C|0.022	0.022	strong	.	NUP153	116	.	NM_005124	exon4	c.A630G	p.P210P	AGCTTCTGGGGAC	.	PASS	Atlas-SNP
DIRC1	116093	hgsc.bcm.edu	37	2	189599373	189599373	+	Missense_Mutation	SNP	A	A	G	rs58846152	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	79	214	0	0.424731	0	A|0.976;G|0.024	0.024	strong	.	DIRC1	13	.	NM_052952	exon2	c.T275C	p.L92S	CCCCTCAATGAGT	.	PASS	Atlas-SNP
ARMC12	221481	hgsc.bcm.edu	37	6	35716613	35716613	+	Missense_Mutation	SNP	A	A	G	rs73729781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	43	69	0	0.573333	0	A|0.995;G|0.005	0.005	strong	.	.	.	.	NM_145028	exon6	c.A1070G	p.Q357R	CCTGCCAGCCCAG	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106813672	106813672	+	Silent	SNP	A	A	G	rs920628	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	71	0	0.46	0	A|0.885;G|0.115	0.115	strong	ZFPM2,NS,carcinoma,+2,1	ZFPM2	219	1	NM_012082	exon8	c.A1362G	p.P454P	GAGACCAGAGATA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370833	26370833	+	Splice_Site	SNP	T	T	G	rs58367598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	81	161	0	0.6	0	T|0.951;G|0.049	0.049	strong	.	BTN3A2	44	.	NM_001197249	exon4	c.589+2T>G	.	CGCAGGTCAGTAC	.	PASS	Atlas-SNP
ZNF770	54989	hgsc.bcm.edu	37	15	35273867	35273867	+	Missense_Mutation	SNP	C	C	A	rs141323293	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	22	60	0	0.458333	0	C|0.996;A|0.004	0.004	strong	.	ZNF770	64	.	NM_014106	exon3	c.G1769T	p.G590V	GTGCTACCAGGAA	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141736732	141736732	+	Missense_Mutation	SNP	G	G	A	rs116034282	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	81	0	0.46	0	G|0.986;A|0.014	0.014	strong	.	MGAM	767	.	NM_004668	exon18	c.G2186A	p.R729H	TCTTCCGTGCTCA	.	PASS	Atlas-SNP
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	43	50	0	0.581081	0	C|0.708;T|0.292	0.292	strong	.	CYB5RL	17	.	NM_001031672	exon3	c.G140A	p.R47K	TCCCACCTTGCCA	.	PASS	Atlas-SNP
FCRL6	343413	hgsc.bcm.edu	37	1	159778983	159778983	+	Silent	SNP	T	T	C	rs12083967	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	147	131	0	1	0	T|0.738;C|0.262	0.262	strong	.	FCRL6	61	.	NM_001004310	exon4	c.T552C	p.P184P	GGCCCCTGAGGGT	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173516915	173516915	+	Silent	SNP	G	G	A	rs114115413	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	37	114	0	0.402174	0	G|0.989;A|0.011	0.011	strong	.	.	.	.	NM_178527	exon13	c.C1470T	p.H490H	TGAAACGTGGGAA	.	PASS	Atlas-SNP
IFNA16	3449	hgsc.bcm.edu	37	9	21216864	21216864	+	Silent	SNP	A	A	G	rs28368164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	122	305	0	0.425087	0	A|0.957;G|0.043	0.043	strong	.	IFNA16	27	.	NM_002173	exon1	c.T441C	p.F147F	TCTTTGAAAGTAT	.	PASS	Atlas-SNP
TPGS1	91978	hgsc.bcm.edu	37	19	507560	507560	+	Silent	SNP	G	G	A	rs61746565	byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	23	18	0	0.958333	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_033513	exon1	c.G54A	p.T18T	TTTCACGGACAGC	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13789	13789	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	5	11	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.T1453C	p.Y485H	CCCCTCTACCTAA	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43680051	43680051	+	Missense_Mutation	SNP	C	C	T	rs1058285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	101	62	0	1	0	C|0.311;T|0.689	0.689	strong	PSG5,NS,carcinoma,+1,1	PSG5	58	1	NM_002781	exon3	c.G680A	p.R227H	TCACTGCGCATGC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	53	132	0	0.438017	0	G|0.783;C|0.217	0.217	strong	.	MYOM2	251	.	NM_003970	exon15	c.G1647C	p.S549S	GTAGTCGGTGGTG	.	PASS	Atlas-SNP
ARHGAP28	79822	hgsc.bcm.edu	37	18	6908976	6908976	+	Missense_Mutation	SNP	G	G	A	rs116232392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	54	149	0	0.382979	0	G|0.979;A|0.021	0.021	strong	.	ARHGAP28	181	.	NM_001010000	exon16	c.G1571A	p.C524Y	CAGAATGTATTAA	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116930013	116930013	+	Missense_Mutation	SNP	G	G	A	rs74339956	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	37	84	0	0.362745	0	G|0.985;A|0.015	0.015	strong	.	COL27A1	200	.	NM_032888	exon3	c.G178A	p.G60R	AAGGCCGGGAGCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113170323	113170323	+	Silent	SNP	G	G	A	rs111722103	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	66	90	0	0.733333	0	G|0.977;A|0.023	0.023	strong	SVEP1,NS,carcinoma,0,1	SVEP1	326	1	NM_153366	exon38	c.C7557T	p.T2519T	GGTAACGGTCTGT	.	PASS	Atlas-SNP
ATAD2B	54454	hgsc.bcm.edu	37	2	23980608	23980608	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	3	216	0	0.0160428	0	.	.	none	ATAD2B_ENST00000238789,NS,carcinoma,+1,1	ATAD2B	110	1	NM_017552	exon25	c.C3758T	p.P1253L	TGCTCCGGGTTTA	.	scavenged	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11222300	11222300	+	Missense_Mutation	SNP	G	G	A	rs11669576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	27	32	0	0.574468	0	G|0.916;A|0.084	0.084	strong	.	LDLR	72	.	NM_001195798	exon8	c.G1171A	p.A391T	ACGAAGGCCTGCA	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71009054	71009054	+	Missense_Mutation	SNP	C	C	T	rs201855097	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	45	151	0	0.264706	0	C|0.999;T|0.001	0.001	weak	LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	NM_001270974	exon31	c.G4757A	p.R1586H	TTGCGGCGACTCC	.	scavenged	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	84	153	0	0.415842	0	T|0.675;C|0.325	0.325	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A706G	p.I236V	GTAATATGAGGAA	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180219838	180219838	+	Missense_Mutation	SNP	C	C	T	rs61743256	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	32	72	0	0.390244	0	C|0.993;T|0.007	0.007	strong	.	MGAT1	48	.	NM_001114617	exon3	c.G134A	p.G45D	GGGTCGCCATCGA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537243	88537243	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	26	216	1	0.109705	0.00462963	.	.	none	DSPP,NS,carcinoma,0,6	DSPP	174	6	NM_014208	exon5	c.C3429A	p.D1143E	CAGTGACAGCAGT	.	scavenged	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88500340	88500340	+	Silent	SNP	G	G	A	rs61472141	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	56	101	0	0.513761	0	G|0.896;A|0.104	0.104	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G6378A	p.P2126P	ATCTCCGTCCTGC	.	PASS	Atlas-SNP
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751128	140751128	+	Missense_Mutation	SNP	C	C	G	rs2240697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	78	0	1	0	C|0.477;G|0.523	0.523	strong	.	PCDHGB3	168	.	NM_018924	exon1	c.C1167G	p.N389K	AGGAAACTTCCCC	.	PASS	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156754895	156754895	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	4	235	0	0.0181818	0	.	.	none	NOM1,NS,carcinoma,+1,1	NOM1	73	1	NM_138400	exon5	c.C1683T	p.R561R	CATGCGCAAAATT	.	scavenged	Atlas-SNP
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297313	28297313	+	Missense_Mutation	SNP	T	T	A	rs853678	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	125	109	0	0.976562	0	T|0.794;N|0.000	.	strong	.	.	.	.	NM_030899	exon2	c.A148T	p.T50S	CAGGAGTCTCTTG	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42742464	42742464	+	Missense_Mutation	SNP	A	A	G	rs12101559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	109	198	0	0.495455	0	A|0.833;G|0.167	0.167	strong	.	ZFP106	117	.	NM_022473	exon2	c.T1937C	p.I646T	CGAACTATGGGAT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149486420	149486420	+	Missense_Mutation	SNP	C	C	G	rs855693	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	46	87	0	0.5	0	C|0.979;G|0.021	0.021	strong	.	.	.	.	NM_198455	exon30	c.C4396G	p.P1466A	TGCCTGCCGCCGG	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57603647	57603647	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	30	45	0	0.576923	0	.	.	none	LRP1,bladder,carcinoma,0,1	LRP1	428	1	NM_002332	exon80	c.C12435T	p.P4145P	GCAGCCCGAAGGT	.	PASS	Atlas-SNP
SMCO2	0	hgsc.bcm.edu	37	12	27641465	27641465	+	Silent	SNP	A	A	G	rs76288777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	17	39	0	0.447368	0	A|0.993;G|0.007	0.007	strong	.	.	.	.	NM_001145010	exon6	c.A585G	p.Q195Q	TGATCAAGGGACA	.	PASS	Atlas-SNP
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955744	18955744	+	Silent	SNP	C	C	T	rs11599929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	101	84	1	0.63522	0.0119048	C|0.741;T|0.259	0.259	strong	MRGPRX1,NS,carcinoma,0,1	MRGPRX1	84	1	NM_147199	exon1	c.G588A	p.L196L	CAGGACCAGGCTG	.	scavenged	Atlas-SNP
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146395	5146395	+	Missense_Mutation	SNP	A	A	G	rs1863968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	42	99	0	0.477273	0	G|0.499;N|0.001	0.499	strong	.	ADAMTS16	543	.	NM_139056	exon3	c.A328G	p.M110V	TTCCACATGGATC	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107457275	107457275	+	Missense_Mutation	SNP	A	A	C	rs10820709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	109	331	1	0.31686	0.00302115	A|0.560;C|0.440	0.440	strong	.	OR13D1	42	.	NM_001004484	exon1	c.A573C	p.Q191H	ATTGCAAACAGTT	.	PASS	Atlas-SNP
INTU	27152	hgsc.bcm.edu	37	4	128565000	128565000	+	Silent	SNP	A	A	G	rs3749507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	150	281	0	0.508475	0	A|0.427;G|0.573	0.573	strong	INTU,NS,carcinoma,+1,1	INTU	92	1	NM_015693	exon2	c.A471G	p.R157R	ACAGCGATACAAA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	28	67	0	0.405797	0	A|0.832;G|0.168	0.168	strong	.	RBM19	117	.	NM_001146699	exon15	c.T1868C	p.I623T	GCAGTGATTCCGC	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84921433	84921433	+	Silent	SNP	A	A	G	rs1192295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	78	200	0	0.443182	0	A|0.904;G|0.096	0.096	strong	.	DNAH6	194	.	NM_001370	exon46	c.A7353G	p.T2451T	AGGCACAGGAAAG	.	PASS	Atlas-SNP
IRF2	3660	hgsc.bcm.edu	37	4	185310218	185310218	+	Silent	SNP	C	C	T	rs1131553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	87	153	0	0.517857	0	C|0.617;T|0.383	0.383	strong	IRF2,NS,carcinoma,0,1	IRF2	53	1	NM_002199	exon9	c.G744A	p.G248G	TGGCCGCCCCTTT	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39343822	39343822	+	Missense_Mutation	SNP	C	C	T	rs9603422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	107	297	0	0.417969	0	C|0.848;T|0.152	0.152	strong	.	FREM2	385	.	NM_207361	exon4	c.C5518T	p.R1840W	CGAGTGCGGATCC	.	PASS	Atlas-SNP
ABCG4	64137	hgsc.bcm.edu	37	11	119027691	119027691	+	Missense_Mutation	SNP	C	C	G	rs12271907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	29	74	0	0.591837	0	C|0.928;G|0.072;T|0.000	0.072	strong	.	ABCG4	77	.	NM_022169	exon9	c.C1035G	p.N345K	GAAGAACGAGGTC	.	PASS	Atlas-SNP
ROGDI	79641	hgsc.bcm.edu	37	16	4847976	4847976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	87	134	0	0.587838	0	.	.	none	.	ROGDI	11	.	NM_024589	exon9	c.G658A	p.A220T	CCCCAGCTGGGCG	.	PASS	Atlas-SNP
OR2C3	81472	hgsc.bcm.edu	37	1	247695427	247695427	+	Missense_Mutation	SNP	C	C	G	rs34220133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	46	105	0	0.396552	0	C|0.891;G|0.109	0.109	strong	OR2C3,NS,carcinoma,0,1	OR2C3	92	1	NM_198074	exon2	c.G387C	p.R129S	GAGTGGCCTGCAG	.	PASS	Atlas-SNP
NDUFAF5	79133	hgsc.bcm.edu	37	20	13797179	13797179	+	Silent	SNP	G	G	A	rs34901599	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	45	108	0	0.478723	0	G|0.960;A|0.040	0.040	strong	.	.	.	.	NM_024120	exon9	c.G849A	p.A283A	AGCTGCGGCAGTG	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714083	32714083	+	Missense_Mutation	SNP	T	T	C	rs9276436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	690	306	611	0	0.443478	0	T|0.882;C|0.118	0.118	strong	.	HLA-DQA2	27	.	NM_020056	exon4	c.T680C	p.V227A	TGTCTGTGGGCCT	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	41	117	0	0.181416	0	G|0.985;T|0.015	0.015	strong	ZDHHC11_ENST00000424784,NS,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon8	c.C1016A	p.T339K	CGTGCCGTCGAAT	.	PASS	Atlas-SNP
CTSB	1508	hgsc.bcm.edu	37	8	11710174	11710174	+	Missense_Mutation	SNP	T	T	C	rs1803250	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	53	0	0.48	0	T|0.896;C|0.103;A|0.000	0.103	strong	.	CTSB	24	.	NM_147780	exon5	c.A157G	p.S53G	AGTAGCTCATGTC	.	PASS	Atlas-SNP
SGIP1	84251	hgsc.bcm.edu	37	1	67105495	67105495	+	Silent	SNP	G	G	A	rs187876611	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	4	255	0	0.0145985	0	G|0.998;A|0.002	0.002	strong	SGIP1_ENST00000371039,right_upper_lobe,carcinoma,+2,2	SGIP1	272	2	NM_032291	exon5	c.G207A	p.A69A	TTATGCGGAAATT	.	scavenged	Atlas-SNP
TSHZ2	128553	hgsc.bcm.edu	37	20	51872038	51872038	+	Missense_Mutation	SNP	G	G	A	rs6097319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	28	45	0	0.583333	0	G|0.935;A|0.065	0.065	strong	.	TSHZ2	209	.	NM_173485	exon2	c.G2041A	p.A681T	GGGTGCGCCCTCG	.	PASS	Atlas-SNP
F9	2158	hgsc.bcm.edu	37	X	138643939	138643939	+	Silent	SNP	A	A	G	rs112057482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	85	140	0	0.625	0	A|0.989;G|0.011	0.011	strong	.	F9	107	.	NM_000133	exon8	c.A1095G	p.S365S	GAGATCAGCTTTA	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	42	0	1	0	C|0.791;T|0.209	0.209	strong	.	PALLD	179	.	NM_001166108	exon2	c.C18T	p.S6S	CTCCTCCCATGAG	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs17855613	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	24	558	1	0.066482	0.00179211	.	.	weak	SIRPA,brain,glioma,-2,4	SIRPA	83	4	NM_001040022	exon3	c.A298G	p.N100D	AAGAGAAACAACA	.	scavenged	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78069129	78069129	+	Missense_Mutation	SNP	G	G	T	rs61686936	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	126	215	0	0.504	0	A|0.000;G|0.981;T|0.019	0.019	strong	CCDC40,colon,carcinoma,0,1	CCDC40	198	1	NM_017950	exon18	c.G2900T	p.R967L	TTGCCCGCAGAGA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107696289	107696289	+	Silent	SNP	C	C	T	rs17154865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	82	133	0	0.565517	0	C|0.806;T|0.194	0.194	strong	.	LAMB4	253	.	NM_007356	exon25	c.G3543A	p.Q1181Q	GTCCCACTGATCA	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3476990	3476990	+	Silent	SNP	G	G	A	rs17706245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	57	116	0	0.504425	0	G|0.942;A|0.058	0.058	strong	.	TRPV1	99	.	NM_018727	exon13	c.C2040T	p.I680I	GAGGGCGATGAGC	.	PASS	Atlas-SNP
RAET1L	154064	hgsc.bcm.edu	37	6	150346532	150346532	+	Missense_Mutation	SNP	T	T	C	rs1543547	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	57	103	0	0.459677	0	C|0.440;N|0.000	0.440	strong	.	RAET1L	21	.	NM_130900	exon1	c.A76G	p.R26G	CTCGCCTAGCCCG	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91827264	91827264	+	Silent	SNP	C	C	T	rs2301664	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	130	119	0	0.992366	0	C|0.870;T|0.130	0.130	strong	.	SV2B	98	.	NM_014848	exon12	c.C1521T	p.H507H	CGAGCACAAGTTC	.	PASS	Atlas-SNP
ABTB2	25841	hgsc.bcm.edu	37	11	34378381	34378381	+	Missense_Mutation	SNP	G	G	C	rs1925368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	51	93	0	0.525773	0	G|0.844;C|0.156	0.156	strong	.	ABTB2	101	.	NM_145804	exon1	c.C750G	p.H250Q	AGGGCTGTGGCTG	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	15	39	0	0.46875	0	C|0.743;T|0.257	0.257	strong	.	TMC4	89	.	NM_001145303	exon11	c.G1572A	p.Q524Q	GAACTCCTGGGTC	.	PASS	Atlas-SNP
DMRTC2	63946	hgsc.bcm.edu	37	19	42354629	42354629	+	Silent	SNP	T	T	C	rs2305809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	43	0	1	0	T|0.398;C|0.602	0.602	strong	.	DMRTC2	31	.	NM_001040283	exon8	c.T852C	p.G284G	ATCTGGTCCCTCA	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786684	75786684	+	Missense_Mutation	SNP	G	G	T	rs201345045		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	11	30	0	0.22	0	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.C2090A	p.T697K	CCCGGTGTGAGTT	.	PASS	Atlas-SNP
MTMR9	66036	hgsc.bcm.edu	37	8	11142529	11142529	+	Silent	SNP	T	T	C	rs61752023	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	53	91	0	0.524752	0	T|0.958;C|0.042	0.042	strong	.	MTMR9	58	.	NM_015458	exon1	c.T132C	p.N44N	GGACAATACGGAG	.	PASS	Atlas-SNP
OR2A14	135941	hgsc.bcm.edu	37	7	143826603	143826603	+	Missense_Mutation	SNP	G	G	T	rs2961160	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	300	324	0	1	0	G|0.367;T|0.633	0.633	strong	OR2A14,NS,carcinoma,+1,1	OR2A14	66	1	NM_001001659	exon1	c.G398T	p.S133I	ACAATAGCCTCAT	.	PASS	Atlas-SNP
SIDT2	51092	hgsc.bcm.edu	37	11	117063020	117063020	+	Silent	SNP	C	C	T	rs12285062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	106	0	0.521277	0	C|0.990;T|0.010	0.010	strong	.	SIDT2	82	.	NM_001040455	exon20	c.C1923T	p.H641H	CATTCACATCATC	.	PASS	Atlas-SNP
FAN1	22909	hgsc.bcm.edu	37	15	31196984	31196984	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	67	134	0	0.496296	0	.	.	none	.	FAN1	77	.	NM_001146095	exon2	c.G118A	p.A40T	CCACCTGCTAAAC	.	PASS	Atlas-SNP
BCAS1	8537	hgsc.bcm.edu	37	20	52611552	52611552	+	Missense_Mutation	SNP	G	G	A	rs60878965	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	24	55	0	0.380952	0	G|0.916;A|0.084	0.084	strong	.	BCAS1	77	.	NM_003657	exon6	c.C926T	p.T309M	CCTACCGTGTCTT	.	PASS	Atlas-SNP
SEL1L	6400	hgsc.bcm.edu	37	14	81969158	81969158	+	Silent	SNP	A	A	G	rs35377988	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	35	78	0	0.37234	0	A|0.957;G|0.043	0.043	strong	.	SEL1L	67	.	NM_001244984	exon6	c.T684C	p.A228A	TAAAAGAGCATAT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50408614	50408614	+	Silent	SNP	A	A	G	rs76870996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	49	125	0	0.418803	0	A|0.988;G|0.012	0.012	strong	.	SALL4	168	.	NM_020436	exon2	c.T408C	p.N136N	GCCGCCATTCTCC	.	PASS	Atlas-SNP
KRT78	196374	hgsc.bcm.edu	37	12	53238387	53238387	+	Missense_Mutation	SNP	C	C	T	rs61764061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	51	107	0	0.962264	0	C|0.918;T|0.082	0.082	strong	.	KRT78	41	.	NM_173352	exon5	c.G877A	p.A293T	TCCGGGCGATCTC	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	105	244	0	0.410156	0	C|0.914;A|0.086	0.086	strong	.	DSC1	240	.	NM_024421	exon16	c.G2547T	p.S849S	GTTATACGAACAA	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74407182	74407182	+	Missense_Mutation	SNP	G	G	T	rs9446983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	51	118	0	0.548387	0	G|0.986;T|0.014	0.014	strong	CD109,NS,carcinoma,-1,1	CD109	170	1	NM_133493	exon2	c.G134T	p.G45V	CTATTGGGGTGGA	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64688335	64688335	+	Silent	SNP	G	G	A	rs75079588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	88	113	0	0.546584	0	G|0.994;A|0.006	0.006	strong	SYNE2,NS,carcinoma,0,1	SYNE2	577	1	NM_182914	exon112	c.G20103A	p.A6701A	GTTAGCGAGTGCC	.	PASS	Atlas-SNP
MICU1	10367	hgsc.bcm.edu	37	10	74183034	74183034	+	Silent	SNP	G	G	A	rs186054834	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	69	164	0	0.43125	0	G|0.999;A|0.001	0.001	strong	.	.	.	.	NM_001195518	exon9	c.C1029T	p.T343T	CATGGCGGTCAGC	.	PASS	Atlas-SNP
ARHGAP30	257106	hgsc.bcm.edu	37	1	161022247	161022247	+	Missense_Mutation	SNP	C	C	T	rs149524176	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	35	87	0	0.393258	0	C|0.999;T|0.001	0.001	strong	LOC257106,NS,carcinoma,-1,2	ARHGAP30	105	2	NM_001025598	exon8	c.G923A	p.R308Q	GCCCCCCGTGGAA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549563	32549563	+	Silent	SNP	G	G	A	rs77689370	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	80	177	0	0.329218	0	A|0.051;C|0.002;G|0.947	0.051	strong	.	HLA-DRB1	41	.	NM_002124	exon3	c.C423T	p.H141H	GAGGTTGTGGTGC	.	PASS	Atlas-SNP
GJB7	375519	hgsc.bcm.edu	37	6	87994101	87994101	+	Missense_Mutation	SNP	G	G	A	rs41273281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	41	111	0	0.383178	0	G|0.918;A|0.082	0.082	strong	GJB7,NS,carcinoma,+1,2	GJB7	28	2	NM_198568	exon3	c.C530T	p.T177M	AAGATCGTCTTCT	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123799974	123799974	+	Silent	SNP	A	A	G	rs6488868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	37	103	0	0.393617	0	A|0.316;G|0.684	0.684	strong	.	SBNO1	138	.	NM_001167856	exon22	c.T3066C	p.G1022G	TCTATCACCATGT	.	PASS	Atlas-SNP
DOC2B	8447	hgsc.bcm.edu	37	17	31199	31199	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	14	47	0	0.368421	0	.	.	none	.	DOC2B	6	.	NM_003585	exon1	c.C72T	p.P24P	GGGGCCGGGGCAC	.	PASS	Atlas-SNP
TTC4	7268	hgsc.bcm.edu	37	1	55188437	55188437	+	Missense_Mutation	SNP	C	C	T	rs62000412	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	46	102	0	0.541176	0	C|0.986;T|0.014	0.014	strong	.	TTC4	21	.	NM_004623	exon5	c.C559T	p.L187F	AAGAAGCTTCTGG	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782165	54782165	+	Missense_Mutation	SNP	C	C	T	rs4993133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	61	190	0	0.429577	0	C|0.995;T|0.005	0.005	strong	.	LILRB2	94	.	NM_005874	exon7	c.G1207A	p.D403N	AGGGGTCGGAGTT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179412452	179412452	+	Missense_Mutation	SNP	C	C	T	rs67665715	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	438	243	387	0	0.554795	0	C|0.967;T|0.033	0.033	strong	.	TTN	18412	.	NM_001267550	exon339	c.G93901A	p.V31301I	CTGTGACGCTAAA	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201012484	201012484	+	Missense_Mutation	SNP	C	C	T	rs13374149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	83	186	0	0.482558	0	C|0.890;T|0.110	0.110	strong	.	CACNA1S	249	.	NM_000069	exon40	c.G4973A	p.R1658H	TTGGCACGAGCCA	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11755316	11755316	+	Silent	SNP	C	C	T	rs16857699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	159	180	0	1	0	C|0.946;T|0.054	0.054	strong	.	GREB1	308	.	NM_014668	exon20	c.C3222T	p.N1074N	GAGCAACGAGGTT	.	PASS	Atlas-SNP
CYP24A1	1591	hgsc.bcm.edu	37	20	52786219	52786219	+	Silent	SNP	G	G	A	rs2296241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	59	115	0	0.475806	0	G|0.500;A|0.500	0.500	strong	CYP24A1,trunk,malignant_melanoma,-1,1	CYP24A1	75	1	NM_000782	exon4	c.C552T	p.A184A	AAAATCGGCCAAG	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503017	140503017	+	Silent	SNP	G	G	A	rs61741162	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	23	207	1	0.0970464	0.00483092	G|0.216;A|0.784	0.784	strong	PCDHB4,right_upper_lobe,carcinoma,+1,1	PCDHB4	177	1	NM_018938	exon1	c.G1437A	p.S479S	AGACTCGGGCACC	.	scavenged	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242054403	242054403	+	Missense_Mutation	SNP	G	G	A	rs3815305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	33	78	0	0.452055	0	G|0.764;A|0.236	0.236	strong	.	PASK	230	.	NM_001252124	exon14	c.C3388T	p.R1130W	GCCACCGGACCCA	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30680608	30680608	+	Missense_Mutation	SNP	C	C	T	rs2075015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	75	133	0	0.510204	0	C|0.939;T|0.061	0.061	strong	.	MDC1	218	.	NM_014641	exon5	c.G1111A	p.E371K	GGCTCTCCTGCAG	.	PASS	Atlas-SNP
MKRN3	7681	hgsc.bcm.edu	37	15	23811592	23811592	+	Silent	SNP	C	C	T	rs2239669	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	28	63	0	0.4375	0	C|0.745;A|0.002	.	strong	.	MKRN3	155	.	NM_005664	exon1	c.C663T	p.P221P	TGCCCCCGAGGCT	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3747496	3747496	+	Missense_Mutation	SNP	G	G	C	rs58583720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	46	72	0	0.567901	0	A|0.002;C|0.001;G|0.997	0.001	strong	.	EFCAB4B	100	.	NM_001144958	exon14	c.C1396G	p.R466G	GCGGCCGGGGGTA	.	PASS	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs806607	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	140	0	1	0	0|0.020;C|0.435	0.435	strong	.	HEPH	224	.	NM_138737	exon14	c.T2457C	p.Y819Y	TAGTTATGGTTAC	.	PASS	Atlas-SNP
KIF18B	146909	hgsc.bcm.edu	37	17	43010064	43010064	+	Silent	SNP	G	G	A	rs57250020	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	23	53	0	0.323944	0	G|0.935;A|0.065	0.065	strong	.	KIF18B	63	.	NM_001264573	exon9	c.C1215T	p.P405P	CGACTTGGGAGAT	.	PASS	Atlas-SNP
MS4A7	58475	hgsc.bcm.edu	37	11	60154242	60154242	+	Missense_Mutation	SNP	C	C	A	rs2233249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	53	90	0	0.473214	0	C|0.973;A|0.027	0.027	strong	.	MS4A7	38	.	NM_021201	exon4	c.C335A	p.P112H	CTAAGCCCTTTGT	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3137674	3137674	+	Missense_Mutation	SNP	G	G	A	rs363075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	134	272	0	0.494465	0	G|0.959;A|0.041	0.041	strong	.	HTT	221	.	NM_002111	exon20	c.G2677A	p.G893R	CACAGAGGGGCTC	.	PASS	Atlas-SNP
COMT	1312	hgsc.bcm.edu	37	22	19950268	19950268	+	Silent	SNP	G	G	A	rs740602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	116	0	0.431193	0	A|0.059;C|0.007	0.059	strong	.	COMT	10	.	NM_000754	exon3	c.G219A	p.Q73Q	CGCACAGAGCGTG	.	PASS	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	114	193	0	0.493506	0	C|0.835;T|0.165	0.165	strong	CD44,colon,carcinoma,0,1	CD44	48	1	NM_001001391	exon3	c.C255T	p.H85H	AGGGCACGTGGTG	.	PASS	Atlas-SNP
ZNF439	90594	hgsc.bcm.edu	37	19	11978130	11978130	+	Silent	SNP	A	A	G	rs10417222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	122	0	0.486486	0	A|0.978;G|0.022	0.022	strong	.	ZNF439	67	.	NM_152262	exon3	c.A246G	p.T82T	TGTCACAGAAGAG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935257	4935257	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	48	152	0	0.355556	0	.	.	none	.	PPL	168	.	NM_002705	exon22	c.C3399T	p.L1133L	GCGGGTGAGATCG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs71563185		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	33	190	0	0.23913	0	A|0.500;G|0.500	0.500	weak	TYW1,NS,carcinoma,0,1	TYW1	71	1	NM_018264	exon15	c.A1895G	p.H632R	TTGTCCACGAGTT	.	PASS	Atlas-SNP
CEACAM21	90273	hgsc.bcm.edu	37	19	42092225	42092225	+	Splice_Site	SNP	G	G	A	rs62119455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	158	140	1	1	0.00714286	G|0.981;A|0.019	0.019	strong	.	CEACAM21	52	.	NM_001098506	exon6	c.882+1G>A	.	TCCTAGGTAAGAC	.	PASS	Atlas-SNP
WDR55	54853	hgsc.bcm.edu	37	5	140048792	140048792	+	Silent	SNP	C	C	A	rs35080423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	32	70	1	0.52459	0.0142857	C|0.991;A|0.009	0.009	strong	WDR55,NS,carcinoma,+2,1	WDR55	27	1	NM_017706	exon6	c.C789A	p.T263T	AGTCACCGAGAGT	.	scavenged	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36351906	36351906	+	Silent	SNP	C	C	A	rs73928338	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	30	50	0	0.434783	0	C|0.994;A|0.006	0.006	strong	.	KIRREL2	170	.	NM_199180	exon8	c.C1024A	p.R342R	CTTCCACGGGTAA	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329093	243329093	+	Silent	SNP	G	G	C	rs2789194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	108	222	0	0.497696	0	G|0.978;C|0.022	0.022	strong	.	CEP170	153	.	NM_014812	exon13	c.C2169G	p.G723G	AGAGCTGCCTAAG	.	PASS	Atlas-SNP
MLL5	55904	hgsc.bcm.edu	37	7	104717517	104717517	+	Silent	SNP	C	C	T	rs2240455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	97	178	0	0.502591	0	C|0.620;T|0.380	0.380	strong	.	MLL5	173	.	NM_018682	exon9	c.C876T	p.Y292Y	CCAGTACAGTGAG	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117659292	117659292	+	Missense_Mutation	SNP	C	C	T	rs76902778	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	35	137	0	0.364583	0	C|0.971;T|0.029	0.029	strong	TRIM45,caecum,carcinoma,+1,1	TRIM45	55	1	NM_025188	exon3	c.G1298A	p.G433D	CCCCTGCCCATGA	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55105727	55105727	+	Silent	SNP	A	A	G	rs28469702	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	229	0	1	0	A|0.789;G|0.211	0.211	strong	.	LILRA1	105	.	NM_006863	exon2	c.A18G	p.T6T	CGTCACAGTCCTG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6549779	6549779	+	Missense_Mutation	SNP	A	A	C	rs4633449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	54	102	0	0.54	0	A|0.272;C|0.728	0.728	strong	.	DNHD1	198	.	NM_144666	exon11	c.A1865C	p.D622A	CAAAAGACGAATT	.	PASS	Atlas-SNP
C16orf62	57020	hgsc.bcm.edu	37	16	19590444	19590444	+	Silent	SNP	T	T	C	rs11866050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	61	95	0	0.564815	0	T|0.937;C|0.063	0.063	strong	.	C16orf62	164	.	NM_020314	exon6	c.T771C	p.F257F	TGACTTTGAGGAG	.	PASS	Atlas-SNP
EGLN2	112398	hgsc.bcm.edu	37	19	41306771	41306771	+	Silent	SNP	G	G	A	rs143206553	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	31	45	0	0.492063	0	G|0.993;A|0.007	0.007	strong	.	EGLN2	31	.	NM_053046	exon2	c.G294A	p.A98A	TGCAGCGCTGGTC	.	PASS	Atlas-SNP
FEV	54738	hgsc.bcm.edu	37	2	219846749	219846749	+	Silent	SNP	G	G	A	rs860573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	50	98	0	0.568182	0	G|0.902;A|0.098	0.098	strong	.	FEV	10	.	NM_017521	exon3	c.C357T	p.G119G	GCGCTTGCCATGC	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528321	20528321	+	Missense_Mutation	SNP	A	A	G	rs1958716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	154	342	1	0.446377	0.00292398	A|0.531;G|0.469	0.469	strong	.	OR4L1	98	.	NM_001004717	exon1	c.A118G	p.M40V	ACTGTGATGGGAA	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234595070	234595070	+	Missense_Mutation	SNP	T	T	C	rs35562024	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	71	0	0.493506	0	T|0.982;C|0.018	0.018	strong	.	TARBP1	111	.	NM_005646	exon8	c.A1538G	p.D513G	ATAACATCCCTGA	.	PASS	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546742	11546742	+	Silent	SNP	T	T	C	rs201044388	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	405	105	424	1	0.259259	0.00235849	T|0.776;C|0.224	0.224	strong	PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	NM_006248	exon3	c.A270G	p.Q90Q	GGGACCTTGAGGT	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74274812	74274812	+	Missense_Mutation	SNP	G	G	A	rs72816199	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	39	70	0	0.428571	0	G|0.986;A|0.014	0.014	strong	.	TET3	101	.	NM_144993	exon1	c.G1363A	p.V455M	GGTCCCGTGGGAA	.	PASS	Atlas-SNP
C17orf85	55421	hgsc.bcm.edu	37	17	3728315	3728315	+	Silent	SNP	C	C	T	rs218719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	11	30	0	0.407407	0	C|0.932;T|0.068	0.068	strong	.	C17orf85	66	.	NM_001114118	exon7	c.G717A	p.E239E	CAAAGACTCCTCT	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	45	89	0	0.454545	0	C|0.908;T|0.092	0.092	strong	.	LRRC16B	120	.	NM_138360	exon23	c.C1899T	p.P633P	CTTCCCCGTGAGC	.	PASS	Atlas-SNP
CUEDC1	404093	hgsc.bcm.edu	37	17	55950082	55950082	+	Silent	SNP	G	G	A	rs16942487	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	47	106	0	0.439252	0	G|0.966;A|0.034	0.034	strong	.	CUEDC1	37	.	NM_001271875	exon5	c.C726T	p.N242N	CTCCTCGTTCTGC	.	PASS	Atlas-SNP
VAV2	7410	hgsc.bcm.edu	37	9	136640122	136640122	+	Silent	SNP	G	G	A	rs7875953	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	86	102	0	0.637037	0	G|0.963;A|0.037	0.037	strong	VAV2_ENST00000371850,colon,carcinoma,0,2	VAV2	165	2	NM_001134398	exon25	c.C2070T	p.H690H	GCTGGCGTGGGAC	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62579907	62579907	+	Silent	SNP	C	C	T	rs7418709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	78	182	0	0.435754	0	C|0.784;T|0.216	0.216	strong	.	INADL	179	.	NM_176877	exon35	c.C4644T	p.I1548I	GAGCATCGTTGGG	.	PASS	Atlas-SNP
C20orf96	140680	hgsc.bcm.edu	37	20	259818	259818	+	Silent	SNP	G	G	A	rs6035541	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	19	41	0	0.542857	0	G|0.679;A|0.321	0.321	strong	C20orf96,NS,carcinoma,0,1	C20orf96	28	1	NM_153269	exon5	c.C460T	p.L154L	CCGCCAGGGTGTC	.	PASS	Atlas-SNP
SPINK2	6691	hgsc.bcm.edu	37	4	57687711	57687711	+	Missense_Mutation	SNP	T	T	C	rs781543	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	10	16	0	0.333333	0	T|0.791;C|0.209	0.209	strong	.	SPINK2	12	.	NM_001271722	exon1	c.A118G	p.T40A	CGCCGGTCTGACT	.	PASS	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35864573	35864573	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	3	145	0	0.0194805	0	.	.	none	NBEA,NS,carcinoma,-2,1	NBEA	340	1	NM_015678	exon35	c.C5824T	p.L1942L	GTTATGCTGCTTT	.	scavenged	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	124	252	0	0.466165	0	C|0.960;T|0.040	0.040	strong	TGM6,NS,carcinoma,0,1	TGM6	126	1	NM_198994	exon4	c.C477T	p.S159S	GCTCAGCGACAGC	.	PASS	Atlas-SNP
IDH3A	3419	hgsc.bcm.edu	37	15	78458638	78458638	+	Silent	SNP	C	C	T	rs2304826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	79	100	0	0.552448	0	C|0.950;T|0.050	0.050	strong	.	IDH3A	24	.	NM_005530	exon10	c.C1011T	p.D337D	TAAGGACGGAAAG	.	PASS	Atlas-SNP
ADPRHL2	54936	hgsc.bcm.edu	37	1	36557619	36557619	+	Missense_Mutation	SNP	G	G	A	rs2236387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	131	257	0	0.511719	0	G|0.871;A|0.129	0.129	strong	.	ADPRHL2	25	.	NM_017825	exon4	c.G625A	p.E209K	TCCAGCGAGCACT	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671663	31671663	+	Silent	SNP	T	T	C	rs2424945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	51	61	0	0.980769	0	T|0.623;C|0.377	0.377	strong	.	.	.	.	NM_182519	exon3	c.T660C	p.T220T	CAGCACTGTGCAA	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	76	183	0	0.466258	0	C|0.615;G|0.385	0.385	strong	.	DDX60L	116	.	NM_001012967	exon10	c.G1225C	p.V409L	TTCCAACGTTAAA	.	PASS	Atlas-SNP
ZFP36L2	678	hgsc.bcm.edu	37	2	43452334	43452334	+	Silent	SNP	G	G	A	rs8098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	20	32	0	0.487805	0	G|0.886;A|0.114	0.114	strong	.	ZFP36L2	56	.	NM_006887	exon2	c.C609T	p.I203I	GAAGCCGATGGTA	.	PASS	Atlas-SNP
LUZP1	7798	hgsc.bcm.edu	37	1	23418576	23418576	+	Missense_Mutation	SNP	T	T	C	rs144862656	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	59	108	0	0.468254	0	T|0.997;C|0.003	0.003	strong	.	LUZP1	83	.	NM_033631	exon4	c.A2179G	p.T727A	CCATGGTATTGGT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114175032	114175032	+	Missense_Mutation	SNP	G	G	A	rs2260335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	53	113	0	0.5	0	G|0.805;A|0.195	0.195	strong	.	TMCO3	77	.	NM_017905	exon8	c.G1327A	p.A443T	GCGGGCGCCAGTG	.	PASS	Atlas-SNP
TUBB2B	347733	hgsc.bcm.edu	37	6	3225759	3225759	+	Silent	SNP	C	C	A	rs62391678	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	562	91	528	2	0.161922	0.00378788	C|0.750;A|0.250	0.250	weak	TUBB2B,caecum,carcinoma,-1,1	TUBB2B	25	1	NM_178012	exon4	c.G564T	p.S188S	GTGGACCGAGAGG	.	scavenged	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919779	28919779	+	Missense_Mutation	SNP	A	A	C	rs8091003	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	152	0	1	0	A|0.796;C|0.204	0.204	strong	.	DSG1	176	.	NM_001942	exon11	c.A1478C	p.N493T	GGACTAATACAGA	.	PASS	Atlas-SNP
BTBD1	53339	hgsc.bcm.edu	37	15	83725291	83725291	+	Silent	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	35	69	0	0.402299	0	.	.	none	BTBD1,NS,carcinoma,-2,1	BTBD1	32	1	NM_025238	exon2	c.A408T	p.L136L	TGAATATAGAAAT	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450003	89450003	+	Silent	SNP	G	G	A	rs2271714	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	65	114	0	0.570175	0	G|0.826;A|0.174	0.174	strong	MFGE8,NS,carcinoma,0,1	MFGE8	60	1	NM_001114614	exon4	c.C394T	p.L132L	GCAGCAGGTTCAC	.	PASS	Atlas-SNP
UGT3A1	133688	hgsc.bcm.edu	37	5	35957462	35957462	+	Silent	SNP	G	G	A	rs10428673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	69	110	0	0.511111	0	G|0.991;A|0.009	0.009	strong	.	UGT3A1	95	.	NM_152404	exon5	c.C903T	p.G301G	CATGGAGCCAAAG	.	PASS	Atlas-SNP
OR5V1	81696	hgsc.bcm.edu	37	6	29323905	29323905	+	Missense_Mutation	SNP	A	A	C	rs6930033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	54	93	0	0.519231	0	A|0.805;C|0.195	0.195	strong	.	OR5V1	63	.	NM_030876	exon1	c.T68G	p.L23W	AACTGCAATTCAT	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66433458	66433458	+	Silent	SNP	G	G	A	rs34042409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	95	0	0.460674	0	G|0.941;A|0.059	0.059	strong	.	LRIG1	138	.	NM_015541	exon15	c.C2439T	p.C813C	GATGATGCACACC	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169622490	169622490	+	Silent	SNP	G	G	A	rs9505895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	86	117	0	0.585034	0	G|0.783;A|0.217	0.217	strong	THBS2,NS,carcinoma,0,1	THBS2	230	1	NM_003247	exon20	c.C3075T	p.A1025A	GAAGCCGGCATAG	.	PASS	Atlas-SNP
ZFP14	57677	hgsc.bcm.edu	37	19	36832427	36832427	+	Missense_Mutation	SNP	A	A	T	rs115297808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	61	136	0	0.516949	0	A|0.990;T|0.010	0.010	strong	.	ZFP14	68	.	NM_020917	exon5	c.T301A	p.F101I	ACTGAAATGAATA	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	55	118	0	0.211538	0	A|0.977;G|0.023	0.023	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.T1005C	p.D335D	ATCCCCATCCTGG	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229773441	229773441	+	Silent	SNP	C	C	T	rs3811475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	68	138	0	0.427673	0	C|0.857;T|0.143	0.143	strong	.	URB2	152	.	NM_014777	exon4	c.C3081T	p.T1027T	AATCACCGCATTC	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77418802	77418802	+	Missense_Mutation	SNP	G	G	A	rs115354606	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	61	82	0	0.693182	0	G|0.969;A|0.031	0.031	strong	.	TRPM6	377	.	NM_017662	exon15	c.C1639T	p.H547Y	TCTGGTGCTGGGA	.	PASS	Atlas-SNP
PYCRL	65263	hgsc.bcm.edu	37	8	144688736	144688736	+	Missense_Mutation	SNP	C	C	G	rs2242090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	89	170	0	0.468421	0	C|0.608;G|0.392	0.392	strong	PYCRL,NS,carcinoma,0,2	PYCRL	14	2	NM_023078	exon4	c.G486C	p.K162N	CAGGAGCTTGGTC	.	PASS	Atlas-SNP
WDR64	128025	hgsc.bcm.edu	37	1	241951329	241951329	+	Missense_Mutation	SNP	C	C	T	rs12074374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	51	98	0	0.607143	0	C|0.837;T|0.163	0.163	strong	WDR64_ENST00000366552,NS,carcinoma,-1,2	WDR64	234	2	NM_144625	exon23	c.C2854T	p.R952W	TTTGACCGGGAAA	.	PASS	Atlas-SNP
RPAP3	79657	hgsc.bcm.edu	37	12	48075597	48075597	+	Silent	SNP	A	A	G	rs36123489	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	68	0	0.479167	0	A|0.952;G|0.048	0.048	strong	.	RPAP3	45	.	NM_024604	exon10	c.T996C	p.Y332Y	TTCTTCATATCTA	.	PASS	Atlas-SNP
GPATCH4	54865	hgsc.bcm.edu	37	1	156567847	156567847	+	Missense_Mutation	SNP	G	G	C	rs141345590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	91	175	0	0.5	0	G|0.988;C|0.012	0.012	strong	.	GPATCH4	34	.	NM_015590	exon5	c.C328G	p.L110V	GATACAGCAAGTT	.	PASS	Atlas-SNP
MASP2	10747	hgsc.bcm.edu	37	1	11103408	11103408	+	Silent	SNP	G	G	A	rs7536030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	21	52	0	0.446809	0	G|0.904;A|0.096	0.096	strong	MASP2,colon,carcinoma,0,1	MASP2	71	1	NM_006610	exon5	c.C729T	p.Y243Y	AAAGTCGTAGGGA	.	PASS	Atlas-SNP
MGA	23269	hgsc.bcm.edu	37	15	42019421	42019421	+	Silent	SNP	A	A	G	rs61736067	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	41	97	0	0.471264	0	A|0.988;G|0.012	0.012	strong	.	MGA	264	.	NM_001080541	exon10	c.A3474G	p.P1158P	TTACCCATTATGG	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71835842	71835842	+	Missense_Mutation	SNP	C	C	A	rs41305539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	54	87	0	0.580645	0	C|0.892;A|0.108	0.108	strong	.	TJP2	120	.	NM_001170416	exon5	c.C475A	p.Q159K	GCACTTCAGGCCA	.	PASS	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125855665	125855665	+	Missense_Mutation	SNP	T	T	G	rs9282691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	79	0	0.526882	0	T|0.935;G|0.065	0.065	strong	.	ALDH1L1	138	.	NM_001270364	exon11	c.A1316C	p.E439A	ACGAACTCCCCCC	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157959888	157959888	+	Silent	SNP	G	G	A	rs73745197	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	40	80	0	0.571429	0	G|0.973;A|0.027	0.027	strong	.	PTPRN2	243	.	NM_130843	exon6	c.C645T	p.D215D	CAGGAGGTCCTCG	.	PASS	Atlas-SNP
PNMT	5409	hgsc.bcm.edu	37	17	37826249	37826249	+	Silent	SNP	A	A	G	rs5638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	23	44	0	0.433962	0	A|0.933;G|0.067	0.067	strong	.	PNMT	17	.	NM_002686	exon3	c.A456G	p.K152K	GGTGAAACGGGTC	.	PASS	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21385427	21385427	+	Missense_Mutation	SNP	G	G	C	rs80061703	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	34	39	0	0.62963	0	G|0.969;C|0.031	0.031	strong	.	SLC7A4	50	.	NM_004173	exon2	c.C675G	p.D225E	GCCTTCGTCAGCG	.	PASS	Atlas-SNP
HCN3	57657	hgsc.bcm.edu	37	1	155247408	155247408	+	Silent	SNP	G	G	T	rs184885598	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	8	2	0	0.615385	0	G|0.983;T|0.017	0.017	strong	.	HCN3	74	.	NM_020897	exon1	c.G27T	p.A9A	GGCGGCGGGGGCC	.	PASS	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161599654	161599654	+	Missense_Mutation	SNP	G	G	T	rs5030738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	405	362	385	2	0.893827	0.00519481	G|0.953;T|0.047	0.047	strong	FCGR3B,NS,carcinoma,-1,2	FCGR3B	35	2	NM_001244753	exon3	c.C341A	p.A114D	GTGGCAGCGTCAA	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160690646	160690646	+	Silent	SNP	T	T	C	rs6722188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	86	182	0	0.573333	0	T|0.880;C|0.120	0.120	strong	.	LY75	151	.	NM_002349	exon27	c.A3750G	p.P1250P	CTGAAATGGTATC	.	PASS	Atlas-SNP
COL1A1	1277	hgsc.bcm.edu	37	17	48264448	48264448	+	Silent	SNP	A	A	G	rs1800218	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	42	93	0	0.47191	0	A|0.952;G|0.048	0.048	strong	.	COL1A1	158	.	NM_000088	exon47	c.T3459C	p.D1153D	GAGTCCATCTTTG	.	PASS	Atlas-SNP
OSBPL1A	114876	hgsc.bcm.edu	37	18	21752366	21752366	+	Silent	SNP	A	A	G	rs2077984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	52	138	0	0.419355	0	A|0.894;G|0.106	0.106	strong	.	OSBPL1A	94	.	NM_080597	exon22	c.T2175C	p.Y725Y	ATTGCCATACTGT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74288421	74288421	+	Missense_Mutation	SNP	A	A	G	rs6501878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	45	143	0	0.314685	0	A|0.636;G|0.364	0.364	strong	.	QRICH2	143	.	NM_032134	exon4	c.T1889C	p.I630T	TGAACTATACCAG	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981516	44981516	+	Silent	SNP	C	C	T	rs16979130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	39	65	0	0.534247	0	C|0.953;T|0.047	0.047	strong	.	ZNF180	103	.	NM_013256	exon5	c.G1182A	p.S394S	AAGGTGCGAGCTC	.	PASS	Atlas-SNP
NCKAP1	10787	hgsc.bcm.edu	37	2	183817154	183817154	+	Silent	SNP	T	T	C	rs111993802	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	97	193	0	0.515957	0	T|0.987;C|0.013	0.013	strong	.	NCKAP1	105	.	NM_205842	exon24	c.A2598G	p.S866S	TTGTGATGAAATA	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52779244	52779244	+	Silent	SNP	A	A	G	rs1732304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	157	0	1	0	A|0.744;G|0.256	0.256	strong	.	KRT84	61	.	NM_033045	exon1	c.T126C	p.P42P	GAATCCAGGCCCA	.	PASS	Atlas-SNP
COL1A2	1278	hgsc.bcm.edu	37	7	94030899	94030899	+	Silent	SNP	T	T	C	rs1800222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	114	0	0.490196	0	T|0.716;C|0.284	0.284	strong	.	COL1A2	240	.	NM_000089	exon6	c.T246C	p.D82D	GTATGATGGAAAA	.	PASS	Atlas-SNP
ITGAD	3681	hgsc.bcm.edu	37	16	31429479	31429479	+	Silent	SNP	T	T	C	rs78517822	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	96	225	0	0.468293	0	T|0.947;C|0.053	0.053	strong	.	ITGAD	154	.	NM_005353	exon21	c.T2583C	p.S861S	CTGCAGTGTCAAC	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605266	32605266	+	Missense_Mutation	SNP	G	G	A	rs1047992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	24	176	0	0.275862	0	G|0.879;A|0.121	0.121	strong	.	HLA-DQA1	52	.	NM_002122	exon1	c.G31A	p.A11T	CTGGGGGCCCTCG	.	PASS	Atlas-SNP
FBXO18	84893	hgsc.bcm.edu	37	10	5979117	5979117	+	Silent	SNP	T	T	C	rs2274033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	106	237	1	0.497653	0.00421941	T|0.958;C|0.042	0.042	strong	.	FBXO18	108	.	NM_032807	exon22	c.T3159C	p.C1053C	CTCCTGTGCGGAG	.	PASS	Atlas-SNP
OR2G2	81470	hgsc.bcm.edu	37	1	247751936	247751936	+	Missense_Mutation	SNP	T	T	G	rs146039934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	347	176	354	0	0.507205	0	T|0.994;G|0.006	0.006	strong	.	OR2G2	88	.	NM_001001915	exon1	c.T275G	p.M92R	AACCCATGAAAAC	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232941215	232941215	+	Missense_Mutation	SNP	A	A	G	rs41271527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	62	97	0	0.459259	0	A|0.951;G|0.049	0.049	strong	.	.	.	.	NM_019090	exon1	c.A446G	p.E149G	TGTCCGAGCGGCT	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11532835	11532835	+	Silent	SNP	A	A	G	rs9895535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	93	0	1	0	A|0.589;G|0.411	0.411	strong	.	DNAH9	695	.	NM_001372	exon7	c.A1452G	p.E484E	GCATGAAGAATTT	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26540951	26540951	+	Silent	SNP	G	G	A	rs116141676	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	59	125	0	0.406897	0	G|0.986;A|0.014	0.014	strong	.	GPR113	134	.	NM_001145168	exon2	c.C219T	p.S73S	GCCAAAGCTAGAA	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	845819	845819	+	Silent	SNP	A	A	G	rs2294446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	55	0	1	0	A|0.862;G|0.138	0.138	strong	.	CHTF18	52	.	NM_022092	exon17	c.A2310G	p.A770A	TCTTGCACCCAAG	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33131227	33131227	+	Silent	SNP	C	C	T	rs10410241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	91	224	0	0.435407	0	C|0.924;T|0.076	0.076	strong	ANKRD27,colon,carcinoma,-1,1	ANKRD27	86	1	NM_032139	exon11	c.G969A	p.T323T	GATCTCCGTTTTC	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12943038	12943038	+	Missense_Mutation	SNP	A	A	C	rs3121081	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	130	321	1	0.970149	0.00311526	A|0.852;C|0.148	0.148	strong	PRAMEF4,caecum,carcinoma,+1,1	PRAMEF4	62	1	NM_001009611	exon2	c.T178G	p.S60A	GCCAGGACTGCAC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505812	195505812	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	4	237	1	0.0159363	0.00421941	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,5	MUC4	1505	5	NM_018406	exon2	c.C12639T	p.D4213D	GGAAGTGTCGGTG	.	scavenged	Atlas-SNP
UPP2	151531	hgsc.bcm.edu	37	2	158971664	158971664	+	Missense_Mutation	SNP	A	A	C	rs7561584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	35	118	0	0.397727	0	A|0.994;C|0.006	0.006	strong	.	UPP2	60	.	NM_001135098	exon5	c.A403C	p.M135L	CTGTTTATGCACA	.	PASS	Atlas-SNP
BPIFB2	80341	hgsc.bcm.edu	37	20	31598909	31598909	+	Silent	SNP	G	G	A	rs61734339	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	116	0	0.451613	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_025227	exon3	c.G189A	p.A63A	AGAGGCGCTTCAG	.	PASS	Atlas-SNP
PVRL1	5818	hgsc.bcm.edu	37	11	119509485	119509485	+	Missense_Mutation	SNP	G	G	A	rs73571271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	21	62	0	0.512195	0	G|0.978;A|0.022	0.022	strong	.	PVRL1	133	.	NM_203285	exon7	c.C1183T	p.P395S	GAGAAGGCTCCGG	.	PASS	Atlas-SNP
FAM186B	84070	hgsc.bcm.edu	37	12	49994658	49994658	+	Missense_Mutation	SNP	C	C	G	rs74086906	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	114	283	0	0.395833	0	C|0.964;G|0.036	0.036	strong	.	FAM186B	72	.	NM_032130	exon4	c.G765C	p.R255S	CAGGCTCCTGTTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228509324	228509324	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	2	92	0	0.017094	0	.	.	none	OBSCN,NS,carcinoma,-1,1	OBSCN	2142	1	NM_001271223	exon66	c.C17653T	p.R5885X	GATGTGCGAGCCC	.	scavenged	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572355	33572355	+	Silent	SNP	C	C	G	rs200701439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	350	14	313	0	0.04	0	C|0.998;G|0.002	0.002	weak	.	ANKRD18B	46	.	NM_001244752	exon16	c.C3030G	p.L1010L	TCTTCTCTAGAAT	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108389111	108389111	+	Silent	SNP	A	A	G	rs3802553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	43	80	0	0.530864	0	A|0.841;G|0.159	0.159	strong	.	SORCS1	534	.	NM_001206572	exon19	c.T2511C	p.F837F	ATCGCCAAAGTCC	.	PASS	Atlas-SNP
C18orf32	497661	hgsc.bcm.edu	37	18	47008736	47008736	+	Silent	SNP	G	G	A	rs148432146	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	56	104	0	0.583333	0	G|0.999;A|0.001	0.001	strong	.	C18orf32	8	.	NM_001199346	exon3	c.C210T	p.I70I	ATCACAGATTTCT	.	PASS	Atlas-SNP
FCRL5	83416	hgsc.bcm.edu	37	1	157497597	157497597	+	Silent	SNP	C	C	T	rs73011545	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	66	214	0	0.370787	0	C|0.972;T|0.028	0.028	strong	FCRL5,NS,carcinoma,-1,1	FCRL5	177	1	NM_031281	exon9	c.G1770A	p.P590P	GCCTCTCGGGGCC	.	PASS	Atlas-SNP
CD8B	926	hgsc.bcm.edu	37	2	87073817	87073817	+	Missense_Mutation	SNP	G	G	C	rs1126874		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	413	29	402	0	0.0702179	0	.	.	weak	CD8B_ENST00000393759,NS,carcinoma,0,2	CD8B	37	2	NM_004931	exon4	c.C573G	p.I191M	CAGGTGGATGGCC	.	scavenged	Atlas-SNP
GPR37	2861	hgsc.bcm.edu	37	7	124404371	124404371	+	Silent	SNP	G	G	A	rs61744942	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	44	80	1	0.488889	0.0125	G|0.889;A|0.111	0.111	strong	GPR37,rectum,carcinoma,-1,1	GPR37	89	1	NM_005302	exon1	c.C660T	p.A220A	ATTCTGGGCCAGC	.	scavenged	Atlas-SNP
NUP50	10762	hgsc.bcm.edu	37	22	45577231	45577231	+	Silent	SNP	T	T	C	rs226524	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	121	0	0.509804	0	T|0.772;C|0.228	0.228	strong	.	NUP50	24	.	NM_007172	exon6	c.T1068C	p.D356D	AGAAGATGCTTTT	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	160047491	160047491	+	Missense_Mutation	SNP	A	A	C	rs375262733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	100	199	0	0.414938	0	.	.	weak	.	ATP10B	201	.	NM_025153	exon15	c.T2279G	p.L760R	CAGAGGAGGCTGA	.	PASS	Atlas-SNP
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	104	208	0	0.429752	0	C|0.963;T|0.037	0.037	strong	.	KRTAP13-4	46	.	NM_181600	exon1	c.C36T	p.S12S	CTCCTCCCGCTCC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40373950	40373950	+	Missense_Mutation	SNP	G	G	T	rs3746010	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	39	808	1	0.174888	0.00123762	G|0.750;T|0.250	0.250	weak	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon26	c.C12128A	p.T4043N	CCTTTGGTGACGC	.	scavenged	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344202	72344202	+	Silent	SNP	T	T	C	rs374837339		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	66	112	0	0.554622	0	.	.	weak	.	ZNF407	231	.	NM_001146190	exon1	c.T1227C	p.S409S	TAACAGTGTAACC	.	PASS	Atlas-SNP
SMAD3	4088	hgsc.bcm.edu	37	15	67457335	67457335	+	Silent	SNP	A	A	G	rs1065080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	113	112	0	0.991228	0	A|0.132;G|0.868	0.868	strong	.	SMAD3	119	.	NM_005902	exon2	c.A309G	p.L103L	CGAGCTACGGGCC	.	PASS	Atlas-SNP
IQCE	23288	hgsc.bcm.edu	37	7	2611908	2611908	+	Silent	SNP	G	G	C	rs147584030	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	29	51	0	0.446154	0	G|0.994;C|0.006	0.006	strong	.	IQCE	66	.	NM_152558	exon5	c.G342C	p.L114L	CTGTCTGACAGAC	.	PASS	Atlas-SNP
OR52M1	119772	hgsc.bcm.edu	37	11	4566870	4566870	+	Silent	SNP	T	T	C	rs61747520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	470	218	432	2	0.46383	0.00462963	T|0.968;C|0.032	0.032	strong	OR52M1,right_upper_lobe,carcinoma,+1,1	OR52M1	53	1	NM_001004137	exon1	c.T450C	p.S150S	TGTTTCTCTCCTC	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92538422	92538422	+	Silent	SNP	C	C	T	rs59542280	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	65	150	0	0.464286	0	C|0.988;T|0.012	0.012	strong	.	FAT3	1822	.	NM_001008781	exon10	c.C9000T	p.L3000L	CTTTCTCAATATC	.	PASS	Atlas-SNP
ZNF616	90317	hgsc.bcm.edu	37	19	52619065	52619065	+	Missense_Mutation	SNP	T	T	C	rs3764537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	186	174	0	1	0	T|0.701;C|0.299	0.299	strong	.	ZNF616	109	.	NM_178523	exon4	c.A1352G	p.H451R	GCAAGATGTGAAT	.	PASS	Atlas-SNP
KIF7	374654	hgsc.bcm.edu	37	15	90192363	90192363	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	32	48	0	0.561404	0	.	.	none	.	KIF7	130	.	NM_198525	exon4	c.C765T	p.G255G	CTCTGAGCCCGCC	.	PASS	Atlas-SNP
CCDC109B	55013	hgsc.bcm.edu	37	4	110581363	110581363	+	Missense_Mutation	SNP	T	T	A	rs4698744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	67	99	0	0.540323	0	T|0.669;A|0.331	0.331	strong	.	CCDC109B	47	.	NM_017918	exon3	c.T188A	p.I63N	CAGTTATTTATAG	.	PASS	Atlas-SNP
ZSCAN2	54993	hgsc.bcm.edu	37	15	85164530	85164530	+	Silent	SNP	C	C	T	rs115131715	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	35	79	0	0.57377	0	C|0.988;T|0.012	0.012	strong	.	ZSCAN2	43	.	NM_181877	exon3	c.C1104T	p.G368G	ATGCGGCGAAAGC	.	PASS	Atlas-SNP
CLYBL	171425	hgsc.bcm.edu	37	13	100511247	100511247	+	Missense_Mutation	SNP	G	G	A	rs35680839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	59	97	0	0.483607	0	G|0.956;A|0.044	0.044	strong	.	CLYBL	48	.	NM_206808	exon3	c.G382A	p.V128I	TCCCGGGTCCTTC	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910431	39910431	+	Missense_Mutation	SNP	A	A	G	rs10152640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	76	0	1	0	A|0.599;G|0.401	0.401	strong	FSIP1,NS,carcinoma,0,2	FSIP1	53	2	NM_152597	exon11	c.T1204C	p.C402R	AGAGACATGATGT	.	PASS	Atlas-SNP
FRMD7	90167	hgsc.bcm.edu	37	X	131212487	131212487	+	Missense_Mutation	SNP	G	G	C	rs61742429	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	84	204	0	0.390698	0	G|0.982;C|0.018	0.018	strong	.	FRMD7	69	.	NM_194277	exon12	c.C1558G	p.H520D	AGCTATGTGGACT	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242012729	242012729	+	Missense_Mutation	SNP	G	G	A	rs6721345	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	72	150	0	0.447205	0	G|0.966;A|0.034	0.034	strong	.	SNED1	76	.	NM_001080437	exon27	c.G3866A	p.R1289Q	CCAAGCGGGTCAG	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7673928	7673928	+	Silent	SNP	C	C	G	rs9909288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	145	1	1	0.00689655	C|0.704;G|0.296	0.296	strong	.	DNAH2	498	.	NM_020877	exon25	c.C4152G	p.P1384P	AGTACCCTACAAG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134628208	134628208	+	Missense_Mutation	SNP	C	C	T	rs61733298	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	99	0	0.468354	0	C|0.968;T|0.032	0.032	strong	.	TTC40	100	.	NM_001200049	exon52	c.G7231A	p.D2411N	CTGAGTCGACTAT	.	PASS	Atlas-SNP
AMDHD2	51005	hgsc.bcm.edu	37	16	2578131	2578131	+	Silent	SNP	C	C	G	rs35816046	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	37	84	0	0.377551	0	G|0.019;C|0.981	0.019	strong	.	AMDHD2	33	.	NM_001145815	exon6	c.C699G	p.L233L	CCACCTCTTCAAC	.	PASS	Atlas-SNP
SMPDL3B	27293	hgsc.bcm.edu	37	1	28282292	28282292	+	Missense_Mutation	SNP	T	T	C	rs3813803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	73	121	0	0.557252	0	T|0.782;C|0.218	0.218	strong	.	SMPDL3B	54	.	NM_001009568	exon6	c.T788C	p.V263A	AGGTGGTCCGGAA	.	PASS	Atlas-SNP
TTC8	123016	hgsc.bcm.edu	37	14	89338786	89338786	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	24	60	0	0.380952	0	.	.	none	.	TTC8	42	.	NM_144596	exon13	c.A1337G	p.H446R	AGGGCCACGTTGA	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106536253	106536253	+	Missense_Mutation	SNP	G	G	A	rs2185379	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	131	243	0	0.479853	0	G|0.948;A|0.052	0.052	strong	.	PRDM1	195	.	NM_001198	exon2	c.G220A	p.G74S	GATGGCGGTACTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416959	105416959	+	Missense_Mutation	SNP	A	A	G	rs2013462	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	286	379	3	1	0.00791557	A|0.579;G|0.421	0.421	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T4829C	p.V1610A	ACTTCCACCTTGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179610477	179610477	+	Silent	SNP	A	A	G	rs16866488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	88	163	0	0.52381	0	A|0.987;G|0.013	0.013	strong	.	TTN	18412	.	NM_133379	exon46	c.T16650C	p.D5550D	TTTTCCATCTTTG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124402677	124402677	+	Silent	SNP	A	A	G	rs1052715	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	157	167	0	1	0	A|0.423;G|0.577	0.577	strong	.	DMBT1	677	.	NM_007329	exon53	c.A7005G	p.P2335P	CTCGCCATCTCTT	.	PASS	Atlas-SNP
MRO	83876	hgsc.bcm.edu	37	18	48333203	48333203	+	Missense_Mutation	SNP	C	C	G	rs4940019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	30	60	0	0.454545	0	C|0.579;G|0.421	0.421	strong	.	MRO	36	.	NM_001127175	exon3	c.G159C	p.R53S	CTGGAACCTCAGT	.	PASS	Atlas-SNP
C11orf82	220042	hgsc.bcm.edu	37	11	82644059	82644059	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	17	42	0	0.515152	0	.	.	none	.	C11orf82	71	.	NM_145018	exon6	c.G1679C	p.R560T	CTATCAGAATCTC	.	PASS	Atlas-SNP
VPS25	84313	hgsc.bcm.edu	37	17	40926695	40926695	+	Silent	SNP	A	A	T	rs2305218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	80	145	0	0.484848	0	A|0.936;T|0.064	0.064	strong	.	VPS25	11	.	NM_032353	exon3	c.A231T	p.V77V	GATTGTATTAGAG	.	PASS	Atlas-SNP
NUP188	23511	hgsc.bcm.edu	37	9	131767668	131767668	+	Silent	SNP	A	A	C	rs2287363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	56	0	1	0	A|0.553;C|0.447	0.447	strong	.	NUP188	140	.	NM_015354	exon40	c.A4596C	p.S1532S	CTCCTCAAAGCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505893	195505893	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	14	167	0	0.0583333	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C12558T	p.S4186S	ACCTGTGGATGCT	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59797235	59797235	+	Silent	SNP	A	A	G	rs941884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	82	155	0	0.550336	0	A|0.377;G|0.623	0.623	strong	.	DAAM1	95	.	NM_001270520	exon13	c.A1389G	p.Q463Q	GCTACAACAGAAA	.	PASS	Atlas-SNP
FAM21B	55747	hgsc.bcm.edu	37	10	47909792	47909792	+	Missense_Mutation	SNP	C	C	T	rs201373575	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	6	934	3	0.0324324	0.00321199	C|0.949;T|0.051	0.051	strong	FAM21B_ENST00000358474,NS,carcinoma,0,2	FAM21B	31	2	NM_018232	exon11	c.C889T	p.R297W	CAGGATCGGCAAG	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283811	152283811	+	Missense_Mutation	SNP	G	G	A	rs3120649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	387	384	387	1	0.992248	0.00258398	G|0.881;A|0.119	0.119	strong	FLG,caecum,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.C3551T	p.S1184L	TCTACCGATTGCT	.	PASS	Atlas-SNP
LYPD3	27076	hgsc.bcm.edu	37	19	43967423	43967423	+	Silent	SNP	G	G	A	rs79420167	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	15	18	0	0.441176	0	G|0.987;A|0.013	0.013	strong	.	LYPD3	24	.	NM_014400	exon4	c.C399T	p.Y133Y	GGGCGGGTATGCA	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21224843	21224843	+	Missense_Mutation	SNP	G	G	A	rs12713450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	100	1	0.508475	0.01	G|0.968;A|0.032	0.032	strong	APOB,NS,carcinoma,+1,1	APOB	761	1	NM_000384	exon29	c.C13451T	p.T4484M	TTCTTCGTCGCAA	.	scavenged	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48506566	48506566	+	Missense_Mutation	SNP	A	A	G	rs4917152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	54	106	0	0.504673	0	A|0.777;G|0.223	0.223	strong	.	ABCA13	1192	.	NM_152701	exon44	c.A12829G	p.N4277D	GGCGACAACTTGG	.	PASS	Atlas-SNP
CHAD	1101	hgsc.bcm.edu	37	17	48542690	48542690	+	Missense_Mutation	SNP	G	G	A	rs2231510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	50	105	0	0.458716	0	G|0.966;A|0.034	0.034	strong	.	CHAD	36	.	NM_001267	exon3	c.C1049T	p.T350I	CTCTTGGTGGGGA	.	PASS	Atlas-SNP
PKN2	5586	hgsc.bcm.edu	37	1	89273241	89273241	+	Missense_Mutation	SNP	A	A	G	rs12085658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	50	103	0	0.49505	0	A|0.992;G|0.008	0.008	strong	.	PKN2	109	.	NM_006256	exon14	c.A1964G	p.Q655R	ATCTACAAGATTT	.	PASS	Atlas-SNP
LRRC14B	389257	hgsc.bcm.edu	37	5	195318	195318	+	Silent	SNP	T	T	C	rs6886707	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	73	0	0.490566	0	T|0.847;C|0.153	0.153	strong	.	LRRC14B	30	.	NM_001080478	exon2	c.T1395C	p.A465A	GCGGGCTGACCGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677457	100677457	+	Silent	SNP	G	G	T	rs59155935	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	44	106	0	0.22335	0	G|0.951;T|0.049	0.049	strong	.	MUC17	804	.	NM_001040105	exon3	c.G2760T	p.G920G	TCCTGGGGAAGGA	.	PASS	Atlas-SNP
CHRM4	1132	hgsc.bcm.edu	37	11	46406767	46406767	+	Silent	SNP	G	G	A	rs2067482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	93	186	0	0.462687	0	G|0.844;T|0.003	.	strong	.	CHRM4	47	.	NM_000741	exon1	c.C1341T	p.T447T	GTTGATGGTGCTG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57180546	57180546	+	Missense_Mutation	SNP	G	G	A	rs145781098	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	24	39	0	0.489796	0	G|0.994;A|0.006	0.006	strong	.	KIAA1211	178	.	NM_020722	exon8	c.G878A	p.R293Q	AGCAGCGGAGCCT	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205811828	205811828	+	Silent	SNP	A	A	T	rs4951025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	36	106	0	0.409091	0	A|0.756;T|0.244	0.244	strong	PM20D1,NS,carcinoma,0,1	PM20D1	56	1	NM_152491	exon7	c.T879A	p.T293T	CAATACAGTCACC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26700700	26700700	+	Missense_Mutation	SNP	G	G	A	rs4665855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	201	190	0	0.985294	0	G|0.410;A|0.590	0.590	strong	OTOF_ENST00000402415,NS,carcinoma,0,2	OTOF	524	2	NM_194322	exon1	c.C62T	p.P21L	ATCAGGGGAGTGA	.	PASS	Atlas-SNP
PRUNE2	158471	hgsc.bcm.edu	37	9	79319725	79319725	+	Missense_Mutation	SNP	T	T	C	rs375144440		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	104	132	0	0.697987	0	.	.	weak	.	PRUNE2	331	.	NM_015225	exon8	c.A7465G	p.T2489A	TATCTGTTTCTAC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43586664	43586664	+	Missense_Mutation	SNP	C	C	G	rs3887660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	35	1	1	0.0285714	C|0.628;G|0.372	0.372	strong	PSG2,NS,carcinoma,0,1	PSG2	84	1	NM_031246	exon1	c.G58C	p.V20L	CTGTGACCAGGAG	.	scavenged	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	101	224	0	0.446903	0	G|0.693;A|0.307	0.307	strong	.	CTNNA1	114	.	NM_001903	exon16	c.G2220A	p.S740S	TACATCGGATGTC	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656805	46656805	+	Silent	SNP	G	G	A	rs6519994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	81	161	0	0.47929	0	G|0.732;A|0.268	0.268	strong	PKDREJ,caecum,carcinoma,0,1	PKDREJ	195	1	NM_006071	exon1	c.C2415T	p.I805I	ACTCACGATTTCT	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40570830	40570830	+	Missense_Mutation	SNP	G	G	C	rs2234547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	84	155	0	0.488372	0	G|0.997;C|0.003	0.003	strong	.	BRWD1	325	.	NM_018963	exon40	c.C5512G	p.H1838D	TTTTATGACATTT	.	PASS	Atlas-SNP
LRRN3	54674	hgsc.bcm.edu	37	7	110763563	110763563	+	Silent	SNP	T	T	C	rs214865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	75	107	0	0.520833	0	T|0.892;C|0.108	0.108	strong	.	LRRN3	132	.	NM_018334	exon2	c.T735C	p.D245D	TTACGATAACAGG	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	98	126	0	0.690141	0	C|0.716;T|0.284	0.284	strong	.	FCN2	55	.	NM_004108	exon8	c.C707T	p.T236M	CCCTGACGTTCCA	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	68	0	1	0	C|0.815;T|0.185	0.185	strong	.	ANKRD6	51	.	NM_001242809	exon15	c.C1518T	p.C506C	CTGGTGCATGTTA	.	PASS	Atlas-SNP
CYB5R1	51706	hgsc.bcm.edu	37	1	202935911	202935911	+	Missense_Mutation	SNP	T	T	C	rs2232842	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	55	163	0	0.443548	0	T|0.886;C|0.114	0.114	strong	.	CYB5R1	25	.	NM_016243	exon2	c.A131G	p.N44S	TTTTCATTGGGGT	.	PASS	Atlas-SNP
SLC9A9	285195	hgsc.bcm.edu	37	3	143185920	143185920	+	Silent	SNP	A	A	G	rs61734421	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	151	311	0	0.480892	0	A|0.993;G|0.007	0.007	strong	.	SLC9A9	117	.	NM_173653	exon12	c.T1428C	p.F476F	TCCTCCAAATACC	.	PASS	Atlas-SNP
OR2A5	393046	hgsc.bcm.edu	37	7	143748364	143748364	+	Silent	SNP	T	T	C	rs4407791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	144	126	0	1	0	T|0.357;C|0.643	0.643	strong	.	OR2A5	78	.	NM_012365	exon1	c.T870C	p.Y290Y	GATCTATAGCCTG	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88396174	88396174	+	Silent	SNP	T	T	C	rs2919881	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	158	236	0	1	0	T|0.654;C|0.346	0.346	strong	.	SMYD1	95	.	NM_198274	exon6	c.T759C	p.I253I	CTATATTGACTTC	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61443871	61443871	+	Missense_Mutation	SNP	C	C	T	rs77478162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	32	60	0	0.492308	0	C|0.984;T|0.016	0.016	strong	.	OGFR	63	.	NM_007346	exon7	c.C904T	p.H302Y	CTGCCCCATCCGC	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167095765	167095765	+	Missense_Mutation	SNP	G	G	A	rs6668826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	46	79	0	0.474227	0	G|0.731;A|0.269	0.269	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G1397A	p.R466H	GGAGGCGCCGCGC	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048661	33048661	+	Missense_Mutation	SNP	A	A	G	rs1042151	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	19	33	9	0.59375	0.272727	A|0.776;G|0.224	0.224	strong	HLA-DPB1,NS,lymphoid_neoplasm,0,1	HLA-DPB1	28	1	NM_002121	exon2	c.A313G	p.M105V	GACAGGATGTGCA	.	scavenged	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31757078	31757078	+	Missense_Mutation	SNP	G	G	A	rs6059139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	31	91	0	0.326316	0	G|0.962;A|0.038	0.038	strong	.	.	.	.	NM_080574	exon2	c.G127A	p.G43R	CACGAGGGACTTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476367	228476367	+	Missense_Mutation	SNP	A	A	T	rs3795790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	63	121	0	0.512195	0	A|0.887;T|0.113	0.113	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.A11404T	p.S3802C	CAAGAGAGCATAG	.	PASS	Atlas-SNP
TRIM49	57093	hgsc.bcm.edu	37	11	89531780	89531780	+	Missense_Mutation	SNP	G	G	C	rs71240006		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	237	0	0.480519	0	G|0.500;C|0.500	0.500	weak	.	TRIM49	45	.	NM_020358	exon8	c.C877G	p.H293D	CTTCATGATGCAG	.	PASS	Atlas-SNP
CLASP2	23122	hgsc.bcm.edu	37	3	33759474	33759474	+	Silent	SNP	C	C	T	rs112019256	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	5	23	0	0.357143	0	C|0.333;T|0.667	0.667	weak	.	CLASP2	138	.	NM_015097	exon1	c.G21A	p.E7E	GAAGTACTCCATG	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62018737	62018737	+	Silent	SNP	G	G	A	rs59081944	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	101	186	0	0.442982	0	G|0.983;A|0.017	0.017	strong	.	SCN4A	205	.	NM_000334	exon24	c.C4905T	p.I1635I	GTAGGCGATGAAC	.	PASS	Atlas-SNP
ZNF684	127396	hgsc.bcm.edu	37	1	41012847	41012847	+	Silent	SNP	A	A	G	rs41268081	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	54	109	0	0.412214	0	A|0.934;G|0.066	0.066	strong	.	ZNF684	37	.	NM_152373	exon5	c.A852G	p.S284S	TAGTTCATCCCTT	.	PASS	Atlas-SNP
RPUSD3	285367	hgsc.bcm.edu	37	3	9881953	9881953	+	Silent	SNP	C	C	T	rs116550290	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	66	139	0	0.519685	0	C|0.979;T|0.021	0.021	strong	.	RPUSD3	19	.	NM_173659	exon7	c.G639A	p.L213L	ACCTTCCAGGATG	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33450806	33450806	+	Missense_Mutation	SNP	C	C	T	rs73926195	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	73	131	0	0.506944	0	C|0.944;T|0.056	0.056	strong	CEP89,colon,carcinoma,-1,4	CEP89	82	4	NM_032816	exon3	c.G305A	p.R102Q	ACCTACCGAGGCC	.	PASS	Atlas-SNP
SOX30	11063	hgsc.bcm.edu	37	5	157053365	157053365	+	Missense_Mutation	SNP	C	C	T	rs889057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	38	97	0	0.487179	0	C|0.998;T|0.002	0.002	strong	.	SOX30	67	.	NM_178424	exon5	c.G2245A	p.V749M	TGAGCACTTTTTC	.	PASS	Atlas-SNP
FAM65C	140876	hgsc.bcm.edu	37	20	49214156	49214156	+	Missense_Mutation	SNP	A	A	G	rs6020624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	136	145	0	0.992701	0	A|0.279;G|0.721	0.721	strong	.	FAM65C	87	.	NM_080829	exon14	c.T1739C	p.L580P	TCATCCAGGGCGA	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39907949	39907949	+	Missense_Mutation	SNP	A	A	G	rs682351	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	72	0	0.5	0	A|0.986;G|0.014	0.014	strong	.	MACF1	909	.	NM_012090	exon73	c.A12728G	p.K4243R	AACTCAAACACCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	701	195	483	1	0.278174	0.00207039	.	.	weak	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G2857C	p.E953Q	GTCCCTCACTGTC	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	96025697	96025697	+	Silent	SNP	G	G	A	rs41291134	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	78	152	0	0.490566	0	G|0.957;A|0.043	0.043	strong	PLCE1_ENST00000371375,NS,carcinoma,+1,3	PLCE1	543	3	NM_016341	exon16	c.G4263A	p.S1421S	ATCCTCGGTAGAA	.	PASS	Atlas-SNP
GLO1	2739	hgsc.bcm.edu	37	6	38650588	38650588	+	Silent	SNP	T	T	A	rs1130534	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	37	85	0	0.435294	0	T|0.811;A|0.189	0.189	strong	.	GLO1	12	.	NM_006708	exon4	c.A372T	p.G124G	ACCGAATCCTCGA	.	PASS	Atlas-SNP
GRHL3	57822	hgsc.bcm.edu	37	1	24658063	24658063	+	Missense_Mutation	SNP	C	C	G	rs2486668	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	195	174	0	1	0	C|0.823;G|0.177	0.177	strong	GRHL3,NS,carcinoma,0,1	GRHL3	69	1	NM_021180	exon2	c.C180G	p.D60E	TGATGACAGTGTT	.	PASS	Atlas-SNP
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	64	140	0	0.503937	0	T|0.778;C|0.222	0.222	strong	.	C1orf168	102	.	NM_001004303	exon2	c.A669G	p.K223K	CCAGCTTTTTCTG	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3759802	3759802	+	Missense_Mutation	SNP	C	C	A	rs35932323	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	32	71	0	0.542373	0	C|0.975;A|0.025	0.025	strong	.	APBA3	28	.	NM_004886	exon2	c.G461T	p.W154L	TCCACCCATTCTG	.	PASS	Atlas-SNP
AJAP1	55966	hgsc.bcm.edu	37	1	4772716	4772716	+	Silent	SNP	C	C	T	rs78250331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	31	72	0	0.476923	0	C|0.978;T|0.022	0.022	strong	.	AJAP1	68	.	NM_018836	exon2	c.C786T	p.N262N	CAACAACGGGGAA	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48248918	48248918	+	Silent	SNP	T	T	C	rs8047091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	120	117	0	0.97561	0	T|0.806;C|0.194	0.194	strong	.	ABCC11	177	.	NM_033151	exon8	c.A1122G	p.K374K	CAATAGTTTCCTT	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657754	49657754	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	6	117	0	0.0441176	0	.	.	none	.	HRC	85	.	NM_002152	exon1	c.C741T	p.D247D	ATCATCGTCATCT	.	PASS	Atlas-SNP
CD180	4064	hgsc.bcm.edu	37	5	66479383	66479383	+	Missense_Mutation	SNP	T	T	C	rs2230523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	66	174	0	0.452055	0	T|0.978;C|0.022	0.022	strong	CD180,NS,carcinoma,+1,2	CD180	78	2	NM_005582	exon3	c.A1288G	p.T430A	AGCGGGTAAATGC	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	92	0	0.463636	0	G|0.679;A|0.321	0.321	strong	SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	NM_001145290	exon3	c.G165A	p.S55S	CTGCTCGGAGCAG	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	127	0	0.45614	0	C|0.734;G|0.266	0.266	strong	.	MORC1	211	.	NM_014429	exon21	c.G2121C	p.L707L	AAAGTTCAGACTC	.	PASS	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	59	0	1	0	T|0.543;A|0.457	0.457	strong	CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	NM_153500	exon2	c.A253T	p.T85S	CGGAGGTGTCAAG	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36351545	36351545	+	Missense_Mutation	SNP	C	C	A	rs73928337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	50	107	0	0.458716	0	C|0.994;A|0.006	0.006	strong	KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	NM_199180	exon7	c.C904A	p.R302S	GCCAACCGCAGTA	.	PASS	Atlas-SNP
SYVN1	84447	hgsc.bcm.edu	37	11	64898226	64898226	+	Silent	SNP	C	C	T	rs9971407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	16	23	0	0.470588	0	C|0.844;T|0.156	0.156	strong	SYVN1,NS,lymphoid_neoplasm,0,1	SYVN1	55	1	NM_172230	exon11	c.G1011A	p.S337S	TGGCAGCGATGCA	.	PASS	Atlas-SNP
NOTO	344022	hgsc.bcm.edu	37	2	73435601	73435601	+	Silent	SNP	T	T	C	rs17008862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	49	92	0	0.544444	0	T|0.920;C|0.080	0.080	strong	.	NOTO	20	.	NM_001134462	exon2	c.T456C	p.T152T	GGACACTGAGAGA	.	PASS	Atlas-SNP
TNPO2	30000	hgsc.bcm.edu	37	19	12816559	12816559	+	Silent	SNP	G	G	T	rs7248726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	78	127	0	0.52349	0	G|0.849;T|0.151	0.151	strong	.	TNPO2	108	.	NM_013433	exon15	c.C1692A	p.P564P	CAGTGGGGGCATC	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	84	243	0	0.4375	0	T|0.955;C|0.045	0.045	strong	.	CLUAP1	32	.	NM_015041	exon2	c.T102C	p.L34L	TGGACTTGTATCT	.	PASS	Atlas-SNP
SPEM1	374768	hgsc.bcm.edu	37	17	7324588	7324588	+	Silent	SNP	G	G	A	rs78583740	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	70	0	0.530612	0	G|0.961;A|0.039	0.039	strong	.	SPEM1	41	.	NM_199339	exon3	c.G594A	p.L198L	CGAGCTGGGCCTA	.	PASS	Atlas-SNP
TIPIN	54962	hgsc.bcm.edu	37	15	66641732	66641732	+	Missense_Mutation	SNP	G	G	C	rs2063690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	44	117	0	0.415094	0	G|0.877;C|0.123	0.123	strong	.	TIPIN	23	.	NM_017858	exon5	c.C332G	p.A111G	CTATGTGCCCAGT	.	PASS	Atlas-SNP
ITGB3	3690	hgsc.bcm.edu	37	17	45368337	45368337	+	Silent	SNP	A	A	C	rs15908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	38	85	0	0.422222	0	A|0.586;C|0.414	0.414	strong	.	ITGB3	157	.	NM_000212	exon9	c.A1143C	p.V381V	TAAAGTAGAGCTG	.	PASS	Atlas-SNP
SRP72	6731	hgsc.bcm.edu	37	4	57361553	57361553	+	Silent	SNP	A	A	G	rs34419325	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	121	209	0	0.562791	0	A|0.915;G|0.085	0.085	strong	.	SRP72	59	.	NM_006947	exon17	c.A1671G	p.K557K	AAAGAAAAAGAAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239116	31239116	+	Missense_Mutation	SNP	G	G	A	rs1131119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	35	64	3	0.336538	0.046875	G|0.815;A|0.185	0.185	strong	HLA-C_ENST00000383329,colon,carcinoma,0,6	HLA-C	92	6	NM_002117	exon3	c.C353T	p.T118I	TGGAGGGTGTGAG	.	scavenged	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167096770	167096770	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	96	0	0.43617	0	.	.	none	.	DUSP27	235	.	NM_001080426	exon5	c.G2402C	p.C801S	TGTCCTGCAACAC	.	PASS	Atlas-SNP
GGTLC2	91227	hgsc.bcm.edu	37	22	22989237	22989237	+	Missense_Mutation	SNP	G	G	A	rs60008056	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	122	257	0	0.465649	0	G|0.952;A|0.048	0.048	strong	.	GGTLC2	20	.	NM_199127	exon2	c.G190A	p.V64I	TCCAAGGTCCGCT	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179020622	179020622	+	Silent	SNP	T	T	C	rs4701135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	67	134	0	0.482014	0	T|0.912;C|0.088	0.088	strong	.	RUFY1	101	.	NM_025158	exon11	c.T1389C	p.N463N	GATTAATTTACAG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41831203	41831203	+	Missense_Mutation	SNP	C	C	T	rs17215589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	48	115	0	0.505263	0	C|0.898;T|0.102	0.102	strong	.	ULK4	150	.	NM_017886	exon21	c.G2143A	p.A715T	TGGCAGCGAATAA	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	64	166	0	0.415584	0	G|0.841;C|0.159	0.159	strong	.	LEPR	284	.	NM_001003680	exon14	c.G1968C	p.K656N	GAAAAAGGAGAAA	.	PASS	Atlas-SNP
PIK3CD	5293	hgsc.bcm.edu	37	1	9784423	9784423	+	Silent	SNP	C	C	T	rs41476649	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	73	140	0	0.51049	0	C|0.800;T|0.200	0.200	strong	.	PIK3CD	86	.	NM_005026	exon22	c.C2808T	p.Y936Y	CACCTACGACTTT	.	PASS	Atlas-SNP
SEC14L5	9717	hgsc.bcm.edu	37	16	5061191	5061191	+	Silent	SNP	C	C	T	rs8055468	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	69	140	0	0.472603	0	C|0.968;T|0.032	0.032	strong	.	SEC14L5	79	.	NM_014692	exon15	c.C1896T	p.D632D	TGTGGACGATGTC	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	37	84	0	0.4625	0	G|0.572;A|0.428	0.428	strong	WWP2,NS,carcinoma,0,1	WWP2	88	1	NM_001270454	exon24	c.G2595A	p.E865E	GACCGAGGGCTTT	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3126811	3126811	+	Missense_Mutation	SNP	A	A	G	rs1071600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	364	165	339	0	0.453297	0	A|0.744;G|0.256	0.256	strong	MYOM1,NS,carcinoma,0,1	MYOM1	192	1	NM_003803	exon19	c.T2879C	p.I960T	CCTCCAATCTTAT	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39908506	39908506	+	Missense_Mutation	SNP	G	G	A	rs587404	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	71	130	0	0.572581	0	G|0.640;A|0.360	0.360	strong	MACF1_ENST00000361689,NS,carcinoid-endocrine_tumour,-1,2	MACF1	909	2	NM_012090	exon75	c.G13048A	p.A4350T	TTGGAAGCCATGA	.	PASS	Atlas-SNP
TBC1D5	9779	hgsc.bcm.edu	37	3	17208267	17208267	+	Missense_Mutation	SNP	T	T	C	rs1138454	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	155	161	0	0.99359	0	T|0.701;C|0.299	0.299	strong	.	TBC1D5	69	.	NM_001134381	exon23	c.A2152G	p.I718V	GTTTAATGGCCCC	.	PASS	Atlas-SNP
KIF1C	10749	hgsc.bcm.edu	37	17	4925674	4925674	+	Silent	SNP	C	C	T	rs73345356	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	42	94	0	0.525	0	C|0.964;T|0.036	0.036	strong	KIF1C,colon,carcinoma,0,1	KIF1C	70	1	NM_006612	exon22	c.C2298T	p.H766H	CCGCCACGGGCGG	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	T	C	rs1881420	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	161	353	0	0.468023	0	T|0.684;G|0.005	.	strong	ALK,NS,carcinoma,0,1	ALK	533	1	NM_004304	exon29	c.A4472G	p.K1491R	TGGACCTTGTGCA	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91805804	91805804	+	Silent	SNP	C	C	T	rs61220159	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	124	193	0	0.53913	0	C|0.968;T|0.032	0.032	strong	.	CCDC88C	192	.	NM_001080414	exon8	c.G627A	p.L209L	CACGATCAGCTGC	.	PASS	Atlas-SNP
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	123	269	0	0.457249	0	G|0.908;C|0.092	0.092	strong	.	SCUBE2	102	.	NM_020974	exon18	c.C2288G	p.T763S	GTCGTAGTATTTC	.	PASS	Atlas-SNP
SORD	6652	hgsc.bcm.edu	37	15	45353365	45353365	+	Silent	SNP	G	G	A	rs11542063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	337	8	221	0	0.0237389	0	G|0.984;A|0.016	0.016	strong	SORD,caecum,carcinoma,0,2	SORD	24	2	NM_003104	exon4	c.G366A	p.T122T	TGCCACGCCCCCC	.	scavenged	Atlas-SNP
CDNF	441549	hgsc.bcm.edu	37	10	14862140	14862140	+	Missense_Mutation	SNP	C	C	A	rs61740068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	60	166	0	0.46875	0	C|0.985;A|0.015	0.015	strong	.	CDNF	19	.	NM_001029954	exon4	c.G403T	p.A135S	CTGATGCCAAGTC	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124841276	124841276	+	Silent	SNP	G	G	A	rs200441401	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	94	182	0	0.489583	0	G|1.000;A|0.000	0.000	strong	.	NCOR2	475	.	NM_006312	exon25	c.C3153T	p.S1051S	CAGGCCGGAAGTC	.	PASS	Atlas-SNP
KIAA1609	57707	hgsc.bcm.edu	37	16	84520496	84520496	+	Missense_Mutation	SNP	C	C	G	rs34244563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	72	149	0	0.496552	0	C|0.989;G|0.011	0.011	strong	.	KIAA1609	39	.	NM_020947	exon5	c.G699C	p.E233D	TTGACGCTCAGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509606	195509606	+	Missense_Mutation	SNP	C	C	T	rs79543693	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	28	295	7	0.137931	0.0237288	C|0.625;T|0.375	0.375	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G8845A	p.D2949N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113233738	113233738	+	Silent	SNP	T	T	C	rs61732942	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	181	249	1	0.677903	0.00401606	T|0.963;C|0.037	0.037	strong	.	SVEP1	326	.	NM_153366	exon16	c.A2904G	p.A968A	TTCTGATGCAAGC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54720967	54720967	+	Missense_Mutation	SNP	G	G	A	rs114510580	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	333	140	280	0	0.42042	0	G|0.962;A|0.038	0.038	strong	.	LILRB3	67	.	NM_001081450	exon13	c.C1894T	p.H632Y	GCTAGTGGATGGC	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166773971	166773971	+	Silent	SNP	G	G	A	rs6750044	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	85	191	1	0.57047	0.0052356	G|0.668;A|0.332	0.332	strong	.	TTC21B	130	.	NM_024753	exon14	c.C1695T	p.Y565Y	CAAATGGTATAAA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76482435	76482435	+	Silent	SNP	C	C	T	rs61743860	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	95	134	0	0.555556	0	C|0.909;T|0.091	0.091	strong	.	DNAH17	347	.	NM_173628	exon45	c.G6972A	p.T2324T	CAGAATCGTTTGG	.	PASS	Atlas-SNP
TBC1D10C	374403	hgsc.bcm.edu	37	11	67176898	67176898	+	Missense_Mutation	SNP	A	A	G	rs11227788	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	37	0	1	0	A|0.659;G|0.341	0.341	strong	.	TBC1D10C	42	.	NM_001256508	exon9	c.A820G	p.R274G	GCTGTCAGAGCGG	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	30	72	0	0.555556	0	A|0.643;G|0.357	0.357	strong	.	IGF2R	251	.	NM_000876	exon9	c.A1050G	p.S350S	AGGTTCATCCTAT	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140811131	140811131	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	7	74	0	0.0752688	0	.	.	none	.	MAML3	192	.	NM_018717	exon2	c.C1459A	p.Q487K	GCTGTTGCTGTTT	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	37	3	183027542	183027542	+	Missense_Mutation	SNP	T	T	G	rs7639705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	74	134	1	0.587302	0.00746269	T|0.718;G|0.282	0.282	strong	MCF2L2,NS,carcinoma,0,1	MCF2L2	164	1	NM_015078	exon10	c.A1075C	p.I359L	TAAGAATCTGCTC	.	scavenged	Atlas-SNP
CACNA1I	8911	hgsc.bcm.edu	37	22	39966856	39966856	+	Silent	SNP	C	C	T	rs3747178	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	68	140	0	0.475524	0	C|0.650;T|0.350	0.350	strong	.	CACNA1I	264	.	NM_001003406	exon1	c.C99T	p.S33S	CCCATCCTCCCCG	.	PASS	Atlas-SNP
TBX15	6913	hgsc.bcm.edu	37	1	119427937	119427937	+	Silent	SNP	G	G	A	rs145938710	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	36	67	0	0.514286	0	G|0.998;A|0.002	0.002	strong	.	TBX15	95	.	NM_152380	exon8	c.C909T	p.A303A	CTGCAAGGCAGCC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96026243	96026243	+	Silent	SNP	G	G	A	rs55981123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	76	0	1	0	G|0.870;A|0.130	0.130	strong	WNK2_ENST00000297954,caecum,carcinoma,0,4	WNK2	277	4	NM_006648	exon15	c.G3624A	p.T1208T	GGAGACGCACAAC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276474	152276474	+	Missense_Mutation	SNP	G	G	A	rs9436065	bycluster;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	572	364	367	0	0.636364	0	G|0.997;A|0.003	0.003	weak	.	FLG	900	.	NM_002016	exon3	c.C10888T	p.H3630Y	GCTGGTGGTGGGA	.	PASS	Atlas-SNP
GAA	2548	hgsc.bcm.edu	37	17	78092081	78092081	+	Silent	SNP	G	G	T	rs17853996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	67	148	0	0.5	0	G|0.997;T|0.003	0.003	strong	.	GAA	66	.	NM_001079803	exon19	c.G2571T	p.L857L	GGAGCTGTTCTGG	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10088271	10088271	+	Missense_Mutation	SNP	C	C	G	rs2161468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	58	101	0	0.517857	0	C|0.631;G|0.369	0.369	strong	.	COL5A3	243	.	NM_015719	exon42	c.G3125C	p.R1042P	CTTACCCGGGACC	.	PASS	Atlas-SNP
IL1RL2	8808	hgsc.bcm.edu	37	2	102851708	102851708	+	Missense_Mutation	SNP	T	T	C	rs2302612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	97	0	1	0	T|0.699;C|0.301	0.301	strong	IL1RL2_ENST00000441515,NS,carcinoma,-1,2	IL1RL2	118	2	NM_003854	exon11	c.T1649C	p.L550P	AGCTGCTGCAGCA	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708751	168708751	+	Silent	SNP	A	A	G	rs10945499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	51	83	0	1	0	A|0.525;G|0.475	0.475	strong	DACT2_ENST00000366795,NS,carcinoma,0,2	DACT2	46	2	NM_214462	exon4	c.T1686C	p.S562S	GGACTCAGAACAG	.	PASS	Atlas-SNP
SMCO2	0	hgsc.bcm.edu	37	12	27641473	27641473	+	Missense_Mutation	SNP	G	G	A	rs412978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	17	41	0	0.404762	0	G|0.691;A|0.309	0.309	strong	.	.	.	.	NM_001145010	exon6	c.G593A	p.S198N	GGACAAGCACTGA	.	PASS	Atlas-SNP
OR2A5	393046	hgsc.bcm.edu	37	7	143747796	143747796	+	Missense_Mutation	SNP	C	C	A	rs61741408	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	85	159	0	0.515152	0	C|0.997;A|0.003	0.003	strong	OR2A5,colon,carcinoma,+1,5	OR2A5	78	5	NM_012365	exon1	c.C302A	p.T101N	TGCAGACCTTTTT	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371085	240371085	+	Silent	SNP	A	A	T	rs71646826	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	31	126	4	0.147619	0.031746	A|0.836;T|0.164	0.164	strong	FMN2,NS,carcinoma,+1,1	FMN2	451	1	NM_020066	exon5	c.A2973T	p.P991P	TCCCCCACTTCCC	.	scavenged	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19870235	19870235	+	Missense_Mutation	SNP	C	C	T	rs56311184	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	29	50	0	0.460317	0	C|0.977;T|0.023	0.023	strong	.	RIN2	126	.	NM_001242581	exon2	c.C137T	p.S46L	GAGCCTCGCTGGG	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56369314	56369314	+	Silent	SNP	G	G	A	rs16986718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	82	156	0	0.450549	0	G|0.718;A|0.281	0.281	strong	NLRP4_ENST00000301295,colon,carcinoma,0,1	NLRP4	331	1	NM_134444	exon3	c.G555A	p.T185T	GTACACGTTCTAT	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901825	129901825	+	Missense_Mutation	SNP	T	T	C	rs10082391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	380	190	347	1	0.5	0.00288184	A|0.005;C|0.218	0.218	strong	.	MKI67	363	.	NM_002417	exon13	c.A8279G	p.D2760G	CCTTTATCTTCAC	.	PASS	Atlas-SNP
ZFYVE9	9372	hgsc.bcm.edu	37	1	52705174	52705174	+	Silent	SNP	A	A	G	rs34437486	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	70	140	0	0.454545	0	A|0.991;G|0.009	0.009	strong	.	ZFYVE9	131	.	NM_007323	exon4	c.A2085G	p.V695V	TCCAGTATGGGTA	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74706943	74706943	+	Silent	SNP	G	G	A	rs1046146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	95	217	0	0.44186	0	G|0.846;A|0.154	0.154	strong	.	SEMA7A	58	.	NM_003612	exon10	c.C1239T	p.V413V	GCGGTGGACGGCC	.	PASS	Atlas-SNP
SHROOM4	57477	hgsc.bcm.edu	37	X	50350778	50350778	+	Missense_Mutation	SNP	T	T	G	rs112781654	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	8	141	0	0.0842105	0	T|0.500;G|0.500	0.500	weak	.	SHROOM4	171	.	NM_020717	exon6	c.A3364C	p.K1122Q	GCTGCTTCTGCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509036	195509036	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	98	144	0	0.382812	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.G9415C	p.V3139L	TGGTGACAGGAAG	.	PASS	Atlas-SNP
OR51M1	390059	hgsc.bcm.edu	37	11	5411398	5411398	+	Missense_Mutation	SNP	T	T	G	rs2736531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	121	0	1	0	T|0.663;G|0.337	0.337	strong	.	OR51M1	60	.	NM_001004756	exon1	c.T770G	p.L257R	CTCCTCTCTGTGC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1075920	1075920	+	Missense_Mutation	SNP	G	G	A	rs11825977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	34	71	0	0.523077	0	G|0.851;A|0.149	0.149	strong	.	MUC2	614	.	NM_002457	exon2	c.G346A	p.V116M	GGGGCCGTGTGAG	.	PASS	Atlas-SNP
IRAK4	51135	hgsc.bcm.edu	37	12	44180295	44180295	+	Missense_Mutation	SNP	G	G	A	rs4251545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	78	167	0	0.590909	0	G|0.843;A|0.157	0.157	strong	.	IRAK4	77	.	NM_016123	exon11	c.G1282A	p.A428T	GTTGAAGCTATGT	.	PASS	Atlas-SNP
MC1R	4157	hgsc.bcm.edu	37	16	89986566	89986566	+	Silent	SNP	C	C	T	rs3212367	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	75	163	0	0.462963	0	C|0.978;T|0.022	0.022	strong	.	MC1R	20	.	NM_002386	exon1	c.C900T	p.F300F	CGCCTTCCACAGC	.	PASS	Atlas-SNP
ABCC10	89845	hgsc.bcm.edu	37	6	43413669	43413669	+	Silent	SNP	G	G	A	rs112977568	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	104	0	0.517241	0	G|0.992;A|0.008	0.008	strong	.	ABCC10	118	.	NM_001198934	exon15	c.G3363A	p.G1121G	CACAGGGGCCACC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79432455	79432455	+	Silent	SNP	A	A	C	rs3749488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	146	275	1	0.466454	0.00363636	A|0.628;C|0.372	0.372	strong	.	FRAS1	779	.	NM_025074	exon64	c.A9808C	p.R3270R	AGCCGGAGGTTCC	.	PASS	Atlas-SNP
UMPS	7372	hgsc.bcm.edu	37	3	124456742	124456742	+	Missense_Mutation	SNP	G	G	C	rs1801019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	42	73	0	0.4375	0	G|0.832;C|0.168	0.168	strong	.	UMPS	43	.	NM_000373	exon3	c.G638C	p.G213A	ATAATGGTTCTCC	.	PASS	Atlas-SNP
TMEM176A	55365	hgsc.bcm.edu	37	7	150498773	150498773	+	Silent	SNP	C	C	T	rs10239586	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	17	28	0	0.566667	0	C|0.993;T|0.007	0.007	strong	.	TMEM176A	35	.	NM_018487	exon2	c.C135T	p.T45T	GGCCACCCAGGCC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037557	33037557	+	Silent	SNP	C	C	T	rs1042177	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	138	161	0	0.992806	0	C|0.814;T|0.186	0.186	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.G207A	p.K69K	CTCCTTCTTGTCC	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053863	95053863	+	Missense_Mutation	SNP	C	C	T	rs6118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	37	87	0	0.430233	0	C|0.764;T|0.236	0.236	strong	.	SERPINA5	69	.	NM_000624	exon3	c.C164T	p.A55V	ACAGGGCCTTGGC	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47086915	47086915	+	Silent	SNP	C	C	T	rs59974223	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	428	114	374	0	0.266355	0	C|0.835;T|0.165	0.165	strong	.	PPYR1	54	.	NM_005972	exon3	c.C132T	p.I44I	CTTCATCGTCACT	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2740798	2740798	+	Silent	SNP	A	A	T	rs115632137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	74	129	0	0.573643	0	A|0.973;T|0.027	0.027	strong	.	SMCHD1	88	.	NM_015295	exon28	c.A3612T	p.S1204S	TAGCTCAAATTTG	.	PASS	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84115393	84115393	+	Silent	SNP	G	G	A	rs12933523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	28	57	0	0.583333	0	G|0.869;A|0.131	0.131	strong	.	MBTPS1	85	.	NM_003791	exon11	c.C1407T	p.L469L	GGCTCTGAGCAGA	.	PASS	Atlas-SNP
SPINK14	408187	hgsc.bcm.edu	37	5	147553829	147553829	+	Silent	SNP	C	C	T	rs79779038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	135	0	1	0	C|0.919;T|0.081	0.081	strong	.	SPINK14	9	.	NM_001001325	exon3	c.C144T	p.S48S	CTTGAGCTGGTAC	.	PASS	Atlas-SNP
GRIPAP1	56850	hgsc.bcm.edu	37	X	48847444	48847444	+	Missense_Mutation	SNP	G	G	A	rs61735977	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	144	233	0	0.525547	0	G|0.945;A|0.055	0.055	strong	.	GRIPAP1	128	.	NM_020137	exon7	c.C536T	p.P179L	GGGGCCGGGCCCC	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30761995	30761995	+	Silent	SNP	G	G	A	rs61732271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	5	21	0	0.25	0	G|0.990;A|0.010	0.010	strong	.	CCDC157	86	.	NM_001017437	exon3	c.G6A	p.A2A	GATGGCGCACCTG	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178231219	178231219	+	Missense_Mutation	SNP	C	C	T	rs34007209	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	33	32	0	0.578947	0	C|0.884;T|0.116	0.116	strong	NEIL3,NS,carcinoma,0,2	NEIL3	89	2	NM_018248	exon1	c.C112T	p.R38C	CAGGGCCGCGCCT	.	PASS	Atlas-SNP
HNRNPA2B1	3181	hgsc.bcm.edu	37	7	26236235	26236235	+	Silent	SNP	T	T	C	rs34317198	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	78	195	0	0.458824	0	T|0.935;C|0.065	0.065	strong	.	HNRNPA2B1	70	.	NM_031243	exon6	c.A555G	p.R185R	AGCCTTTCTTACT	.	PASS	Atlas-SNP
MFSD6L	162387	hgsc.bcm.edu	37	17	8701701	8701701	+	Silent	SNP	A	A	G	rs16957601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	9	15	0	0.75	0	A|0.974;G|0.026	0.026	strong	.	MFSD6L	46	.	NM_152599	exon1	c.T738C	p.F246F	GAGGATAAAAGTC	.	PASS	Atlas-SNP
BAI1	575	hgsc.bcm.edu	37	8	143599594	143599594	+	Silent	SNP	C	C	T	rs75573695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	67	160	0	0.462069	0	C|0.964;T|0.036	0.036	strong	.	BAI1	146	.	NM_001702	exon18	c.C2913T	p.S971S	CGTGTCCGTGTGG	.	PASS	Atlas-SNP
GPC2	221914	hgsc.bcm.edu	37	7	99773879	99773879	+	Silent	SNP	G	G	A	rs74662631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	136	231	0	0.492754	0	G|0.985;A|0.015	0.015	strong	.	GPC2	49	.	NM_152742	exon2	c.C276T	p.S92S	GGAGCCGCTGTCC	.	PASS	Atlas-SNP
TAS2R30	259293	hgsc.bcm.edu	37	12	11286214	11286214	+	Missense_Mutation	SNP	C	C	G	rs200082783	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	25	271	0	0.0883392	0	C|0.944;G|0.055	0.055	strong	TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	NM_001097643	exon1	c.G630C	p.Q210H	ATGGAGCTGCATC	.	scavenged	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2578181	2578181	+	Missense_Mutation	SNP	C	C	T	rs61627394	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	17	11	0	0.515152	0	C|0.936;T|0.064	0.064	strong	.	BRAT1	57	.	NM_152743	exon14	c.G1988A	p.G663D	GTCTGGCCCAGGA	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140707590	140707590	+	Silent	SNP	C	C	T	rs35943616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	64	47	0	1	0	C|0.899;T|0.101	0.101	strong	.	EHMT1	196	.	NM_024757	exon20	c.C3000T	p.P1000P	GGCCCCCGACAGG	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650054	+	Missense_Mutation	SNP	T	T	C	rs111934125	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	8	86	0	0.0952381	0	C|1.000;|0.000	1.000	weak	CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	NM_001141947	exon13	c.T1816C	p.S606P	ACGACTTCTAAGA	.	PASS	Atlas-SNP
CBFB	865	hgsc.bcm.edu	37	16	67116169	67116169	+	Silent	SNP	C	C	T	rs78053453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	38	80	0	0.431818	0	C|0.951;T|0.049	0.049	strong	CBFB_ENST00000412916,NS,carcinoma,+1,2	CBFB	52	2	NM_022845	exon5	c.C453T	p.R151R	GACACGCGAATTT	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1737502	1737502	+	Silent	SNP	C	C	T	rs11248073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	28	74	0	0.459016	0	C|0.661;T|0.339	0.339	strong	.	TACC3	69	.	NM_006342	exon8	c.C1689T	p.F563F	CAAGTTCGACCCC	.	PASS	Atlas-SNP
LNX2	222484	hgsc.bcm.edu	37	13	28130473	28130473	+	Silent	SNP	G	G	A	rs115119970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	29	73	0	0.341176	0	G|0.988;A|0.012	0.012	strong	.	LNX2	70	.	NM_153371	exon7	c.C1446T	p.T482T	AGCAACGGTCATG	.	PASS	Atlas-SNP
FBF1	85302	hgsc.bcm.edu	37	17	73929118	73929118	+	Missense_Mutation	SNP	G	G	A	rs149283443	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	35	61	0	0.636364	0	G|0.997;A|0.003	0.003	strong	.	FBF1	48	.	NM_001080542	exon4	c.C83T	p.T28I	ACACCTGTGGTGT	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	127	0	0.486486	0	C|0.950;T|0.050	0.050	strong	ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	NM_005845	exon28	c.G3609A	p.A1203A	TGCCGTCGCTTCA	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26834833	26834833	+	Silent	SNP	G	G	A	rs35412320	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	44	101	0	0.369748	0	G|0.991;A|0.009	0.009	strong	ITPR2,colon,carcinoma,-2,1	ITPR2	270	1	NM_002223	exon13	c.C1383T	p.N461N	TGTGCCGTTTTCT	.	PASS	Atlas-SNP
CALM3	808	hgsc.bcm.edu	37	19	47112207	47112207	+	Silent	SNP	C	C	T	rs35617141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	47	86	0	0.566265	0	C|0.990;T|0.010	0.010	strong	.	CALM3	9	.	NM_005184	exon5	c.C390T	p.D130D	GGCTGACATCGAT	.	PASS	Atlas-SNP
OR4D2	124538	hgsc.bcm.edu	37	17	56247794	56247794	+	Missense_Mutation	SNP	C	C	T	rs148697791	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	191	361	1	0.527624	0.00277008	C|0.995;T|0.005	0.005	strong	.	OR4D2	48	.	NM_001004707	exon1	c.C778T	p.R260W	TATGCCCGGCCCT	.	PASS	Atlas-SNP
RINT1	60561	hgsc.bcm.edu	37	7	105182995	105182995	+	Silent	SNP	G	G	A	rs7805216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	106	180	0	0.486239	0	G|0.939;A|0.061	0.061	strong	.	RINT1	65	.	NM_021930	exon4	c.G414A	p.A138A	GACTGCGCAACCT	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89421327	89421327	+	Silent	SNP	A	A	G	rs2280463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	104	0	0.515152	0	A|0.561;G|0.439	0.439	strong	.	HAPLN3	43	.	NM_178232	exon5	c.T957C	p.G319G	GACGCTACCATCT	.	PASS	Atlas-SNP
RNASE4	6038	hgsc.bcm.edu	37	14	21167837	21167837	+	Missense_Mutation	SNP	G	G	A	rs59543367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	22	36	0	0.733333	0	G|0.994;A|0.006	0.006	strong	.	RNASE4	18	.	NM_002937	exon2	c.G307A	p.V103I	GAGGGTGTAGTGA	.	PASS	Atlas-SNP
LRCH4	4034	hgsc.bcm.edu	37	7	100175853	100175853	+	Silent	SNP	G	G	T	rs187288824	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	3	108	0	0.0232558	0	G|0.999;A|0.001	.	alt	LRCH4,NS,carcinoma,0,1	LRCH4	53	1	NM_002319	exon7	c.C877A	p.R293R	CGTACCGATGTCC	.	scavenged	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	136	0	0.508475	0	G|0.862;A|0.138	0.138	strong	.	UBXN11	54	.	NM_183008	exon10	c.C628T	p.L210L	CCACCAGCTCACT	.	PASS	Atlas-SNP
SECTM1	6398	hgsc.bcm.edu	37	17	80285085	80285085	+	Missense_Mutation	SNP	T	T	G	rs73999869	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	90	272	1	0.40724	0.00367647	T|0.943;G|0.057	0.057	strong	.	SECTM1	14	.	NM_003004	exon2	c.A32C	p.H11P	GAAACGTGGCCAG	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49658084	49658084	+	Silent	SNP	G	G	A	rs57897109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	352	185	308	1	0.525568	0.00324675	G|0.903;A|0.097	0.097	strong	.	HRC	85	.	NM_002152	exon1	c.C411T	p.H137H	ACTCCCGTGGCCT	.	PASS	Atlas-SNP
AKAP8L	26993	hgsc.bcm.edu	37	19	15512393	15512393	+	Silent	SNP	G	G	A	rs61739315	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	19	42	0	0.395833	0	G|0.991;A|0.009	0.009	strong	.	AKAP8L	64	.	NM_014371	exon5	c.C384T	p.C128C	CGAGTCGCAGGAC	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642823	1642823	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	10	185	1	0.0497512	0.00540541	.	.	none	KRTAP5-4,colon,carcinoma,0,1	KRTAP5-4	78	1	NM_001012709	exon1	c.C501T	p.S167S	ACCTGAGGAGGAG	.	scavenged	Atlas-SNP
GPNMB	10457	hgsc.bcm.edu	37	7	23300352	23300352	+	Silent	SNP	G	G	T	rs35115002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	83	0	0.547945	0	G|0.995;T|0.005	0.005	strong	.	GPNMB	88	.	NM_002510	exon6	c.G978T	p.P326P	GCCACCGCCACCA	.	PASS	Atlas-SNP
PMS2	5395	hgsc.bcm.edu	37	7	6026959	6026959	+	Missense_Mutation	SNP	G	G	C	rs63750685	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	40	78	0	0.454545	0	G|0.994;C|0.006	0.006	strong	.	PMS2	88	.	NM_000535	exon11	c.C1437G	p.H479Q	GGGTCCGTGACTG	.	PASS	Atlas-SNP
ZNF446	55663	hgsc.bcm.edu	37	19	58991075	58991075	+	Silent	SNP	C	C	T	rs140158663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	43	87	0	0.434343	0	C|0.998;T|0.002	0.002	strong	.	ZNF446	22	.	NM_017908	exon5	c.C693T	p.Y231Y	GAAGTACGGCACA	.	PASS	Atlas-SNP
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	421	200	412	0	0.475059	0	G|0.754;A|0.246	0.246	strong	HHLA1,NS,carcinoma,0,1	HHLA1	35	1	NM_001145095	exon10	c.C752T	p.P251L	TGTCCGGGGCTTG	.	PASS	Atlas-SNP
ZC3H6	376940	hgsc.bcm.edu	37	2	113089267	113089267	+	Silent	SNP	T	T	C	rs7601200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	91	0	1	0	T|0.273;C|0.727	0.727	strong	.	ZC3H6	93	.	NM_198581	exon12	c.T2772C	p.N924N	TCAAAATACAGTG	.	PASS	Atlas-SNP
OR2AE1	81392	hgsc.bcm.edu	37	7	99473858	99473858	+	Missense_Mutation	SNP	G	G	C	rs17161997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	46	108	0	0.425926	0	G|0.862;C|0.138	0.138	strong	.	OR2AE1	32	.	NM_001005276	exon1	c.C799G	p.L267V	GCAATAGAGTGCA	.	PASS	Atlas-SNP
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227027	99227027	+	Missense_Mutation	SNP	C	C	T	rs142120776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	28	57	0	0.474576	0	C|0.998;T|0.002	0.002	strong	.	.	.	.	NM_145115	exon8	c.C1019T	p.T340I	TCAAAACCCACAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179414318	179414318	+	Missense_Mutation	SNP	C	C	T	rs747122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	58	85	0	0.568627	0	C|0.882;T|0.118	0.118	strong	.	TTN	18412	.	NM_001267550	exon338	c.G92131A	p.V30711M	CAACCACTGGATC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368520	40368520	+	Silent	SNP	G	G	C	rs36079378	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	130	167	2	0.702703	0.011976	G|0.500;C|0.500	0.500	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon28	c.C12828G	p.G4276G	GCCAGGGCCCTCG	.	scavenged	Atlas-SNP
HDAC9	9734	hgsc.bcm.edu	37	7	18914209	18914209	+	Silent	SNP	G	G	T	rs17140166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	35	64	0	0.4375	0	G|0.975;T|0.025	0.025	strong	.	HDAC9	560	.	NM_178425	exon21	c.G2793T	p.V931V	CAAAGTGACGGCA	.	PASS	Atlas-SNP
KIF2B	84643	hgsc.bcm.edu	37	17	51900836	51900836	+	Missense_Mutation	SNP	C	C	T	rs59657238	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	19	49	0	0.513514	0	C|0.931;T|0.069	0.069	strong	.	KIF2B	254	.	NM_032559	exon1	c.C442T	p.P148S	AAGTCTCCCTGCC	.	PASS	Atlas-SNP
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	104	220	0	0.490566	0	A|0.821;G|0.179	0.179	strong	.	MC1R	20	.	NM_002386	exon1	c.A942G	p.T314T	GCTGACATGCTCC	.	PASS	Atlas-SNP
THRSP	7069	hgsc.bcm.edu	37	11	77775157	77775157	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	62	128	0	0.516667	0	.	.	none	.	THRSP	18	.	NM_003251	exon1	c.G230A	p.R77Q	TGCCGCGGGAGGA	.	PASS	Atlas-SNP
C6orf25	80739	hgsc.bcm.edu	37	6	31692558	31692558	+	Nonsense_Mutation	SNP	C	C	T	rs34741956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	77	130	0	0.506579	0	C|0.997;T|0.003	0.003	strong	.	C6orf25	52	.	NM_138277	exon5	c.C577T	p.R193X	GAAAACCGAGCCC	.	PASS	Atlas-SNP
CD164L2	388611	hgsc.bcm.edu	37	1	27709020	27709020	+	Missense_Mutation	SNP	T	T	C	rs2504779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	50	78	0	0.549451	0	T|0.731;C|0.269	0.269	strong	.	CD164L2	13	.	NM_207397	exon2	c.A226G	p.M76V	CCCACATGCAGCT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46763671	46763671	+	Silent	SNP	A	A	G	rs7285515	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	195	207	0	1	0	A|0.740;G|0.260	0.260	strong	.	CELSR1	242	.	NM_014246	exon28	c.T8034C	p.D2678D	CAGTGCATCGCGG	.	PASS	Atlas-SNP
TAS2R31	259290	hgsc.bcm.edu	37	12	11183708	11183708	+	Missense_Mutation	SNP	T	T	C	rs80125932	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	54	336	0	0.156977	0	T|0.871;C|0.129	0.129	strong	.	TAS2R31	24	.	NM_176885	exon1	c.A227G	p.Y76C	ACACTATAAAAAG	.	PASS	Atlas-SNP
CBLN3	643866	hgsc.bcm.edu	37	14	24898135	24898135	+	Silent	SNP	C	C	T	rs57646536	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	50	121	0	0.50505	0	C|0.963;T|0.037	0.037	strong	.	CBLN3	21	.	NM_001039771	exon1	c.G126A	p.E42E	CTCCCCCTCCAGC	.	PASS	Atlas-SNP
RGAG4	340526	hgsc.bcm.edu	37	X	71350294	71350294	+	Missense_Mutation	SNP	A	A	G	rs146618350	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	237	205	0	0.995798	0	A|0.994;G|0.006	0.006	strong	.	RGAG4	63	.	NM_001024455	exon1	c.T1097C	p.M366T	GCCCTCATGCGCT	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98201527	98201527	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1172	406	1252	1	0.346416	0.000798722	.	.	none	.	.	.	.	NM_025190	exon3	c.C330T	p.A110A	TGGATCGGCGCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678568	100678568	+	Missense_Mutation	SNP	A	A	T	rs75492258	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	31	103	0	0.213793	0	A|0.934;T|0.066	0.066	strong	MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A3871T	p.T1291S	CTGGTGACCAGTC	.	PASS	Atlas-SNP
MS4A15	219995	hgsc.bcm.edu	37	11	60531264	60531264	+	Missense_Mutation	SNP	A	A	G	rs12363342	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	33	89	0	0.388235	0	A|0.709;G|0.291	0.291	strong	.	MS4A15	37	.	NM_001098835	exon2	c.A58G	p.S20G	AACGCCAGTGGCC	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	157	244	0	0.489097	0	G|0.796;A|0.204	0.204	strong	.	DHRS4	22	.	NM_021004	exon2	c.G252A	p.T84T	CGTGACGGGCACC	.	PASS	Atlas-SNP
PRSS36	146547	hgsc.bcm.edu	37	16	31151927	31151927	+	Silent	SNP	G	G	A	rs61976958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	28	75	0	0.405797	0	G|0.983;A|0.017	0.017	strong	.	PRSS36	50	.	NM_173502	exon13	c.C2053T	p.L685L	AGCTCAGCTCCAG	.	PASS	Atlas-SNP
ROBO4	54538	hgsc.bcm.edu	37	11	124764176	124764176	+	Silent	SNP	T	T	C	rs11820142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	38	97	0	0.422222	0	T|0.971;C|0.029	0.029	strong	.	ROBO4	130	.	NM_019055	exon8	c.A1239G	p.P413P	GGAGCCTGGCATA	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16340289	16340289	+	Silent	SNP	C	C	T	rs2229741	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	64	82	0	0.537815	0	C|0.443;T|0.557	0.557	strong	NRIP1,NS,carcinoma,0,1	NRIP1	103	1	NM_003489	exon4	c.G225A	p.G75G	GCCAGACCCCTGA	.	PASS	Atlas-SNP
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	26	50	0	0.684211	0	A|0.902;G|0.098	0.098	strong	.	ROR2	167	.	NM_004560	exon5	c.T498C	p.D166D	GTAATCATCCCTG	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730427	61730427	+	Missense_Mutation	SNP	G	G	T	rs115979721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	81	193	0	0.490909	0	G|0.977;T|0.023	0.023	strong	.	BEST1	85	.	NM_001139443	exon9	c.G1621T	p.A541S	TCCCTTGCTCTGA	.	PASS	Atlas-SNP
POTEG	404785	hgsc.bcm.edu	37	14	19563532	19563532	+	Missense_Mutation	SNP	A	A	G	rs79385954		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	320	10	293	1	0.03125	0.00341297	A|0.250;G|0.750	0.750	weak	POTEG,NS,carcinoma,-1,2	POTEG	118	2	NM_001005356	exon5	c.A1046G	p.H349R	CTAGTCATCATAA	.	scavenged	Atlas-SNP
ANKUB1	389161	hgsc.bcm.edu	37	3	149485581	149485581	+	Missense_Mutation	SNP	C	C	T	rs75855073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	76	0	0.493506	0	C|0.974;T|0.026	0.026	strong	.	ANKUB1	27	.	NM_001144960	exon5	c.G868A	p.V290I	ATAATACACAGTC	.	PASS	Atlas-SNP
MED13	9969	hgsc.bcm.edu	37	17	60087932	60087932	+	Missense_Mutation	SNP	T	T	C	rs114223275	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	121	0	0.441176	0	T|0.999;C|0.001	0.001	strong	.	MED13	181	.	NM_005121	exon9	c.A1946G	p.E649G	ACACTTTCCTGTC	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377120	49377120	+	Silent	SNP	C	C	T	rs34899467	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	93	0	0.460526	0	C|0.984;T|0.016	0.016	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.C630T	p.A210A	TTCTGCCTTGTCT	.	PASS	Atlas-SNP
COPE	11316	hgsc.bcm.edu	37	19	19030120	19030120	+	Missense_Mutation	SNP	G	G	C	rs2231987	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	36	62	0	0.521739	0	G|0.928;C|0.072	0.072	strong	.	COPE	26	.	NM_007263	exon1	c.C38G	p.S13C	TCCCCGGAGCCGC	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232942276	232942276	+	Missense_Mutation	SNP	G	G	A	rs61735495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	50	67	0	0.555556	0	G|0.988;A|0.012	0.012	strong	.	.	.	.	NM_019090	exon1	c.G1507A	p.E503K	GCACACGAACATC	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464736	39464736	+	Missense_Mutation	SNP	C	C	G	rs2074284	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	105	140	0	0.990566	0	C|0.672;G|0.328	0.328	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.G770C	p.S257T	GAGCAACTTGGCT	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55450727	55450727	+	Missense_Mutation	SNP	C	C	T	rs775881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	42	125	0	0.424242	0	C|0.869;T|0.131	0.131	strong	.	NLRP7	411	.	NM_001127255	exon4	c.G1460A	p.G487E	TCCTCCCCCTCCT	.	PASS	Atlas-SNP
URI1	8725	hgsc.bcm.edu	37	19	30500195	30500195	+	Missense_Mutation	SNP	G	G	C	rs151025990	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	88	0	0.494737	0	G|0.998;C|0.002	0.002	strong	.	.	.	.	NM_003796	exon8	c.G970C	p.A324P	CATGAGGCTTTAG	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117051020	117051020	+	Silent	SNP	A	A	G	rs1687410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	69	120	0	0.69	0	A|0.790;G|0.210	0.210	strong	.	COL27A1	200	.	NM_032888	exon43	c.A4083G	p.G1361G	ACCGGGAGACCCT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092841	1092841	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	37	124	26	0.284615	0.209677	.	.	none	MUC2_ENST00000441003,trunk,malignant_melanoma,-1,2	MUC2	614	2	NM_002457	exon30	c.G4660A	p.G1554S	CCCACCGGCACAC	.	scavenged	Atlas-SNP
ZBTB4	57659	hgsc.bcm.edu	37	17	7365289	7365289	+	Silent	SNP	A	A	T	rs114898274	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	40	110	0	0.430108	0	A|0.992;T|0.008	0.008	strong	.	ZBTB4	163	.	NM_001128833	exon4	c.T3012A	p.V1004V	TCTCTCAACCCCT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123970513	123970513	+	Silent	SNP	G	G	A	rs35913854	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	23	54	0	0.442308	0	G|0.936;A|0.064	0.064	strong	.	TACC2	271	.	NM_206862	exon9	c.G6573A	p.T2191T	GGAGACGCCCCTT	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559350	140559350	+	Missense_Mutation	SNP	C	C	T	rs17844499		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	2	18	0	0.181818	0	.	.	weak	PCDHB8,NS,carcinoma,-1,1	PCDHB8	199	1	NM_019120	exon1	c.C1735T	p.R579W	GTGCCCCGGGCGG	.	scavenged	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167301338	167301338	+	Silent	SNP	A	A	G	rs35213258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	59	164	0	0.406897	0	A|0.967;G|0.033	0.033	strong	.	SCN7A	410	.	NM_002976	exon12	c.T1560C	p.C520C	CAGAAAACATACG	.	PASS	Atlas-SNP
OPRL1	4987	hgsc.bcm.edu	37	20	62729272	62729272	+	Silent	SNP	G	G	A	rs61742883	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	94	161	0	0.489583	0	G|0.982;A|0.018	0.018	strong	.	OPRL1	47	.	NM_000913	exon3	c.G351A	p.P117P	CTGGCCGTTTGGG	.	PASS	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26085931	26085931	+	Silent	SNP	G	G	A	rs75831953		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	451	212	422	0	0.470067	0	.	.	weak	.	NOS2	113	.	NM_000625	exon26	c.C3330T	p.V1110V	GTCCTCGACCTGC	.	PASS	Atlas-SNP
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	54	97	0	0.556701	0	C|0.726;A|0.274	0.274	strong	.	INPP5J	94	.	NM_001002837	exon11	c.C1299A	p.T433T	GAATACCTACCAG	.	PASS	Atlas-SNP
ARHGEF4	50649	hgsc.bcm.edu	37	2	131803624	131803624	+	Silent	SNP	C	C	T	rs114004756	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	73	166	0	0.405556	0	C|0.996;T|0.004	0.004	strong	.	ARHGEF4	89	.	NM_015320	exon14	c.C1935T	p.P645P	CCGGCCCTGCTAC	.	PASS	Atlas-SNP
PNKD	25953	hgsc.bcm.edu	37	2	219205471	219205471	+	Silent	SNP	G	G	A	rs34014804	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	67	119	0	0.540323	0	G|0.939;A|0.061	0.061	strong	.	PNKD	58	.	NM_015488	exon5	c.G486A	p.G162G	GGAAGGGGTCACC	.	PASS	Atlas-SNP
CHRNA4	1137	hgsc.bcm.edu	37	20	61990939	61990939	+	Silent	SNP	G	G	A	rs2273506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	47	103	0	0.5	0	G|0.910;A|0.090	0.090	strong	.	CHRNA4	98	.	NM_000744	exon2	c.C189T	p.L63L	GCGGACGAGGACC	.	PASS	Atlas-SNP
COL11A2	1302	hgsc.bcm.edu	37	6	33153528	33153528	+	Missense_Mutation	SNP	C	C	T	rs9277934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	42	88	0	0.531646	0	C|0.684;N|0.000	.	strong	COL11A2,NS,lymphoid_neoplasm,+1,1	COL11A2	124	1	NM_080680	exon6	c.G826A	p.E276K	GGGGCTCGTAGTC	.	PASS	Atlas-SNP
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158456	26158456	+	Missense_Mutation	SNP	C	C	T	rs62623440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	61	174	0	0.42069	0	C|0.990;T|0.010	0.010	strong	.	HIST1H2BD	45	.	NM_021063	exon1	c.C59T	p.T20I	CGGTGACTAAGGC	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43237080	43237080	+	Missense_Mutation	SNP	T	T	C	rs76931703	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	116	237	0	0.493617	0	T|0.988;C|0.012	0.012	strong	.	PSG3	82	.	NM_021016	exon3	c.A565G	p.M189V	GAGTCATAGGGAG	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232941677	232941677	+	Missense_Mutation	SNP	G	G	T	rs3766497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	140	143	0	0.979021	0	G|0.897;T|0.103	0.103	strong	.	.	.	.	NM_019090	exon1	c.G908T	p.R303L	GGGGACGTTTCCC	.	PASS	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10297658	10297658	+	Missense_Mutation	SNP	A	A	G	rs8069834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	60	116	0	0.465116	0	A|0.408;G|0.592	0.592	strong	.	MYH8	346	.	NM_002472	exon35	c.T5074C	p.W1692R	TGGCCCACAGCTC	.	PASS	Atlas-SNP
PI4K2A	55361	hgsc.bcm.edu	37	10	99410790	99410790	+	Silent	SNP	T	T	C	rs7915721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	65	154	1	0.5	0.00649351	T|0.663;C|0.337	0.337	strong	PI4K2A_ENST00000555577,NS,carcinoma,0,2	PI4K2A	57	2	NM_018425	exon2	c.T528C	p.P176P	CTGTCCTTGCTGC	.	scavenged	Atlas-SNP
ROBO4	54538	hgsc.bcm.edu	37	11	124766128	124766128	+	Silent	SNP	A	A	G	rs4078313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	45	159	0	0.36	0	A|0.539;G|0.461	0.461	strong	.	ROBO4	130	.	NM_019055	exon4	c.T645C	p.H215H	CTCCCTATGTCCT	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167674370	167674370	+	Silent	SNP	C	C	T	rs3733988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	69	0	1	0	C|0.592;T|0.408	0.408	strong	ODZ2,NS,carcinoma,0,1	.	.	1	NM_001122679	exon27	c.C6399T	p.I2133I	CCAGATCATCACC	.	PASS	Atlas-SNP
FCRL6	343413	hgsc.bcm.edu	37	1	159785370	159785370	+	Silent	SNP	T	T	C	rs4301626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	156	0	0.991304	0	T|0.814;C|0.186	0.186	strong	FCRL6,NS,carcinoma,0,1	FCRL6	61	1	NM_001004310	exon10	c.T1224C	p.S408S	GCCCAGTGAGGTT	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6903920	6903920	+	Missense_Mutation	SNP	A	A	G	rs443658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	38	88	0	0.413043	0	T|0.001;G|0.397	0.397	strong	EMR1,NS,carcinoma,+1,1	EMR1	153	1	NM_001256253	exon7	c.A761G	p.N254S	CAAGCAATGGACA	.	PASS	Atlas-SNP
CLEC2D	29121	hgsc.bcm.edu	37	12	9833524	9833524	+	Missense_Mutation	SNP	C	C	G	rs3764022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	26	36	0	0.52	0	C|0.732;G|0.268	0.268	strong	.	CLEC2D	54	.	NM_001004419	exon2	c.C67G	p.L23V	GGTTGTCTGCATT	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192328	102192328	+	Missense_Mutation	SNP	A	A	G	rs61745026	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	279	340	0	0.996429	0	A|0.823;G|0.177	0.177	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.A82G	p.S28G	GGCAAGAGTGAGA	.	PASS	Atlas-SNP
CXCR6	10663	hgsc.bcm.edu	37	3	45987980	45987980	+	Missense_Mutation	SNP	G	G	A	rs2234355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	67	171	0	0.489051	0	G|0.857;A|0.143	0.143	strong	.	CXCR6	17	.	NM_006564	exon2	c.G7A	p.E3K	ATGGCAGAGCATG	.	PASS	Atlas-SNP
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	109	190	1	0.469828	0.00526316	C|0.830;T|0.170	0.170	strong	OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	NM_001001912	exon1	c.C722T	p.S241L	CCTGCTCGGCCCA	.	scavenged	Atlas-SNP
GNA12	2768	hgsc.bcm.edu	37	7	2834754	2834754	+	Silent	SNP	T	T	C	rs2230877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	47	70	0	0.522222	0	T|0.980;C|0.020	0.020	strong	.	GNA12	35	.	NM_007353	exon2	c.A333G	p.A111A	ATCTCGTGCATCA	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	37	5	82400773	82400773	+	Missense_Mutation	SNP	C	C	G	rs28383138	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	69	136	0	0.479167	0	C|0.993;G|0.007	0.007	strong	.	XRCC4	37	.	NM_003401	exon2	c.C35G	p.S12C	TTGTTTCTGAACC	.	PASS	Atlas-SNP
DMGDH	29958	hgsc.bcm.edu	37	5	78326750	78326750	+	Missense_Mutation	SNP	G	G	C	rs1805073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	53	95	0	0.504762	0	G|0.677;C|0.323	0.323	strong	DMGDH,colon,adenoma,+1,1	DMGDH	88	1	NM_013391	exon10	c.C1589G	p.A530G	GTTACCGCTACTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512412	195512412	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	15	343	5	0.130435	0.0145773	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	NM_018406	exon2	c.G6039C	p.Q2013H	GGTGGCCTGTCCT	.	scavenged	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	21	44	0	0.538462	0	G|0.631;A|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.C1700T	p.P567L	GCCAGCGGTGACA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132549300	132549300	+	Missense_Mutation	SNP	A	A	G	rs7136109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	28	36	0	0.5	0	A|0.883;G|0.117	0.117	strong	.	EP400	370	.	NM_015409	exon48	c.A8422G	p.T2808A	CAGCCAACAGCCC	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68612556	68612556	+	Silent	SNP	T	T	C	rs2271724	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	56	90	0	0.474576	0	T|0.827;C|0.173	0.173	strong	.	ITGA11	110	.	NM_001004439	exon20	c.A2583G	p.S861S	GTTTGCTGACTGC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6958609	6958609	+	Missense_Mutation	SNP	T	T	C	rs543355	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	76	227	0	0.406417	0	C|0.157;G|0.000;T|0.843	0.157	strong	LAMA1,colon,carcinoma,0,1	LAMA1	458	1	NM_005559	exon55	c.A7831G	p.T2611A	CTAATGTGCCCAA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228469870	228469870	+	Missense_Mutation	SNP	C	C	T	rs3795785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	88	175	0	0.389381	0	C|0.882;T|0.118	0.118	strong	.	OBSCN	2142	.	NM_001271223	exon36	c.C9721T	p.R3241W	TCTGTGCGGGGCC	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79875104	79875104	+	Silent	SNP	A	A	G	rs73466058	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	93	145	0	0.62	0	A|0.987;G|0.013	0.013	strong	.	VPS13A	735	.	NM_001018038	exon23	c.A2391G	p.P797P	TGAACCAGTAACT	.	PASS	Atlas-SNP
GCAT	23464	hgsc.bcm.edu	37	22	38205989	38205989	+	Missense_Mutation	SNP	T	T	C	rs2285178	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	83	146	0	0.479769	0	T|0.723;C|0.277	0.277	strong	.	GCAT	27	.	NM_001171690	exon2	c.T230C	p.L77S	TGCCCTTGCCCCA	.	PASS	Atlas-SNP
ITIH6	347365	hgsc.bcm.edu	37	X	54783952	54783952	+	Missense_Mutation	SNP	A	A	G	rs150850201	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	115	153	0	0.506608	0	A|0.982;G|0.018	0.018	strong	.	.	.	.	NM_198510	exon8	c.T2555C	p.I852T	AATAAGATTTTAG	.	PASS	Atlas-SNP
UGGT1	56886	hgsc.bcm.edu	37	2	128939817	128939817	+	Silent	SNP	G	G	A	rs1699	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	148	1	1	0.00675676	G|0.589;A|0.411	0.411	strong	.	UGGT1	126	.	NM_020120	exon37	c.G4197A	p.K1399K	CTGGAAGTCAGGG	.	PASS	Atlas-SNP
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	35	82	0	0.360825	0	A|0.354;G|0.646	0.646	strong	.	ARHGAP4	103	.	NM_001164741	exon16	c.T1836C	p.H612H	CAGGTCATGGGCA	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89645360	89645360	+	Silent	SNP	G	G	A	rs149812493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	37	72	0	0.430233	0	G|0.988;A|0.012	0.012	strong	.	CPNE7	56	.	NM_014427	exon3	c.G453A	p.T151T	CTGCACGGAATCC	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408476	29408476	+	Silent	SNP	A	A	G	rs2074465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	80	229	0	0.410256	0	A|0.939;G|0.061	0.061	strong	.	OR10C1	58	.	NM_013941	exon1	c.A684G	p.P228P	GATCCCATCTGTT	.	PASS	Atlas-SNP
HEXIM2	124790	hgsc.bcm.edu	37	17	43246456	43246456	+	Silent	SNP	G	G	A	rs34207107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	101	1	1	0.00990099	G|0.962;A|0.038	0.038	strong	.	HEXIM2	19	.	NM_144608	exon4	c.G141A	p.P47P	GACACCGCGGATG	.	PASS	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	37	11	47431703	47431703	+	Missense_Mutation	SNP	A	A	G	rs61897432	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	58	142	0	0.471545	0	A|0.882;G|0.118	0.118	strong	.	SLC39A13	18	.	NM_152264	exon2	c.A58G	p.T20A	TTCCTCACTGCCC	.	PASS	Atlas-SNP
VPS39	23339	hgsc.bcm.edu	37	15	42459034	42459034	+	Silent	SNP	T	T	C	rs1619030	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	164	162	0	0.993939	0	T|0.694;C|0.306	0.306	strong	.	VPS39	53	.	NM_015289	exon14	c.A1455G	p.L485L	CTTCTTTAGCACG	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43575928	43575928	+	Silent	SNP	G	G	A	rs1064935	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	89	200	0	0.421801	0	T|0.002;G|0.976;A|0.023	0.023	strong	PSG2,NS,carcinoma,0,1	PSG2	84	1	NM_031246	exon4	c.C888T	p.S296S	GAGCCCGCTATGC	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58757668	58757668	+	Silent	SNP	A	A	C	rs14221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	77	261	0	0.420765	0	A|0.293;C|0.707;G|0.000	0.707	strong	.	GOT2	42	.	NM_002080	exon2	c.T228G	p.V76V	AGGCAGAACGTAA	.	PASS	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	37	4	94344042	94344042	+	Missense_Mutation	SNP	G	G	A	rs10034345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	58	121	0	0.432836	0	G|0.911;A|0.089	0.089	strong	.	GRID2	233	.	NM_001510	exon10	c.G1468A	p.V490I	ATTTACGTAGCAC	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39623496	39623496	+	Missense_Mutation	SNP	C	C	T	rs115680799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	80	0	0.494737	0	C|0.981;T|0.019	0.019	strong	.	KRT32	57	.	NM_002278	exon1	c.G82A	p.G28S	TCACGCCGCTGGA	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617094	183617094	+	Missense_Mutation	SNP	G	G	A	rs10911391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	395	202	386	0	0.511392	0	G|0.933;A|0.067	0.067	strong	.	APOBEC4	45	.	NM_203454	exon2	c.C823T	p.P275S	CACTCGGCATTTG	.	PASS	Atlas-SNP
TSPEAR	54084	hgsc.bcm.edu	37	21	45953576	45953576	+	Silent	SNP	C	C	T	rs148713881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	44	85	0	0.435644	0	C|0.990;T|0.010	0.010	strong	TSPEAR,caecum,carcinoma,0,1	TSPEAR	110	1	NM_144991	exon3	c.G534A	p.P178P	GTCCACCGGGAGG	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220427395	220427395	+	Silent	SNP	G	G	A	rs3183099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	56	0	0.493151	0	G|0.802;A|0.198	0.198	strong	.	OBSL1	120	.	NM_001173431	exon8	c.C2682T	p.D894D	GGAGACGTCTGGA	.	PASS	Atlas-SNP
PRSS45	377047	hgsc.bcm.edu	37	3	46784467	46784467	+	Missense_Mutation	SNP	G	G	A	rs58943210	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	62	117	0	0.534483	0	G|0.801;A|0.199	0.199	strong	.	PRSS45	12	.	NM_199183	exon3	c.C389T	p.P130L	ACAACTGGGGGGA	.	PASS	Atlas-SNP
PENK	5179	hgsc.bcm.edu	37	8	57354380	57354380	+	Silent	SNP	T	T	C	rs76702938	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	58	115	0	0.542056	0	T|0.999;C|0.001	0.001	strong	.	PENK	59	.	NM_001135690	exon4	c.A255G	p.R85R	ATTTTCTCTGAGG	.	PASS	Atlas-SNP
BPIFB1	92747	hgsc.bcm.edu	37	20	31890175	31890175	+	Missense_Mutation	SNP	G	G	T	rs6120222	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	74	151	0	0.459627	0	G|0.875;T|0.125	0.125	strong	.	.	.	.	NM_033197	exon10	c.G938T	p.S313I	CTGAGAGTGCCCA	.	PASS	Atlas-SNP
CASKIN2	57513	hgsc.bcm.edu	37	17	73498483	73498483	+	Missense_Mutation	SNP	T	T	C	rs7503373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	28	36	0	0.965517	0	T|0.224;C|0.776	0.776	strong	.	CASKIN2	66	.	NM_020753	exon18	c.A2672G	p.E891G	GGGCTCTCATCTA	.	PASS	Atlas-SNP
RUFY4	285180	hgsc.bcm.edu	37	2	218954716	218954716	+	Missense_Mutation	SNP	A	A	G	rs116710266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	153	214	0	0.546429	0	A|0.982;G|0.018	0.018	strong	.	RUFY4	59	.	NM_198483	exon13	c.A1655G	p.Y552C	TGGATTACAAGAA	.	PASS	Atlas-SNP
MUC1	4582	hgsc.bcm.edu	37	1	155161714	155161714	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	4	5	0	0.666667	0	.	.	none	.	MUC1	94	.	NM_001204286	exon2	c.C446T	p.S149L	GGGGCCGAGGTGA	.	PASS	Atlas-SNP
SIDT2	51092	hgsc.bcm.edu	37	11	117050007	117050007	+	Missense_Mutation	SNP	G	G	A	rs61729992	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	15	43	0	0.340909	0	G|0.991;A|0.009	0.009	strong	.	SIDT2	82	.	NM_001040455	exon1	c.G28A	p.V10M	TTCTTGGTGCTCT	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	130007388	130007388	+	Missense_Mutation	SNP	G	G	T	rs17854248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	138	326	0	0.445161	0	G|0.810;T|0.190	0.190	strong	.	CPA5	61	.	NM_080385	exon11	c.G1014T	p.E338D	GCTGGAGCCCGTT	.	PASS	Atlas-SNP
TRAF3	7187	hgsc.bcm.edu	37	14	103342049	103342049	+	Missense_Mutation	SNP	T	T	C	rs1131877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	53	0	1	0	T|0.550;C|0.450	0.450	strong	.	TRAF3	60	.	NM_145726	exon5	c.T386C	p.M129T	AGTTAATGCTGGG	.	PASS	Atlas-SNP
RAB19	401409	hgsc.bcm.edu	37	7	140125878	140125878	+	Silent	SNP	C	C	T	rs4585665	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	81	0	0.450549	0	C|0.989;T|0.011	0.011	strong	.	RAB19	21	.	NM_001008749	exon4	c.C582T	p.N194N	CCTGAACGGCCTC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176919	8176919	+	Silent	SNP	C	C	T	rs4804264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	80	175	0	0.432432	0	C|0.388;N|0.000	.	strong	.	FBN3	300	.	NM_032447	exon30	c.G3903A	p.P1301P	ACTCCCCGGGATG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs2231093	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	377	118	226	0	0.312997	0	G|0.860;T|0.140	0.140	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G808T	p.A270S	TGGGCGGCTGTGG	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49743010	49743010	+	Silent	SNP	C	C	G	rs76989089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	103	179	0	0.492823	0	C|0.974;G|0.026	0.026	strong	.	RNF123	100	.	NM_022064	exon24	c.C2202G	p.P734P	GCGGCCCCCCGAG	.	PASS	Atlas-SNP
OR10G8	219869	hgsc.bcm.edu	37	11	123900694	123900694	+	Missense_Mutation	SNP	A	A	G	rs75994039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	571	308	641	0	0.539405	0	A|0.966;G|0.034	0.034	strong	OR10G8,NS,carcinoma,0,1	OR10G8	132	1	NM_001004464	exon1	c.A365G	p.Y122C	ATCGCTACCTGGC	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107586753	107586753	+	Missense_Mutation	SNP	T	T	C	rs2066714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	156	211	2	0.681223	0.00947867	T|0.686;C|0.314	0.314	strong	ABCA1,NS,adenoma,0,1	ABCA1	244	1	NM_005502	exon18	c.A2649G	p.I883M	TTCTGATATTCTC	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274212	39274212	+	Missense_Mutation	SNP	C	C	T	rs187464255	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	37	120	0	0.313559	0	C|0.982;T|0.018	0.018	strong	.	KRTAP4-11	94	.	NM_033059	exon1	c.G356A	p.C119Y	CTGCAGCAGCTGG	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52282060	52282060	+	Silent	SNP	C	C	T	rs697634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	71	127	0	0.533835	0	C|0.719;T|0.281	0.281	strong	.	ANKRD33	33	.	NM_182608	exon1	c.C90T	p.R30R	GCTCCGCGGAGCC	.	PASS	Atlas-SNP
CCDC150	284992	hgsc.bcm.edu	37	2	197521750	197521750	+	Missense_Mutation	SNP	G	G	A	rs34133636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	71	97	0	0.533835	0	G|0.924;A|0.076	0.076	strong	CCDC150,NS,carcinoma,0,1	CCDC150	96	1	NM_001080539	exon4	c.G466A	p.E156K	CATCTCGAAGTTA	.	PASS	Atlas-SNP
ZNF213	7760	hgsc.bcm.edu	37	16	3188789	3188789	+	Silent	SNP	G	G	A	rs35931391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	62	95	0	0.553571	0	G|0.949;A|0.051	0.051	strong	.	ZNF213	36	.	NM_004220	exon4	c.G567A	p.T189T	AGAGACGACGGAC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225339732	225339732	+	Missense_Mutation	SNP	C	C	T	rs115743416	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	62	138	0	0.492063	0	C|0.993;T|0.007	0.007	strong	DNAH14_ENST00000430092,colon,carcinoma,-1,2	DNAH14	300	2	NM_001373	exon31	c.C4915T	p.R1639C	GAAATTCGTATCA	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361449	107361449	+	Silent	SNP	T	T	C	rs79797302		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	705	293	752	2	0.415603	0.00265957	.	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.A246G	p.L82L	GCTCACTAGCGTG	.	PASS	Atlas-SNP
ELMO2	63916	hgsc.bcm.edu	37	20	45014804	45014804	+	Silent	SNP	G	G	A	rs201990540	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	5	95	1	0.045045	0.0105263	G|0.998;A|0.002	0.002	strong	ELMO2,NS,carcinoma,-1,1	ELMO2	51	1	NM_182764	exon8	c.C636T	p.A212A	TTCCTCGGCTATC	.	scavenged	Atlas-SNP
TEAD2	8463	hgsc.bcm.edu	37	19	49852070	49852070	+	Missense_Mutation	SNP	G	G	A	rs201393859	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	57	114	0	0.448819	0	G|0.995;A|0.005	0.005	strong	.	TEAD2	70	.	NM_001256660	exon9	c.C637T	p.P213S	GTGGGGGCAGGGG	.	PASS	Atlas-SNP
GPRIN3	285513	hgsc.bcm.edu	37	4	90168945	90168945	+	Missense_Mutation	SNP	A	A	C	rs34322172	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	93	173	0	0.508197	0	A|0.992;C|0.008	0.008	strong	.	GPRIN3	90	.	NM_198281	exon2	c.T2317G	p.S773A	ACACAGAAGACGG	.	PASS	Atlas-SNP
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	103	0	0.526882	0	C|0.986;A|0.014	0.014	strong	.	MLKL	51	.	NM_001142497	exon4	c.G605T	p.G202V	GCTGAGCCAGTCT	.	PASS	Atlas-SNP
TMEM201	199953	hgsc.bcm.edu	37	1	9671935	9671935	+	Silent	SNP	C	C	T	rs4073292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	44	82	0	0.511628	0	C|0.934;T|0.066	0.066	strong	.	TMEM201	63	.	NM_001130924	exon10	c.C1890T	p.A630A	GGAGGCCGCCACC	.	PASS	Atlas-SNP
LRRC4C	57689	hgsc.bcm.edu	37	11	40137543	40137543	+	Silent	SNP	T	T	C	rs2953310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	81	167	1	0.503106	0.00598802	T|0.478;C|0.522	0.522	strong	LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	NM_001258419	exon7	c.A300G	p.R100R	CAAGTGTCTCAAG	.	scavenged	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21386019	21386019	+	Missense_Mutation	SNP	G	G	A	rs2072550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	38	81	0	0.413043	0	G|0.786;A|0.214	0.214	strong	SLC7A4,NS,carcinoma,0,1	SLC7A4	50	1	NM_004173	exon2	c.C83T	p.T28I	TCCATGGTGGAGT	.	PASS	Atlas-SNP
CNDP1	84735	hgsc.bcm.edu	37	18	72226578	72226578	+	Silent	SNP	C	C	A	rs9807352	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	41	77	0	0.621212	0	C|0.934;A|0.066	0.066	strong	.	CNDP1	98	.	NM_032649	exon3	c.C174A	p.A58A	GGTGGCCATCGAG	.	PASS	Atlas-SNP
ZNF195	7748	hgsc.bcm.edu	37	11	3383015	3383015	+	Missense_Mutation	SNP	G	G	A	rs7125523	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	29	39	0	0.58	0	G|0.980;A|0.020	0.020	strong	.	ZNF195	77	.	NM_001242841	exon5	c.C343T	p.R115C	GGGCACGGTGGTT	.	PASS	Atlas-SNP
IFI16	3428	hgsc.bcm.edu	37	1	159024668	159024668	+	Missense_Mutation	SNP	A	A	T	rs6940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	297	254	0	0.996644	0	A|0.827;T|0.173	0.173	strong	.	IFI16	111	.	NM_001206567	exon11	c.A2167T	p.T723S	ATGGAAACTTCAC	.	PASS	Atlas-SNP
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73339675	73339675	+	Silent	SNP	C	C	T	rs143108301		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	30	44	0	0.434783	0	C|1.000;T|0.000	0.000	weak	.	RAB11FIP5	66	.	NM_015470	exon1	c.G231A	p.L77L	CGGCGGCAGCTCG	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150553605	150553605	+	Missense_Mutation	SNP	C	C	T	rs10156191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	34	82	0	0.4	0	C|0.708;T|0.292	0.292	strong	.	ABP1	92	.	NM_001091	exon2	c.C47T	p.T16M	TGCAGACGGCCAT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4508960	4508960	+	Silent	SNP	C	C	T	rs112037560	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	26	31	0	0.604651	0	C|0.974;T|0.026	0.026	strong	.	PLIN4	191	.	NM_001080400	exon4	c.G3480A	p.L1160L	GGCAGCCAGCTGA	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133487000	133487000	+	Silent	SNP	C	C	T	rs8177286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	71	0	0.547945	0	C|0.987;T|0.013	0.013	strong	.	TF	116	.	NM_001063	exon13	c.C1614T	p.G538G	CACAGGCGCTTTC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51720838	51720838	+	Silent	SNP	T	T	C	rs9349603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	74	176	0	0.445783	0	T|0.577;C|0.423	0.423	strong	.	PKHD1	927	.	NM_170724	exon49	c.A7764G	p.L2588L	CATGGTTAAATCA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159654408	159654408	+	Missense_Mutation	SNP	G	G	A	rs73799344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	25	50	0	0.454545	0	G|0.959;A|0.041	0.041	strong	.	FNDC1	250	.	NM_032532	exon11	c.G2864A	p.S955N	AACAGAGCACAGA	.	PASS	Atlas-SNP
MRPL9	65005	hgsc.bcm.edu	37	1	151733335	151733335	+	Missense_Mutation	SNP	T	T	G	rs8480	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	14	22	0	0.56	0	T|0.485;G|0.515	0.515	strong	.	MRPL9	21	.	NM_031420	exon6	c.A629C	p.E210A	GGCTCTTCTGGTA	.	PASS	Atlas-SNP
OR5D14	219436	hgsc.bcm.edu	37	11	55563602	55563602	+	Missense_Mutation	SNP	G	G	A	rs68042892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	315	157	275	0	0.498413	0	G|0.896;A|0.104	0.104	strong	OR5D14,NS,carcinoma,0,1	OR5D14	116	1	NM_001004735	exon1	c.G571A	p.G191S	GTGTCTGGCTCTG	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84816015	84816015	+	Silent	SNP	A	A	G	rs1006244	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	144	282	0	0.464516	0	A|0.901;G|0.099	0.099	strong	.	DNAH6	194	.	NM_001370	exon16	c.A2547G	p.Q849Q	TCTGCAATCTGTT	.	PASS	Atlas-SNP
SLC14A1	6563	hgsc.bcm.edu	37	18	43319519	43319519	+	Missense_Mutation	SNP	G	G	A	rs1058396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	164	147	0	0.993939	0	G|0.587;A|0.413	0.413	strong	.	SLC14A1	84	.	NM_001146037	exon7	c.G1006A	p.D336N	TTTGAGGACATCT	.	PASS	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	37041439	37041439	+	Missense_Mutation	SNP	C	C	T	rs11901202	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	53	85	0	0.546392	0	C|0.932;T|0.068	0.068	strong	VIT,mouth,carcinoma,0,1	VIT	138	1	NM_053276	exon16	c.C2017T	p.H673Y	AACCTCCATCAGT	.	PASS	Atlas-SNP
CXCR2	3579	hgsc.bcm.edu	37	2	219000193	219000193	+	Silent	SNP	A	A	G	rs2228414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	124	253	0	0.579439	0	A|0.985;G|0.015	0.015	strong	.	CXCR2	54	.	NM_001168298	exon4	c.A669G	p.P223P	CGTGCCACTGCTG	.	PASS	Atlas-SNP
ND3	0	hgsc.bcm.edu	37	MT	10321	10321	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	8	8	0	1	0	.	.	none	.	.	.	.	ENST00000361227	exon1	c.T263C	p.V88A	TAATAGTTATGTC	.	PASS	Atlas-SNP
NLRP10	338322	hgsc.bcm.edu	37	11	7982432	7982432	+	Missense_Mutation	SNP	G	G	A	rs59039403	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	86	0	0.518519	0	G|0.976;A|0.024	0.024	strong	.	NLRP10	146	.	NM_176821	exon2	c.C727T	p.R243W	GGAGCCGCTCTGG	.	PASS	Atlas-SNP
FAM83D	81610	hgsc.bcm.edu	37	20	37555116	37555116	+	Missense_Mutation	SNP	G	G	C	rs3752290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	2	21	0	0.166667	0	G|0.618;C|0.382	0.382	strong	FAM83D,NS,carcinoma,0,2	FAM83D	60	2	NM_030919	exon1	c.G121C	p.V41L	GACGAGGTGCCCG	.	scavenged	Atlas-SNP
RETSAT	54884	hgsc.bcm.edu	37	2	85570857	85570857	+	Missense_Mutation	SNP	G	G	A	rs4832169	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	47	545	0	0.110329	0	G|0.786;A|0.214	0.214	strong	.	RETSAT	56	.	NM_017750	exon10	c.C1598T	p.A533V	TAGCAGGCACCTC	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs2020862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	124	184	0	0.534483	0	C|0.606;T|0.394	0.394	strong	FMO2,NS,carcinoma,-1,2	FMO2	66	2	NM_001460	exon5	c.C584T	p.S195L	GAAACTCAGGCTC	.	PASS	Atlas-SNP
KCNH5	27133	hgsc.bcm.edu	37	14	63269180	63269180	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	3	104	0	0.0208333	0	.	.	none	KCNH5_ENST00000394968,caecum,carcinoma,0,3	KCNH5	320	3	NM_172375	exon9	c.G1689A	p.A563A	CTCTACCGCCAAG	.	scavenged	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941938	22941938	+	Missense_Mutation	SNP	T	T	G	rs6511379	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	24	17	0	0.96	0	T|0.901;G|0.099	0.099	strong	.	ZNF99	273	.	NM_001080409	exon4	c.A773C	p.K258T	TCACATTTGCAGG	.	PASS	Atlas-SNP
C1orf64	149563	hgsc.bcm.edu	37	1	16332679	16332679	+	Silent	SNP	T	T	C	rs3738646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	51	99	0	0.481132	0	T|0.916;C|0.084	0.084	strong	.	C1orf64	16	.	NM_178840	exon2	c.T348C	p.S116S	AGGGTCTGTGGCC	.	PASS	Atlas-SNP
CEP85L	387119	hgsc.bcm.edu	37	6	118803091	118803091	+	Missense_Mutation	SNP	C	C	G	rs9489410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	32	59	0	0.444444	0	C|0.982;G|0.018	0.018	strong	.	CEP85L	26	.	NM_001178035	exon9	c.G1605C	p.Q535H	CAGAATCTGCAGC	.	PASS	Atlas-SNP
SLC35B3	51000	hgsc.bcm.edu	37	6	8413890	8413890	+	Silent	SNP	A	A	G	rs3757099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	29	32	0	0.630435	0	A|0.639;G|0.360	0.360	strong	.	SLC35B3	38	.	NM_001142540	exon11	c.T1098C	p.L366L	AACATTAAGAAAT	.	PASS	Atlas-SNP
LIPI	149998	hgsc.bcm.edu	37	21	15516948	15516948	+	Missense_Mutation	SNP	C	C	T	rs2822432	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	51	177	0	0.386364	0	C|0.629;T|0.371	0.371	strong	.	LIPI	95	.	NM_198996	exon9	c.G1354A	p.E452K	ACCTTTCTGGGTA	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	35	63	0	0.454545	0	G|0.791;A|0.209	0.209	strong	.	TRIM3	67	.	NM_001248006	exon5	c.C603T	p.I201I	TGCACTGATCTGG	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140579358	140579358	+	Missense_Mutation	SNP	A	A	G	rs3756323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	44	61	0	0.628571	0	A|0.818;G|0.182	0.182	strong	.	PCDHB11	162	.	NM_018931	exon1	c.A11G	p.Q4R	AGAACCAAGGGAC	.	PASS	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs76491286		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	878	396	1118	0	0.451025	0	.	.	weak	ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	NM_005435	exon2	c.C1040T	p.T347I	GTCAAACCTTTTT	.	scavenged	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138379608	138379608	+	Silent	SNP	C	C	T	rs139160467	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	8	24	0	0.363636	0	C|0.989;T|0.011	0.011	strong	.	.	.	.	NM_014811	exon4	c.C3252T	p.T1084T	GTCCACCCAGCTC	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	14	182	1	0.0636364	0.00549451	G|0.994;A|0.006	0.006	strong	LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	NM_001081442	exon13	c.C1648T	p.P550S	CCTGGGGGGCTTC	.	scavenged	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161152240	161152240	+	Missense_Mutation	SNP	G	G	A	rs4252125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	128	0	1	0	G|0.784;A|0.216	0.216	strong	.	PLG	150	.	NM_000301	exon11	c.G1414A	p.D472N	CTTCCAGATGTAG	.	PASS	Atlas-SNP
FBXO33	254170	hgsc.bcm.edu	37	14	39871017	39871017	+	Silent	SNP	T	T	C	rs7156962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	82	0	0.515789	0	T|0.825;C|0.175	0.175	strong	.	FBXO33	21	.	NM_203301	exon3	c.A759G	p.K253K	CAGCCATTTCAGT	.	PASS	Atlas-SNP
OR3A1	4994	hgsc.bcm.edu	37	17	3195603	3195603	+	Nonsense_Mutation	SNP	T	T	A	rs7218125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	148	254	0	0.534296	0	T|0.972;A|0.028	0.028	strong	.	OR3A1	46	.	NM_002550	exon1	c.A274T	p.K92X	CACGCTTGCGGGA	.	PASS	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239059610	239059610	+	Silent	SNP	C	C	T	rs61736173	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	95	169	0	0.552326	0	C|0.961;T|0.039	0.039	strong	.	KLHL30	79	.	NM_198582	exon8	c.C1641T	p.G547G	CCACGGCGCCCTG	.	PASS	Atlas-SNP
CYBA	1535	hgsc.bcm.edu	37	16	88713213	88713213	+	Silent	SNP	C	C	G	rs2228472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	36	65	0	0.537313	0	C|0.949;G|0.051	0.051	strong	.	CYBA	12	.	NM_000101	exon4	c.G237C	p.L79L	CCCGAACAGCTTC	.	PASS	Atlas-SNP
OR1J2	26740	hgsc.bcm.edu	37	9	125273435	125273435	+	Missense_Mutation	SNP	G	G	A	rs41277120	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	77	222	0	0.308	0	G|0.948;A|0.052	0.052	strong	.	OR1J2	64	.	NM_054107	exon1	c.G355A	p.A119T	TCAATGGCATATG	.	PASS	Atlas-SNP
IFNA10	3446	hgsc.bcm.edu	37	9	21206724	21206724	+	Nonsense_Mutation	SNP	G	G	A	rs145785282	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	702	210	599	0	0.299145	0	G|0.996;A|0.004	0.004	strong	.	IFNA10	29	.	NM_002171	exon1	c.C373T	p.Q125X	CCTCCTGTATCAC	.	PASS	Atlas-SNP
DIRAS3	9077	hgsc.bcm.edu	37	1	68512441	68512441	+	Silent	SNP	A	A	G	rs61736596	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	91	169	0	0.532164	0	A|0.900;G|0.100	0.100	strong	.	DIRAS3	31	.	NM_004675	exon2	c.T540C	p.I180I	GGCTGAAATCTCC	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90103487	90103487	+	Missense_Mutation	SNP	T	T	C	rs7729495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	84	0	1	0	T|0.926;C|0.074	0.074	strong	.	GPR98	605	.	NM_032119	exon73	c.T14905C	p.W4969R	CCTGGTTGGCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507227	195507227	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	46	283	0	0.657143	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G11224A	p.V3742I	GGGTGACGTGACC	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36269946	36269946	+	Missense_Mutation	SNP	A	A	G	rs145856102	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	63	132	0	0.473684	0	A|0.998;G|0.002	0.002	strong	.	PNPLA1	92	.	NM_001145717	exon6	c.A1084G	p.T362A	TCTTCAACTCCAC	.	PASS	Atlas-SNP
FAM118A	55007	hgsc.bcm.edu	37	22	45728370	45728370	+	Missense_Mutation	SNP	G	G	A	rs6007594	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	107	260	2	0.479821	0.00769231	G|0.536;A|0.464	0.464	strong	FAM118A,NS,carcinoma,0,1	FAM118A	32	1	NM_017911	exon6	c.G716A	p.R239H	CCCTTCGTGATCA	.	scavenged	Atlas-SNP
PRSS45	377047	hgsc.bcm.edu	37	3	46783959	46783959	+	Missense_Mutation	SNP	T	T	C	rs58830807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	440	214	446	0	0.486364	0	T|0.801;C|0.199	0.199	strong	.	PRSS45	12	.	NM_199183	exon4	c.A568G	p.I190V	TGGTGATGCGGGT	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	124	184	0	0.525424	0	A|0.536;G|0.464	0.464	strong	FMO2,NS,carcinoma,0,2	FMO2	66	2	NM_001460	exon5	c.A585G	p.S195S	AAACTCAGGCTCA	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112437438	112437438	+	Silent	SNP	T	T	G	rs62374708	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	29	60	0	0.527273	0	T|0.933;G|0.067	0.067	strong	MCC_ENST00000408903,NS,carcinoma,+1,2	MCC	234	2	NM_001085377	exon8	c.A1396C	p.R466R	TCACCCTCCTCCG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76547634	76547634	+	Missense_Mutation	SNP	T	T	C	rs16971526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	64	163	0	0.418301	0	T|0.904;C|0.096	0.096	strong	.	DNAH17	347	.	NM_173628	exon16	c.A2374G	p.I792V	GGGAAATTCCTTC	.	PASS	Atlas-SNP
MIA2	117153	hgsc.bcm.edu	37	14	39703324	39703324	+	Silent	SNP	A	A	G	rs7141840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	117	0	1	0	A|0.389;G|0.611	0.611	strong	.	MIA2	82	.	NM_054024	exon1	c.A6G	p.A2A	CATGGCAAAATTT	.	PASS	Atlas-SNP
BRAF	673	hgsc.bcm.edu	37	7	140481425	140481425	+	Silent	SNP	T	T	C	rs56216404	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	59	103	0	0.526786	0	T|0.995;C|0.005	0.005	strong	.	BRAF	36346	.	NM_004333	exon11	c.A1383G	p.Q461Q	AATTCTTTGTCCC	.	PASS	Atlas-SNP
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201866	32201866	+	Missense_Mutation	SNP	A	A	G	rs9982755	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	117	253	1	0.471774	0.00395257	A|0.480;G|0.520	0.520	strong	.	.	.	.	NM_181606	exon2	c.T151C	p.S51P	CCAGGGAGCTGTA	.	PASS	Atlas-SNP
NPL	80896	hgsc.bcm.edu	37	1	182787797	182787797	+	Silent	SNP	G	G	A	rs58343016	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	30	59	0	0.5	0	G|0.983;A|0.017	0.017	strong	.	NPL	55	.	NM_001200052	exon9	c.G579A	p.Q193Q	GCAACAGTTTGCT	.	PASS	Atlas-SNP
DGUOK	1716	hgsc.bcm.edu	37	2	74174013	74174013	+	Silent	SNP	G	G	A	rs1804599	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	64	0	0.542857	0	G|0.986;A|0.014	0.014	strong	.	DGUOK	16	.	NM_080918	exon3	c.G423A	p.E141E	CTTTGAGAGGTCT	.	PASS	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	37	4	148594177	148594177	+	Missense_Mutation	SNP	C	C	T	rs73853975	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	77	114	0	0.509934	0	C|0.946;T|0.054	0.054	strong	.	PRMT10	68	.	NM_138364	exon4	c.G676A	p.E226K	CTGCTTCCATCTT	.	PASS	Atlas-SNP
ARMC2	84071	hgsc.bcm.edu	37	6	109274527	109274527	+	Missense_Mutation	SNP	A	A	G	rs113651966	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	40	0	0.530612	0	A|0.969;G|0.031	0.031	strong	.	ARMC2	56	.	NM_032131	exon13	c.A1888G	p.I630V	CCGGGGATAGTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511690	195511690	+	Missense_Mutation	SNP	G	G	C	rs199920095	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	100	536	0	0.413223	0	G|0.945;C|0.055	0.055	strong	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.C6761G	p.T2254S	GGGGTGGTGTCAC	.	PASS	Atlas-SNP
AGAP7	653268	hgsc.bcm.edu	37	10	51465429	51465429	+	Missense_Mutation	SNP	C	C	T	rs183573385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	650	348	591	0	0.535385	0	C|0.996;T|0.004	0.004	strong	.	AGAP7	33	.	NM_001077685	exon7	c.G1027A	p.D343N	CCATGTCCTTGGA	.	PASS	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	117877	117877	+	Silent	SNP	C	C	T	rs71509933		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	170	325	0	0.487106	0	C|0.500;T|0.500	0.500	weak	.	FOXD4	75	.	NM_207305	exon1	c.G243A	p.E81E	GCCAAACTCTGAG	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78177668	78177668	+	Missense_Mutation	SNP	G	G	A	rs34822755	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	139	287	0	0.491166	0	G|0.991;A|0.009	0.009	strong	.	CARD14	98	.	NM_024110	exon16	c.G2267A	p.C756Y	AGCAGTGCACCGT	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19192332	19192332	+	Silent	SNP	G	G	T	rs56005620	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	31	74	0	0.397436	0	G|0.718;T|0.282	0.282	strong	SH2D4A,NS,carcinoma,+1,3	SH2D4A	49	3	NM_022071	exon4	c.G477T	p.S159S	AGGATCGAGGCCA	.	PASS	Atlas-SNP
GRIK1	2897	hgsc.bcm.edu	37	21	30925928	30925928	+	Missense_Mutation	SNP	A	A	G	rs363504	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	59	85	0	0.561905	0	T|0.000;G|0.095	0.095	strong	.	GRIK1	293	.	NM_000830	exon17	c.T2705C	p.L902S	CGAATTAATTTAC	.	PASS	Atlas-SNP
USP24	23358	hgsc.bcm.edu	37	1	55545240	55545240	+	Missense_Mutation	SNP	T	T	C	rs116203669	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	81	0	0.460674	0	T|0.996;C|0.004	0.004	strong	.	USP24	323	.	NM_015306	exon60	c.A7171G	p.M2391V	CAGACATGAACAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9071916	9071916	+	Missense_Mutation	SNP	G	G	A	rs35346115	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	85	164	0	0.502959	0	G|0.980;A|0.020	0.020	strong	.	MUC16	4315	.	NM_024690	exon3	c.C15530T	p.T5177I	TTTGTAGTCTCAG	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	650371	650371	+	Silent	SNP	C	C	T	rs61735317	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	66	100	0	0.559322	0	C|0.978;T|0.022	0.022	strong	.	GEMIN4	116	.	NM_015721	exon2	c.G912A	p.S304S	GGCCAGCGAGGTC	.	PASS	Atlas-SNP
C1orf61	10485	hgsc.bcm.edu	37	1	156377720	156377720	+	Silent	SNP	G	G	A	rs141938076	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	53	106	0	0.427419	0	G|0.998;A|0.002	0.002	strong	.	C1orf61	15	.	NM_006365	exon5	c.C219T	p.S73S	CCTGGTGGAGATT	.	PASS	Atlas-SNP
ABCA12	26154	hgsc.bcm.edu	37	2	215851303	215851303	+	Silent	SNP	A	A	G	rs34351934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	85	0	0.551282	0	A|0.807;G|0.193	0.193	strong	ABCA12,NS,carcinoma,+2,1	ABCA12	368	1	NM_173076	exon28	c.T4126C	p.L1376L	CCAGCAATGAAGT	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	814058	814058	+	Missense_Mutation	SNP	C	C	T	rs9927389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	16	50	1	0.5	0.02	C|0.941;T|0.059	0.059	strong	MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	NM_005823	exon6	c.C215T	p.A72V	CGTGTGCGGAGGT	.	scavenged	Atlas-SNP
LSM4	25804	hgsc.bcm.edu	37	19	18420501	18420501	+	Silent	SNP	G	G	A	rs148380214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	26	17	0	0.742857	0	G|0.997;A|0.003	0.003	strong	.	LSM4	15	.	NM_012321	exon4	c.C315T	p.G105G	AGCGCCGCCCATG	.	PASS	Atlas-SNP
ZNF610	162963	hgsc.bcm.edu	37	19	52869278	52869278	+	Missense_Mutation	SNP	G	G	C	rs321937	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	133	220	0	0.992537	0	G|0.176;C|0.824	0.824	strong	.	ZNF610	84	.	NM_001161426	exon6	c.G647C	p.R216P	GAGTCCGTGCAAG	.	PASS	Atlas-SNP
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	44	86	1	0.586667	0.0116279	A|0.981;G|0.019	0.019	strong	RFWD3,NS,carcinoma,0,1	RFWD3	49	1	NM_018124	exon10	c.T1735C	p.L579L	CTACTAACTCCTG	.	scavenged	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101090924	101090924	+	Missense_Mutation	SNP	T	T	A	rs116197973	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	73	145	0	0.462025	0	T|0.988;A|0.012	0.012	strong	.	SENP7	170	.	NM_020654	exon7	c.A724T	p.T242S	GCGCAGTCTGCTT	.	PASS	Atlas-SNP
PRSS38	339501	hgsc.bcm.edu	37	1	228003879	228003879	+	Silent	SNP	C	C	T	rs112241411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	131	190	0	0.515748	0	C|0.982;T|0.018	0.018	strong	PRSS38,colon,carcinoma,0,1	PRSS38	55	1	NM_183062	exon2	c.C237T	p.Y79Y	GCACTACGCAGGC	.	PASS	Atlas-SNP
CRYBB2	1415	hgsc.bcm.edu	37	22	25627604	25627604	+	Silent	SNP	G	G	A	rs8140949	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	95	168	0	0.530726	0	G|0.756;A|0.244	0.244	strong	.	CRYBB2	18	.	NM_000496	exon6	c.G483A	p.G161G	CCGTGGGCTGCAG	.	PASS	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	37	19	56321517	56321517	+	Silent	SNP	T	T	C	rs7249635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	148	0	1	0	T|0.849;C|0.151	0.151	strong	.	NLRP11	139	.	NM_145007	exon5	c.A459G	p.G153G	TCTCTCTCCCATC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	Silent	SNP	G	G	A	rs16824585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	60	112	0	0.465116	0	G|0.764;A|0.236	0.236	strong	.	KIAA1751	92	.	NM_001080484	exon13	c.C1462T	p.L488L	GCTCCAGGATGTC	.	PASS	Atlas-SNP
KHDC1	80759	hgsc.bcm.edu	37	6	74019376	74019376	+	Missense_Mutation	SNP	T	T	C	rs16883573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	78	0	0.527027	0	T|0.846;C|0.154	0.154	strong	.	KHDC1	10	.	NM_001251874	exon1	c.A62G	p.Y21C	ACTCCGTATTCTG	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	259	217	0	1	0	A|0.859;G|0.141	0.141	strong	.	TMEM232	57	.	NM_001039763	exon7	c.T747C	p.Y249Y	GTTCTCATATCTT	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28908178	28908178	+	Missense_Mutation	SNP	G	G	C	rs74368609	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	56	81	0	0.538462	0	G|0.992;C|0.008	0.008	strong	.	DSG1	176	.	NM_001942	exon4	c.G243C	p.Q81H	AAACCAGCAAGTT	.	PASS	Atlas-SNP
KRTAP4-2	85291	hgsc.bcm.edu	37	17	39334314	39334314	+	Missense_Mutation	SNP	A	A	T	rs200720939		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	26	179	0	0.105691	0	.	.	weak	KRTAP4-2_ENST00000458321,NS,haematopoietic_neoplasm,0,4	KRTAP4-2	93	4	NM_033062	exon1	c.T103A	p.C35S	GGCAGCAGGTGGT	.	scavenged	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371136	58371136	+	Silent	SNP	G	G	C	rs61747108	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	80	263	0	0.414508	0	G|0.742;C|0.258	0.258	strong	.	ZNF587	53	.	NM_032828	exon3	c.G1356C	p.L452L	TCTTCTGGTTCAT	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	24	45	0	0.387097	0	C|0.689;T|0.311	0.311	strong	PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	NM_001134316	exon3	c.G546A	p.P182P	TGGCAGCGGGGCC	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049916	69049916	+	Missense_Mutation	SNP	G	G	A	rs61734450	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	31	69	0	0.455882	0	G|0.998;A|0.002	0.002	strong	ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	NM_001007231	exon10	c.G1645A	p.E549K	GGAGAAGAGGAAA	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552942	43552942	+	Silent	SNP	G	G	A	rs71373588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	131	247	1	0.466192	0.00404858	G|0.993;A|0.007	0.007	strong	.	PLEKHM1	69	.	NM_014798	exon4	c.C447T	p.Y149Y	GGGCTGGTAGTAC	.	PASS	Atlas-SNP
KIAA1456	57604	hgsc.bcm.edu	37	8	12879198	12879198	+	Missense_Mutation	SNP	A	A	T	rs34995506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	45	76	0	0.6	0	A|0.832;T|0.168	0.168	strong	.	KIAA1456	20	.	NM_020844	exon5	c.A1010T	p.H337L	GAGACCATCAAGG	.	PASS	Atlas-SNP
C20orf27	54976	hgsc.bcm.edu	37	20	3736160	3736160	+	Missense_Mutation	SNP	G	G	A	rs140915844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	27	48	0	0.415385	0	G|0.999;A|0.001	0.001	strong	.	C20orf27	17	.	NM_001039140	exon4	c.C332T	p.P111L	AGGCTGGGGACAG	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119466025	119466025	+	Missense_Mutation	SNP	G	G	A	rs9853426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	75	134	0	0.513699	0	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_033364	exon15	c.G1966A	p.A656T	ACCGAAGCGAATA	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72517830	72517830	+	Missense_Mutation	SNP	G	G	A	rs10999516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	30	85	0	0.352941	0	G|0.824;A|0.176	0.176	strong	.	ADAMTS14	148	.	NM_139155	exon20	c.G3059A	p.S1020N	TCTGCAGCCTGCC	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4721376	4721376	+	Missense_Mutation	SNP	A	A	G	rs17854914	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	48	90	0	0.527473	0	A|0.896;G|0.104	0.104	strong	PLD2,NS,carcinoma,0,1	PLD2	138	1	NM_001243108	exon18	c.A1895G	p.E632G	TCAGGGAGAGCCA	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57797414	57797414	+	Missense_Mutation	SNP	C	C	T	rs3796529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	54	87	0	0.453782	0	C|0.784;T|0.216	0.216	strong	REST,NS,carcinoma,0,1	REST	104	1	NM_001193508	exon4	c.C2390T	p.P797L	GGGAGCCACCTCC	.	PASS	Atlas-SNP
MFSD8	256471	hgsc.bcm.edu	37	4	128842761	128842761	+	Missense_Mutation	SNP	G	G	A	rs3733319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	110	208	1	0.497738	0.00480769	G|0.894;A|0.106	0.106	strong	.	MFSD8	46	.	NM_152778	exon12	c.C1268T	p.A423V	AGCACAGCTGATG	.	PASS	Atlas-SNP
KIAA0319L	79932	hgsc.bcm.edu	37	1	35919979	35919979	+	Silent	SNP	A	A	G	rs10796920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	80	145	0	0.484848	0	A|0.959;G|0.041	0.041	strong	.	KIAA0319L	156	.	NM_024874	exon11	c.T1764C	p.T588T	AATAACAGTCACT	.	PASS	Atlas-SNP
TEX13A	56157	hgsc.bcm.edu	37	X	104464674	104464674	+	Silent	SNP	G	G	A	rs183606927	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	25	71	0	0.3125	0	G|0.992;A|0.008	0.008	strong	.	TEX13A	55	.	NM_031274	exon2	c.C408T	p.L136L	CTCCACGAGGCTG	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157098756	157098756	+	Missense_Mutation	SNP	G	G	T	rs11740603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	209	184	0	0.985849	0	G|0.814;T|0.186	0.186	strong	.	C5orf52	17	.	NM_001145132	exon1	c.G134T	p.R45L	GCCGCCGCCCAGA	.	PASS	Atlas-SNP
PIF1	80119	hgsc.bcm.edu	37	15	65112116	65112116	+	Silent	SNP	C	C	T	rs145376177	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	45	71	0	0.5	0	C|1.000;T|0.000	0.000	weak	.	PIF1	43	.	NM_025049	exon8	c.G1263A	p.V421V	CGTGGCCACAATC	.	PASS	Atlas-SNP
IGFALS	3483	hgsc.bcm.edu	37	16	1842454	1842454	+	Missense_Mutation	SNP	G	G	A	rs34680334	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	9	11	0	0.692308	0	G|0.947;A|0.053	0.053	strong	.	IGFALS	29	.	NM_001146006	exon2	c.C79T	p.H27Y	CCGAGTGAGCCTG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65622463	65622463	+	Missense_Mutation	SNP	A	A	G	rs9294631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	283	246	1	1	0.00406504	A|0.375;G|0.625	0.625	strong	.	EYS	527	.	NM_001142800	exon16	c.T2555C	p.L852P	TCACAAAGGTTAT	.	PASS	Atlas-SNP
C5AR2	27202	hgsc.bcm.edu	37	19	47844899	47844899	+	Silent	SNP	C	C	T	rs34085015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	48	107	0	0.55814	0	C|0.992;T|0.008	0.008	strong	.	.	.	.	NM_001271750	exon2	c.C843T	p.L281L	TGCCCTCGCTCAC	.	PASS	Atlas-SNP
AES	166	hgsc.bcm.edu	37	19	3062857	3062857	+	Silent	SNP	T	T	C	rs11539938	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	48	56	0	0.539326	0	T|0.607;C|0.393	0.393	strong	.	AES	14	.	NM_198969	exon1	c.A69G	p.L23L	GAGCCTTAGTTTC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17087474	17087474	+	Missense_Mutation	SNP	C	C	T	rs71193817		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	868	93	684	0	0.107143	0	C|0.500;T|0.500	0.500	weak	.	.	.	.	NM_001271733	exon2	c.G191A	p.R64H	CCACAGCGACCAG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249471	71249471	+	Missense_Mutation	SNP	A	A	T	rs112605265		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	12	173	2	0.0497925	0.0115607	A|0.500;T|0.500	0.500	weak	KRTAP5-8,extremity,malignant_melanoma,0,1	KRTAP5-8	28	1	NM_021046	exon1	c.A370T	p.S124C	CCCTGCAGCTGCT	.	scavenged	Atlas-SNP
KRT31	3881	hgsc.bcm.edu	37	17	39551533	39551533	+	Silent	SNP	G	G	A	rs6503626	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	101	236	0	0.480952	0	G|0.988;A|0.012	0.012	strong	.	KRT31	158	.	NM_002277	exon5	c.C840T	p.N280N	CAGGGCGTTGACT	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71235647	71235647	+	Missense_Mutation	SNP	C	C	T	rs16869301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	41	96	0	0.414141	0	C|0.974;T|0.026	0.026	strong	.	FAM135A	181	.	NM_001162529	exon13	c.C2860T	p.P954S	CAGAGTCCTGATA	.	PASS	Atlas-SNP
C9	735	hgsc.bcm.edu	37	5	39364554	39364554	+	Missense_Mutation	SNP	G	G	A	rs700233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	10	37	0	0.384615	0	G|0.675;A|0.325	0.325	strong	.	C9	116	.	NM_001737	exon1	c.C13T	p.R5W	AGCTCCGGCAGGC	.	PASS	Atlas-SNP
TPSD1	23430	hgsc.bcm.edu	37	16	1306671	1306671	+	Silent	SNP	G	G	A	rs71384641		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	97	172	0	0.535912	0	G|1.000;|0.000	.	weak	.	TPSD1	47	.	NM_012217	exon2	c.G237A	p.A79A	AACCGCGGCGCAC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376226	52376226	+	Silent	SNP	C	C	T	rs9807840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	38	76	0	0.527778	0	C|0.891;T|0.109	0.109	strong	.	ZNF577	63	.	NM_032679	exon7	c.G1017A	p.S339S	GAGCTTCGACTTG	.	PASS	Atlas-SNP
GPR137	56834	hgsc.bcm.edu	37	11	64051853	64051853	+	Silent	SNP	G	G	A	rs75052600	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	26	38	0	0.541667	0	G|0.986;A|0.014	0.014	strong	.	GPR137	52	.	NM_001170726	exon1	c.G15A	p.V5V	GGCTGTGAGGACA	.	PASS	Atlas-SNP
FAM159A	348378	hgsc.bcm.edu	37	1	53099242	53099242	+	Missense_Mutation	SNP	G	G	A	rs182623287	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	23	41	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	FAM159A	22	.	NM_001042693	exon1	c.G77A	p.G26D	CGGGGGGCGAGGC	.	PASS	Atlas-SNP
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	115	0	1	0	G|0.714;A|0.286	0.286	strong	ITGA6,NS,NS,-1,1	ITGA6	171	1	NM_001079818	exon7	c.G1138A	p.A380T	GGCATTGCAGTAA	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38825329	38825329	+	Silent	SNP	C	C	T	rs2061907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	75	141	1	0.454545	0.0070922	C|0.559;T|0.441	0.441	strong	DNAH8_ENST00000359357,NS,carcinoma,0,4	DNAH8	1239	4	NM_001206927	exon42	c.C5769T	p.H1923H	GACACACGATTCA	.	scavenged	Atlas-SNP
HK2	3099	hgsc.bcm.edu	37	2	75101454	75101454	+	Silent	SNP	T	T	C	rs2229622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	300	289	1	0.996678	0.00346021	T|0.680;C|0.320	0.320	strong	.	HK2	85	.	NM_000189	exon7	c.T753C	p.D251D	AGGCGATGAGGGG	.	PASS	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	16	52	0	0.333333	0	T|0.898;C|0.102	0.102	strong	GPR146,NS,carcinoma,0,3	GPR146	20	3	NM_138445	exon1	c.T243C	p.P81P	GGCCCCTGTGCAC	.	PASS	Atlas-SNP
C15orf40	123207	hgsc.bcm.edu	37	15	83673653	83673653	+	Silent	SNP	A	A	C	rs74028206	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	53	122	0	0.524752	0	A|0.985;C|0.015	0.015	strong	.	C15orf40	18	.	NM_001160114	exon4	c.T438G	p.V146V	GCATTCAACAAGT	.	PASS	Atlas-SNP
SNX21	90203	hgsc.bcm.edu	37	20	44469290	44469290	+	Missense_Mutation	SNP	G	G	A	rs4638862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	44	118	0	0.407407	0	G|0.611;A|0.389	0.389	strong	.	SNX21	23	.	NM_033421	exon4	c.G460A	p.A154T	ACCCTCGCCGTGA	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39521752	39521752	+	Silent	SNP	G	G	A	rs61741664	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	100	168	0	0.5	0	G|0.981;A|0.019	0.019	strong	.	KRT33B	46	.	NM_002279	exon4	c.C642T	p.D214D	AGCAGCGTCCACC	.	PASS	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172766822	172766822	+	Silent	SNP	G	G	A	rs508508	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	70	97	0	0.588235	0	G|0.824;A|0.176	0.176	strong	SPATA16,NS,haematopoietic_neoplasm,-1,2	SPATA16	111	2	NM_031955	exon3	c.C675T	p.S225S	TGCCACGCTTGCT	.	PASS	Atlas-SNP
TMEM255B	348013	hgsc.bcm.edu	37	13	114507956	114507956	+	Silent	SNP	G	G	A	rs56032548	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	29	54	0	0.483333	0	G|0.922;A|0.078	0.078	strong	.	.	.	.	NM_182614	exon8	c.G768A	p.T256T	CCTGACGCCCGAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152282113	152282113	+	Missense_Mutation	SNP	G	G	A	rs3120647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	467	464	464	3	0.993576	0.00646552	G|0.884;A|0.116	0.116	strong	.	FLG	900	.	NM_002016	exon3	c.C5249T	p.S1750F	CGTGTGGACTCTT	.	PASS	Atlas-SNP
HUS1	3364	hgsc.bcm.edu	37	7	48008869	48008869	+	Missense_Mutation	SNP	G	G	C	rs138848570	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	21	51	0	0.396226	0	G|0.996;C|0.004	0.004	strong	.	HUS1	36	.	NM_004507	exon6	c.C587G	p.T196S	AATTCAGTTTCTA	.	PASS	Atlas-SNP
IGSF11	152404	hgsc.bcm.edu	37	3	118621664	118621664	+	Missense_Mutation	SNP	C	C	A	rs36052974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	95	216	0	0.487179	0	C|0.777;A|0.223	0.223	strong	.	IGSF11	122	.	NM_001015887	exon7	c.G999T	p.E333D	GACTGACTCTGTG	.	PASS	Atlas-SNP
OR5D18	219438	hgsc.bcm.edu	37	11	55587591	55587591	+	Silent	SNP	C	C	T	rs142792552	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	163	309	1	0.472464	0.00323625	C|0.997;T|0.003	0.003	strong	.	OR5D18	121	.	NM_001001952	exon1	c.C486T	p.C162C	GACGTGCTCTGCT	.	PASS	Atlas-SNP
ACSBG1	23205	hgsc.bcm.edu	37	15	78466006	78466006	+	Missense_Mutation	SNP	G	G	A	rs11072735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	44	102	1	0.407407	0.00980392	G|0.954;A|0.046	0.046	strong	ACSBG1,mouth,carcinoma,+1,1	ACSBG1	79	1	NM_015162	exon13	c.C2018T	p.A673V	CGGGCCGCCGCGT	.	scavenged	Atlas-SNP
VPS33B	26276	hgsc.bcm.edu	37	15	91550232	91550232	+	Silent	SNP	G	G	A	rs59648701	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	32	14	0	0.969697	0	G|0.978;A|0.022	0.022	strong	.	VPS33B	42	.	NM_018668	exon9	c.C648T	p.G216G	GGTTTCGCCATCC	.	PASS	Atlas-SNP
PAPSS1	9061	hgsc.bcm.edu	37	4	108574677	108574677	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	4	194	0	0.0193237	0	.	.	none	PAPSS1,NS,carcinoma,+1,1	PAPSS1	57	1	NM_005443	exon9	c.C1207A	p.L403I	GCTTTAGCTCAGT	.	scavenged	Atlas-SNP
MYBPC1	4604	hgsc.bcm.edu	37	12	102036305	102036305	+	Silent	SNP	C	C	T	rs2293468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	64	0	0.48	0	C|0.704;T|0.296	0.296	strong	.	MYBPC1	235	.	NM_206819	exon11	c.C774T	p.D258D	CACCGACCTGCGC	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	rs9877201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	36	73	0	0.423529	0	C|0.879;T|0.121	0.121	strong	LRIG1,NS,carcinoma,0,1	LRIG1	138	1	NM_015541	exon18	c.G2776A	p.G926S	GGCCACCGTGTTC	.	PASS	Atlas-SNP
KIAA1328	57536	hgsc.bcm.edu	37	18	34647176	34647176	+	Silent	SNP	T	T	C	rs3747895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	173	171	0	0.994253	0	T|0.749;C|0.251	0.251	strong	.	KIAA1328	39	.	NM_020776	exon7	c.T900C	p.P300P	TAAGCCTACTCCT	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55578987	55578987	+	Silent	SNP	T	T	C	rs67727364	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	63	114	1	0.557522	0.00877193	T|0.898;C|0.102	0.102	strong	OR5L1,NS,carcinoma,0,1	OR5L1	145	1	NM_001004738	exon1	c.T45C	p.L15L	TCTCCTTGGACTA	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152476028	152476028	+	Missense_Mutation	SNP	C	C	G	rs10172023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	90	181	1	0.584416	0.00552486	C|0.769;G|0.231	0.231	strong	.	NEB	1697	.	NM_001271208	exon73	c.G10809C	p.W3603C	GCAGATCCATTCA	.	PASS	Atlas-SNP
LY6G5B	58496	hgsc.bcm.edu	37	6	31639845	31639845	+	Missense_Mutation	SNP	C	C	A	rs11758242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	57	156	0	0.416058	0	C|0.932;A|0.068	0.068	strong	LY6G5B,NS,carcinoma,0,1	LY6G5B	8	1	NM_021221	exon3	c.C392A	p.S131Y	CTGACTCCCAGAT	.	PASS	Atlas-SNP
CDH13	1012	hgsc.bcm.edu	37	16	83378487	83378487	+	Silent	SNP	T	T	C	rs145120824	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	48	126	0	0.4	0	T|0.996;C|0.004	0.004	strong	.	CDH13	97	.	NM_001220488	exon7	c.T798C	p.D266D	CACTGATGTCAAT	.	PASS	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	89	180	0	0.475936	0	T|0.680;C|0.320	0.320	strong	ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	NM_147195	exon9	c.A1451G	p.N484S	AAGGTATTGAACT	.	PASS	Atlas-SNP
TFDP1	7027	hgsc.bcm.edu	37	13	114265331	114265331	+	Silent	SNP	C	C	T	rs4150731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	94	186	0	0.497355	0	C|0.975;T|0.025	0.025	strong	.	TFDP1	70	.	NM_007111	exon3	c.C33T	p.N11N	AGCCAACGGAGAA	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43243217	43243217	+	Missense_Mutation	SNP	A	A	G	rs34721205	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	214	287	0	0.986175	0	.	.	alt	PSG3,NS,carcinoma,-1,1	PSG3	82	1	NM_021016	exon2	c.T89C	p.L30S	GTAGGCAAGTTCC	.	PASS	Atlas-SNP
VASN	114990	hgsc.bcm.edu	37	16	4431880	4431880	+	Silent	SNP	C	C	T	rs13333950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	31	45	0	0.534483	0	C|0.962;T|0.038	0.038	strong	.	VASN	21	.	NM_138440	exon2	c.C1002T	p.N334N	CAAGAACGCTGGC	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3421897	3421897	+	Missense_Mutation	SNP	A	A	G	rs2821008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	70	148	0	0.463576	0	A|0.775;G|0.225	0.225	strong	.	MEGF6	91	.	NM_001409	exon17	c.T2063C	p.L688P	TAGCCCAGCTCAC	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36486004	36486004	+	Missense_Mutation	SNP	T	T	C	rs55727040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	106	0	1	0	T|0.897;C|0.103	0.103	strong	.	GPR179	170	.	NM_001004334	exon11	c.A3448G	p.K1150E	ACTCCTTGTCATC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906364	129906364	+	Missense_Mutation	SNP	G	G	A	rs4750685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	121	289	2	0.444853	0.00692042	G|0.915;A|0.085	0.085	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.C3740T	p.T1247I	ATTTTAGTGGTTT	.	scavenged	Atlas-SNP
UQCRH	7388	hgsc.bcm.edu	37	1	46775856	46775856	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	100	182	0	0.518135	0	.	.	none	.	UQCRH	4	.	NM_006004	exon3	c.C111A	p.C37X	GCAATGCGAGCAG	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94937446	94937446	+	Missense_Mutation	SNP	T	T	C	rs662	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	52	101	0	0.485981	0	T|0.544;C|0.456	0.456	strong	PON1,NS,carcinoma,0,1	PON1	55	1	NM_000446	exon6	c.A575G	p.Q192R	CAGGATTGTAAGT	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43970602	43970602	+	Silent	SNP	G	G	C	rs117880737	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	7	13	0	0.466667	0	G|0.957;C|0.043	0.043	strong	.	C6orf223	14	.	NM_153246	exon4	c.G468C	p.P156P	GAGCCCGGGACAG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	8	159	2	0.0490798	0.0125786	.	.	none	MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	NM_002457	exon30	c.C4709T	p.T1570I	CGGTGACCCCAAC	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149509419	149509419	+	Missense_Mutation	SNP	C	C	T	rs740109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	10	25	0	0.4	0	C|0.776;T|0.224	0.224	strong	.	.	.	.	NM_198455	exon69	c.C9817T	p.R3273W	GGCCTGCGGAGCC	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808292	18808292	+	Missense_Mutation	SNP	C	C	A	rs2992753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	91	0	1	0	C|0.325;A|0.675	0.675	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.C817A	p.H273N	GAGGAGCATTTCA	.	PASS	Atlas-SNP
HMOX1	3162	hgsc.bcm.edu	37	22	35777185	35777185	+	Missense_Mutation	SNP	G	G	C	rs2071747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	8	4	0	0.421053	0	G|0.952;C|0.048	0.048	strong	.	HMOX1	32	.	NM_002133	exon1	c.G19C	p.D7H	CAACCCGACAGGC	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764731	17764731	+	Silent	SNP	G	G	C	rs6459569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	152	144	0	1	0	G|0.857;C|0.143	0.143	strong	.	KIF13A	276	.	NM_022113	exon39	c.C5028G	p.A1676A	CCCTTTGGCTAAG	.	PASS	Atlas-SNP
ARL5C	390790	hgsc.bcm.edu	37	17	37319103	37319103	+	Missense_Mutation	SNP	T	T	C	rs657723	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	39	79	0	0.506494	0	T|0.644;C|0.356	0.356	strong	.	ARL5C	3	.	NM_001143968	exon3	c.A116G	p.N39S	ACCTCATTGGTCA	.	PASS	Atlas-SNP
GGTLC1	92086	hgsc.bcm.edu	37	20	23966316	23966316	+	Silent	SNP	T	T	C	rs111546926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	73	0	0.517241	0	T|0.937;C|0.063	0.063	strong	.	GGTLC1	37	.	NM_178311	exon5	c.A519G	p.R173R	AATGTTTCTCTCC	.	PASS	Atlas-SNP
GIMAP8	155038	hgsc.bcm.edu	37	7	150164189	150164189	+	Silent	SNP	C	C	A	rs143212982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	104	180	0	0.517413	0	A|0.002;C|0.998;G|0.001	0.002	strong	GIMAP8,NS,carcinoma,-1,1	GIMAP8	136	1	NM_175571	exon2	c.C403A	p.R135R	TTCACTCGGAAGG	.	PASS	Atlas-SNP
BACE1	23621	hgsc.bcm.edu	37	11	117163824	117163824	+	Silent	SNP	C	C	G	rs638405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	66	161	0	0.578947	0	C|0.533;G|0.467	0.467	strong	.	BACE1	33	.	NM_012104	exon5	c.G786C	p.V262V	AATGATCACCTCA	.	PASS	Atlas-SNP
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	47	99	0	0.47	0	T|0.000;G|0.355;C|0.645	0.355	strong	TRPV2,NS,carcinoma,0,1	TRPV2	74	1	NM_016113	exon13	c.C2094G	p.P698P	CAGCCCCGATGAG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	rs34500739	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	71	100	0	0.550388	0	T|0.949;G|0.051	0.051	strong	.	PCNT	283	.	NM_006031	exon4	c.T711G	p.H237Q	CCTGCATCAGAGT	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120589064	120589064	+	Silent	SNP	G	G	C	rs2286045	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	54	108	0	0.495413	0	G|0.685;C|0.315	0.315	strong	GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	NM_006836	exon34	c.C4194G	p.A1398A	GCCATAGGCGGCC	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170070348	170070348	+	Silent	SNP	T	T	C	rs11886219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	67	144	0	0.482014	0	T|0.827;C|0.173	0.173	strong	.	LRP2	751	.	NM_004525	exon36	c.A5859G	p.R1953R	GATCATTCGATCT	.	PASS	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826003	125826003	+	Missense_Mutation	SNP	T	T	C	rs4646750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	60	0	0.490909	0	T|0.919;C|0.081	0.081	strong	.	ALDH1L1	138	.	NM_001270364	exon21	c.A2464G	p.I822V	GAGAGATGATCAT	.	PASS	Atlas-SNP
PPP3CA	5530	hgsc.bcm.edu	37	4	102117083	102117083	+	Silent	SNP	C	C	T	rs3730251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	42	125	0	0.442105	0	C|0.936;T|0.064	0.064	strong	PPP3CA,NS,carcinoma,-1,1	PPP3CA	51	1	NM_000944	exon2	c.G249A	p.A83A	GACTGGCGCATCA	.	PASS	Atlas-SNP
KRTAP19-4	337971	hgsc.bcm.edu	37	21	31869286	31869286	+	Missense_Mutation	SNP	T	T	C	rs2298437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	56	115	0	0.470588	0	T|0.392;C|0.608	0.608	strong	KRTAP19-4,uveal_tract,malignant_melanoma,+1,1	KRTAP19-4	22	1	NM_181610	exon1	c.A143G	p.Y48C	CGGCAGTAGCCAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508692	195508692	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	74	154	1	0.643478	0.00649351	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9759G	p.D3253E	GGAAGTGTCGGTG	.	scavenged	Atlas-SNP
STK10	6793	hgsc.bcm.edu	37	5	171533629	171533629	+	Silent	SNP	A	A	G	rs2306963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	66	114	0	0.540984	0	A|0.272;G|0.728	0.728	strong	.	STK10	100	.	NM_005990	exon6	c.T783C	p.S261S	CCACTTAGAGGGC	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744777	54744777	+	Silent	SNP	C	C	T	rs76127474		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	477	65	396	0	0.136268	0	.	.	weak	.	LILRA6	75	.	NM_024318	exon5	c.G885A	p.R295R	ATAGCACCTGTAC	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652993	38652993	+	Silent	SNP	C	C	T	rs332864	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	115	233	2	0.529954	0.00858369	C|0.679;T|0.321	0.321	strong	SIPA1L3,NS,adenoma,0,1	SIPA1L3	150	1	NM_015073	exon14	c.C3762T	p.S1254S	AGATTCCCCCAAC	.	scavenged	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42232475	42232475	+	Silent	SNP	G	G	A	rs2295274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	110	102	0	0.990991	0	G|0.848;A|0.152	0.152	strong	.	TRERF1	124	.	NM_033502	exon7	c.C1602T	p.H534H	TCCCCCGTGGGAC	.	PASS	Atlas-SNP
HHLA3	11147	hgsc.bcm.edu	37	1	70820802	70820802	+	Silent	SNP	G	G	A	rs17131261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	50	87	0	0.515464	0	G|0.971;A|0.029	0.029	strong	.	HHLA3	11	.	NM_001036645	exon1	c.G168A	p.K56K	TACGAAGCTAGCA	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109377070	109377070	+	Missense_Mutation	SNP	C	C	A	rs12060255	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	18	55	0	0.418605	0	C|0.870;A|0.130	0.130	strong	.	AKNAD1	83	.	NM_152763	exon9	c.G1745T	p.G582V	ATTACCCCAGAGT	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43576029	43576029	+	Missense_Mutation	SNP	C	C	T	rs112235686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	89	194	0	0.45641	0	C|0.998;T|0.002	0.002	strong	PSG2,colon,carcinoma,+1,2	PSG2	84	2	NM_031246	exon4	c.G787A	p.A263T	AGTTCGCGAAGCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678527	100678527	+	Missense_Mutation	SNP	G	G	T	rs73402889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	36	120	0	0.235294	0	G|0.918;T|0.082	0.082	strong	MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	NM_001040105	exon3	c.G3830T	p.S1277I	AAGGAAGTACTCT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016960	1016960	+	Silent	SNP	G	G	T	rs113980831	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1031	130	918	5	0.126091	0.00544662	G|0.500;T|0.500	0.500	weak	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.C5841A	p.T1947T	GGTTCTGGTGCCT	.	scavenged	Atlas-SNP
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	63	102	0	0.5625	0	T|0.959;C|0.041	0.041	strong	.	TRPC4	389	.	NM_003306	exon11	c.A2943G	p.R981R	TCACAATCTTGTG	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581889	84581889	+	Silent	SNP	G	G	A	rs12439867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	144	0	1	0	G|0.688;A|0.312	0.312	strong	.	ADAMTSL3	290	.	NM_207517	exon16	c.G1746A	p.P582P	TGGGCCGGGTGTG	.	PASS	Atlas-SNP
TEX33	339669	hgsc.bcm.edu	37	22	37397876	37397876	+	Splice_Site	SNP	A	A	G	rs148258673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	44	107	0	0.435644	0	A|0.997;G|0.003	0.003	strong	.	TEX33	25	.	NM_001163857	exon4	c.489+2T>C	.	TATGACACCTGCT	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114182353	114182353	+	Silent	SNP	C	C	T	rs16916080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	36	70	0	0.62069	0	C|0.908;T|0.092	0.092	strong	KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	NM_001080398	exon17	c.G2037A	p.V679V	GGGAAACACCGTA	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90281381	90281381	+	Silent	SNP	T	T	C	rs35017767	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	90	151	0	0.588235	0	T|0.955;C|0.045	0.045	strong	.	WDR93	63	.	NM_020212	exon16	c.T1875C	p.C625C	AAATTGTACCATT	.	PASS	Atlas-SNP
MRPS11	64963	hgsc.bcm.edu	37	15	89011226	89011226	+	Missense_Mutation	SNP	G	G	C	rs16941907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	79	188	0	0.456647	0	G|0.980;C|0.020	0.020	strong	.	MRPS11	14	.	NM_176805	exon2	c.G153C	p.Q51H	TGAACAGAACGCG	.	PASS	Atlas-SNP
ND6	0	hgsc.bcm.edu	37	MT	14178	14178	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	16	17	0	1	0	.	.	none	.	.	.	.	ENST00000361681	exon1	c.A496G	p.I166V	TTACAATATATAC	.	PASS	Atlas-SNP
KRBA2	124751	hgsc.bcm.edu	37	17	8273654	8273654	+	Missense_Mutation	SNP	G	G	A	rs74532943	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	65	158	0	0.532787	0	G|0.969;A|0.031	0.031	strong	.	KRBA2	34	.	NM_213597	exon2	c.C277T	p.P93S	CCCCAGGTGGATC	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433333	169433333	+	Silent	SNP	C	C	T	rs7673220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	92	0	1	0	C|0.724;T|0.276	0.276	strong	.	PALLD	179	.	NM_001166108	exon2	c.C678T	p.D226D	GGAAGACCAAGGG	.	PASS	Atlas-SNP
HRASLS5	117245	hgsc.bcm.edu	37	11	63256441	63256441	+	Missense_Mutation	SNP	C	C	G	rs940611	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	89	198	0	0.508571	0	C|0.786;G|0.214	0.214	strong	.	HRASLS5	28	.	NM_001146728	exon3	c.G277C	p.A93P	CTACAGCCTTCTC	.	PASS	Atlas-SNP
SPATA6L	55064	hgsc.bcm.edu	37	9	4625546	4625546	+	Silent	SNP	C	C	T	rs12338523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	78	0	0.530612	0	C|0.994;T|0.006	0.006	strong	.	SPATA6L	3	.	NM_001039395	exon5	c.G276A	p.R92R	AGGCCTCCGTGAC	.	PASS	Atlas-SNP
FAM186B	84070	hgsc.bcm.edu	37	12	49993766	49993766	+	Missense_Mutation	SNP	C	C	G	rs12299908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	27	73	0	0.54	0	C|0.909;G|0.091	0.091	strong	.	FAM186B	72	.	NM_032130	exon4	c.G1657C	p.E553Q	CATCCTCCCCTAG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41877414	41877414	+	Missense_Mutation	SNP	T	T	C	rs3774372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	120	274	0	0.542986	0	T|0.818;C|0.182	0.182	strong	.	ULK4	150	.	NM_017886	exon18	c.A1706G	p.K569R	TTTAATTTGCTGT	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	328144	328144	+	Silent	SNP	G	G	A	rs35746964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	80	157	0	0.547945	0	G|0.996;A|0.004	0.004	strong	DOCK8_ENST00000453981,colon,carcinoma,0,2	DOCK8	401	2	NM_203447	exon9	c.G1017A	p.P339P	CTACCCGTCCTCA	.	PASS	Atlas-SNP
CD1B	910	hgsc.bcm.edu	37	1	158299299	158299299	+	Silent	SNP	C	C	T	rs11806249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	151	286	0	0.464615	0	C|0.984;T|0.016	0.016	strong	.	CD1B	78	.	NM_001764	exon4	c.G747A	p.Q249Q	CCCTAGCTGAGTG	.	PASS	Atlas-SNP
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661653	31661653	+	Silent	SNP	A	A	G	rs2832759	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	98	209	0	0.396761	0	A|0.846;G|0.154	0.154	strong	.	KRTAP25-1	13	.	NM_001128598	exon1	c.T156C	p.G52G	TTGATTACCATAG	.	PASS	Atlas-SNP
ZFYVE19	84936	hgsc.bcm.edu	37	15	41105979	41105979	+	Silent	SNP	C	C	G	rs116749518	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	51	90	0	0.51	0	C|0.997;G|0.003	0.003	strong	.	ZFYVE19	31	.	NM_001077268	exon9	c.C1179G	p.P393P	TCGACCCTGGACG	.	PASS	Atlas-SNP
BBS9	27241	hgsc.bcm.edu	37	7	33545253	33545253	+	Missense_Mutation	SNP	A	A	G	rs140882212	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	34	41	0	0.576271	0	A|1.000;G|0.000	0.000	strong	.	BBS9	194	.	NM_198428	exon20	c.A2294G	p.E765G	CTCAAGAATTGGT	.	PASS	Atlas-SNP
CPT1B	1375	hgsc.bcm.edu	37	22	51009953	51009953	+	Missense_Mutation	SNP	C	C	T	rs470117	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	39	36	0	1	0	C|0.649;T|0.351	0.351	strong	.	CPT1B	61	.	NM_001145135	exon14	c.G1591A	p.E531K	AACTCTCGATGAC	.	PASS	Atlas-SNP
XYLT2	64132	hgsc.bcm.edu	37	17	48434008	48434008	+	Missense_Mutation	SNP	C	C	T	rs151294421	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	9	35	0	0.428571	0	C|0.996;T|0.004	0.004	strong	.	XYLT2	51	.	NM_022167	exon8	c.C1619T	p.T540I	AGAACACCTACGA	.	PASS	Atlas-SNP
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126578	19126578	+	Silent	SNP	T	T	C	rs114869688	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	38	106	0	0.431818	0	T|0.995;C|0.005	0.005	strong	ITPRIPL2,colon,carcinoma,+1,1	ITPRIPL2	40	1	NM_001034841	exon1	c.T795C	p.T265T	GGCCACTGTGCGT	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742807	39742807	+	Missense_Mutation	SNP	C	C	T	rs3826550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	111	0	0.523364	0	C|0.705;T|0.295	0.295	strong	.	KRT14	65	.	NM_000526	exon1	c.G280A	p.A94T	AGCCAGCACCAAG	.	PASS	Atlas-SNP
VRK2	7444	hgsc.bcm.edu	37	2	58350340	58350340	+	Silent	SNP	T	T	C	rs17049354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	38	76	0	0.527778	0	T|0.962;C|0.038	0.038	strong	.	VRK2	46	.	NM_001130480	exon8	c.T648C	p.F216F	AGAGTTTACCAGC	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170143	58170143	+	Missense_Mutation	SNP	C	C	G	rs11229409	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	57	104	1	0.504425	0.00961538	C|0.674;G|0.326	0.326	strong	OR5B3,colon,carcinoma,-1,2	OR5B3	65	2	NM_001005469	exon1	c.G740C	p.G247A	AAGATGCCGACTG	.	scavenged	Atlas-SNP
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	53	76	0	0.540816	0	C|0.772;T|0.228	0.228	strong	DCPS,NS,carcinoma,+2,1	DCPS	33	1	NM_014026	exon1	c.C189T	p.F63F	CATTTTCCTACAC	.	PASS	Atlas-SNP
FGF12	2257	hgsc.bcm.edu	37	3	192078253	192078253	+	Missense_Mutation	SNP	T	T	C	rs142373936	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	92	214	0	0.431925	0	T|1.000;C|0.000	0.000	strong	.	FGF12	88	.	NM_021032	exon2	c.A274G	p.T92A	CAATGGTACCATC	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263657	263657	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	329	4	309	2	0.0121581	0.00647249	.	.	none	C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	NM_001013672	exon2	c.C1023T	p.A341A	CGAGGCCCTCAAG	.	scavenged	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241828012	241828012	+	Silent	SNP	T	T	C	rs6708304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	97	0	1	0	T|0.464;C|0.536	0.536	strong	C2orf54,colon,carcinoma,0,1	C2orf54	14	1	NM_001085437	exon4	c.A948G	p.E316E	CTGCAGTTCTGCC	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48601454	48601454	+	Silent	SNP	T	T	C	rs251684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	85	151	0	0.469613	0	T|0.337;C|0.663	0.663	strong	.	PLA2G4C	76	.	NM_001159322	exon6	c.A540G	p.P180P	AAATATTGGGTAG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491801	110491801	+	Silent	SNP	T	T	C	rs116618272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	40	89	0	0.45977	0	T|0.993;C|0.007	0.007	strong	.	PKHD1L1	522	.	NM_177531	exon54	c.T9111C	p.F3037F	TTCTTTTTGGCAA	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383351	39383351	+	Missense_Mutation	SNP	T	T	C	rs146532415	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	400	149	336	1	0.3725	0.00297619	T|0.993;C|0.007	0.007	strong	.	KRTAP9-2	24	.	NM_031961	exon1	c.T445C	p.C149R	CCAGCCTGCTGTG	.	PASS	Atlas-SNP
AADAC	13	hgsc.bcm.edu	37	3	151545601	151545601	+	Missense_Mutation	SNP	G	G	A	rs1803155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	75	0	1	0	G|0.250;A|0.750	0.750	strong	.	AADAC	49	.	NM_001086	exon5	c.G841A	p.V281I	AAATTTGTTAATT	.	PASS	Atlas-SNP
IFNAR1	3454	hgsc.bcm.edu	37	21	34715699	34715699	+	Missense_Mutation	SNP	G	G	C	rs2257167	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	47	95	0	0.419643	0	G|0.831;C|0.169	0.169	strong	.	IFNAR1	44	.	NM_000629	exon4	c.G502C	p.V168L	AGCTTAGTTATCT	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	25	59	0	0.520833	0	C|0.770;T|0.230	0.230	strong	.	COL5A3	243	.	NM_015719	exon66	c.G5071A	p.V1691I	GGGGGACGCTGAC	.	PASS	Atlas-SNP
CSF2RB	1439	hgsc.bcm.edu	37	22	37326443	37326443	+	Missense_Mutation	SNP	G	G	C	rs16845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	43	83	0	0.438776	0	G|0.901;C|0.099	0.099	strong	.	CSF2RB	104	.	NM_000395	exon7	c.G745C	p.E249Q	AACCTGGAGTGCT	.	PASS	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	37	1	38186189	38186189	+	Missense_Mutation	SNP	C	C	T	rs6671088	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	109	238	0	0.424125	0	C|0.875;T|0.125	0.125	strong	EPHA10,NS,carcinoma,0,2	EPHA10	120	2	NM_001099439	exon13	c.G2246A	p.G749E	AGCAACCCCATCA	.	PASS	Atlas-SNP
CATSPER1	117144	hgsc.bcm.edu	37	11	65787666	65787666	+	Silent	SNP	G	G	A	rs3829937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	58	131	0	0.402778	0	G|0.834;A|0.166	0.166	strong	.	CATSPER1	101	.	NM_053054	exon9	c.C2070T	p.A690A	CCGGGCGGCCCTC	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	65	0	0.460526	0	T|0.830;C|0.170	0.170	strong	.	RBM19	117	.	NM_001146699	exon15	c.A1826G	p.H609R	CCAAAATGGCCGA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158626378	158626378	+	Silent	SNP	C	C	T	rs857691	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	84	0	1	0	C|0.581;T|0.419	0.419	strong	.	SPTA1	720	.	NM_003126	exon20	c.G2874A	p.L958L	ATTCCGCAGAGCT	.	PASS	Atlas-SNP
CRYZ	1429	hgsc.bcm.edu	37	1	75175865	75175865	+	Missense_Mutation	SNP	C	C	T	rs17095822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	145	229	0	0.478548	0	C|0.979;T|0.021	0.021	strong	.	CRYZ	28	.	NM_001130043	exon6	c.G547A	p.E183K	CTTCCTCAGTACC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15794411	15794411	+	Silent	SNP	C	C	T	rs61731191	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	58	140	0	0.27619	0	C|0.985;T|0.015	0.015	strong	.	CYP4F12	89	.	NM_023944	exon7	c.C756T	p.D252D	CCATGACGGGCGG	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216298084	216298084	+	Silent	SNP	G	G	A	rs2289202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	57	152	0	0.401408	0	G|0.783;A|0.217	0.217	strong	FN1,NS,carcinoma,-2,1	FN1	521	1	NM_212476	exon3	c.C378T	p.I126I	AGCCCCGATGCAG	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21945530	21945530	+	Silent	SNP	C	C	T	rs77539762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	130	0	0.483516	0	C|0.939;T|0.061	0.061	strong	.	RAP1GAP	119	.	NM_001145658	exon5	c.G246A	p.P82P	GGGCGGCGGGAAG	.	PASS	Atlas-SNP
HELT	391723	hgsc.bcm.edu	37	4	185940196	185940196	+	Silent	SNP	A	A	T	rs370662812		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	60	112	0	0.526316	0	.	.	weak	.	HELT	34	.	NM_001029887	exon1	c.A114T	p.A38A	GATGGCAGGGAAG	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	37	4	25849329	25849329	+	Missense_Mutation	SNP	T	T	C	rs16877661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	52	107	0	0.504854	0	T|0.984;C|0.016	0.016	strong	.	SEL1L3	62	.	NM_015187	exon2	c.A320G	p.Q107R	CAAGGCTGAGAGC	.	PASS	Atlas-SNP
MPZL3	196264	hgsc.bcm.edu	37	11	118100634	118100634	+	Missense_Mutation	SNP	T	T	A	rs7105729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	49	69	0	0.662162	0	T|0.954;A|0.046	0.046	strong	.	MPZL3	22	.	NM_198275	exon6	c.A683T	p.D228V	TCTGAATCCTGGA	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	37	17	15968887	15968887	+	Silent	SNP	T	T	C	rs7210057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	150	299	1	0.477707	0.00334448	T|0.979;C|0.021	0.021	strong	.	NCOR1	240	.	NM_001190440	exon32	c.A4911G	p.Q1637Q	CATCTGTTGTGAG	.	PASS	Atlas-SNP
C5orf47	133491	hgsc.bcm.edu	37	5	173416508	173416508	+	Missense_Mutation	SNP	C	C	T	rs115473626	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	55	0	0.428571	0	C|0.984;T|0.016	0.016	strong	.	C5orf47	14	.	NM_001144954	exon1	c.C242T	p.P81L	CGACCCCTGGTGT	.	PASS	Atlas-SNP
C10orf95	79946	hgsc.bcm.edu	37	10	104210861	104210861	+	Missense_Mutation	SNP	C	C	A	rs73349055	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	7	27	0	0.4375	0	C|0.954;A|0.046	0.046	strong	.	C10orf95	5	.	NM_024886	exon2	c.G127T	p.G43W	GGCCCCCCAGGCG	.	PASS	Atlas-SNP
NPL	80896	hgsc.bcm.edu	37	1	182785865	182785865	+	Silent	SNP	C	C	T	rs1128759	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	45	115	0	0.478723	0	C|0.921;T|0.079	0.079	strong	.	NPL	55	.	NM_001200052	exon8	c.C381T	p.F127F	TAATTTCCTAAAG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6961950	6961950	+	Silent	SNP	T	T	C	rs145257845	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	163	310	0	0.543333	0	T|0.998;C|0.002	0.002	strong	.	LAMA1	458	.	NM_005559	exon52	c.A7446G	p.L2482L	CTCCAGTAAACAG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093600	1093600	+	Missense_Mutation	SNP	G	G	A	rs74193969	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	55	127	2	0.390071	0.015748	G|0.965;A|0.036	0.036	strong	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.G5419A	p.G1807S	CCCACCGGCACAC	.	scavenged	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81592384	81592384	+	Missense_Mutation	SNP	C	C	T	rs17875513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	58	0	0.42	0	C|0.955;T|0.045	0.045	strong	.	IL16	254	.	NM_001172128	exon14	c.C2717T	p.S906L	TGTCCTCGGGGTC	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234727	45234727	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	6	191	5	0.0365854	0.026178	.	.	none	CDC27_ENST00000531206,NS,carcinoma,+2,10	CDC27	337	10	NM_001114091	exon6	c.A499T	p.T167S	TAAATGTTTGGTC	.	scavenged	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71654450	71654450	+	Silent	SNP	A	A	G	rs60163900	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	58	43	0	0.983051	0	A|0.893;G|0.107	0.107	strong	.	ZNF638	179	.	NM_014497	exon24	c.A5451G	p.K1817K	CACAAAAAAGACA	.	PASS	Atlas-SNP
PTH1R	5745	hgsc.bcm.edu	37	3	46945000	46945000	+	Missense_Mutation	SNP	G	G	A	rs77048718	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	80	170	0	0.493827	0	A|0.019;C|0.000;G|0.981	0.019	strong	.	PTH1R	49	.	NM_001184744	exon15	c.G1636A	p.E546K	GCCCTGGAGACCC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129921195	129921195	+	Silent	SNP	A	A	T	rs1063536	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	80	185	0	0.496894	0	A|0.894;T|0.106	0.106	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_001145966	exon4	c.T237A	p.P79P	CCGTACAGGCTCA	.	PASS	Atlas-SNP
TINAG	27283	hgsc.bcm.edu	37	6	54254589	54254589	+	Missense_Mutation	SNP	A	A	C	rs3736352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	29	40	0	0.54717	0	A|0.919;C|0.081	0.081	strong	.	TINAG	102	.	NM_014464	exon11	c.A1297C	p.I433L	CTGCAGATTGCTG	.	PASS	Atlas-SNP
ZYG11B	79699	hgsc.bcm.edu	37	1	53262456	53262456	+	Silent	SNP	G	G	A	rs11206020	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	55	126	0	0.419847	0	G|0.962;A|0.038	0.038	strong	.	ZYG11B	61	.	NM_024646	exon8	c.G1485A	p.R495R	TGTCAGGGTAAGT	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19196449	19196449	+	Missense_Mutation	SNP	T	T	C	rs182543131	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	53	103	0	0.552083	0	T|0.999;C|0.001	0.001	strong	.	CLTCL1	115	.	NM_001835	exon21	c.A3425G	p.Q1142R	GCTGACTGAACAA	.	PASS	Atlas-SNP
BCO2	83875	hgsc.bcm.edu	37	11	112071464	112071464	+	Missense_Mutation	SNP	C	C	T	rs115780398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	35	78	0	0.546875	0	C|0.994;T|0.006	0.006	strong	BCO2,colon,carcinoma,0,1	BCO2	44	1	NM_031938	exon7	c.C994T	p.R332W	AATACGCGGTTTC	.	PASS	Atlas-SNP
DPAGT1	1798	hgsc.bcm.edu	37	11	118967758	118967758	+	Missense_Mutation	SNP	T	T	C	rs643788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	59	181	0	0.409722	0	A|0.003;C|0.413	0.413	strong	.	DPAGT1	43	.	NM_001382	exon9	c.A1177G	p.I393V	AGGTGATGGCACT	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43897499	43897499	+	Missense_Mutation	SNP	T	T	C	rs56042996		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	358	128	346	0	0.357542	0	.	.	weak	.	STRC	58	.	NM_153700	exon19	c.A3893G	p.H1298R	GCCTGGTGGAGGG	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	37	10	135012583	135012583	+	Missense_Mutation	SNP	C	C	A	rs111276772	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	23	0	0.509091	0	C|0.983;A|0.017	0.017	strong	.	KNDC1	155	.	NM_152643	exon14	c.C2571A	p.D857E	TGATGACCAGAGT	.	PASS	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	37	5	140725828	140725828	+	Missense_Mutation	SNP	C	C	T	rs7736541	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	202	140	0	0.980583	0	C|0.492;T|0.508	0.508	strong	.	PCDHGA3	246	.	NM_032011	exon1	c.C2228T	p.A743V	TGGGCGCGGACGG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82786194	82786194	+	Silent	SNP	T	T	C	rs12332199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	70	0	1	0	T|0.613;C|0.387	0.387	strong	.	VCAN	498	.	NM_004385	exon3	c.T348C	p.T116T	CCTCACTGTGGTC	.	PASS	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124658203	124658203	+	Missense_Mutation	SNP	T	T	C	rs72711231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	95	152	0	0.484694	0	T|0.924;C|0.076	0.076	strong	.	KLHL38	81	.	NM_001081675	exon3	c.A1522G	p.K508E	GGTCTTTCATGTC	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	37	7	75615006	75615006	+	Missense_Mutation	SNP	C	C	T	rs1057868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	52	63	0	0.55914	0	C|0.723;T|0.277	0.277	strong	.	POR	46	.	NM_000941	exon13	c.C1508T	p.A503V	AGCCTGCCGGGGA	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167145106	167145106	+	Silent	SNP	C	C	A	rs58465962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	89	0	1	0	C|0.964;A|0.036	0.036	strong	.	SCN9A	296	.	NM_002977	exon10	c.G1155T	p.V385V	GAAAATCACTACG	.	PASS	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	37	1	120480583	120480583	+	Silent	SNP	G	G	A	rs7543643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	62	135	0	0.504065	0	G|0.925;A|0.075	0.075	strong	.	NOTCH2	348	.	NM_001200001	exon20	c.C3234T	p.C1078C	CTGAACGCAAGTA	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118644430	118644430	+	Silent	SNP	A	A	G	rs10754367	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	99	206	0	0.473684	0	A|0.430;G|0.570	0.570	strong	.	SPAG17	263	.	NM_206996	exon5	c.T567C	p.N189N	TGGTGCATTTGCC	.	PASS	Atlas-SNP
CNGA2	1260	hgsc.bcm.edu	37	X	150912171	150912171	+	Missense_Mutation	SNP	G	G	A	rs150539917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	34	91	0	0.425	0	G|0.964;A|0.036	0.036	strong	.	CNGA2	136	.	NM_005140	exon7	c.G1196A	p.R399Q	AGTTCCGAAAGGT	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55450696	55450696	+	Silent	SNP	G	G	A	rs775880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	64	158	0	0.470588	0	G|0.908;A|0.092	0.092	strong	.	NLRP7	411	.	NM_001127255	exon4	c.C1491T	p.I497I	GTCCCCGATGTCC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1214	88	1007	23	0.0724876	0.0228401	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	NM_005961	exon31	c.C5235T	p.T1745T	TGTAGAGGTTTTG	.	scavenged	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378425	31378425	+	Missense_Mutation	SNP	A	A	G	rs1051786	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	184	230	0	1	0	A|0.641;G|0.359	0.359	strong	.	MICA	21	.	NM_001177519	exon2	c.A176G	p.Y59C	TGCGCTATGACAG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15791074	15791074	+	Missense_Mutation	SNP	A	A	G	rs114254919	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	372	95	266	0	0.255376	0	A|0.989;G|0.011	0.011	strong	CYP4F12,colon,carcinoma,-1,1	CYP4F12	89	1	NM_023944	exon4	c.A364G	p.N122D	AAGGATAATCTCT	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	57935443	57935443	+	Missense_Mutation	SNP	C	C	A	rs16942445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	97	0	0.494624	0	C|0.957;A|0.043	0.043	strong	.	CNGB1	105	.	NM_001297	exon28	c.G2881T	p.A961S	AGAGTGCGACTTT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149489037	149489037	+	Missense_Mutation	SNP	T	T	C	rs1635802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	60	0	0.506667	0	T|0.977;C|0.023	0.023	strong	.	.	.	.	NM_198455	exon35	c.T5378C	p.L1793P	GAGGCCTGCACAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	12049	12049	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	5	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C1290T	p.F430F	CTCATTCACACGA	.	PASS	Atlas-SNP
SEBOX	645832	hgsc.bcm.edu	37	17	26691321	26691321	+	Missense_Mutation	SNP	A	A	G	rs9910163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	86	70	0	0.988506	0	A|0.120;G|0.880	0.880	strong	.	SEBOX	20	.	NM_001080837	exon3	c.T620C	p.L207S	ATGGCCAAGGCAT	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105776792	105776792	+	Silent	SNP	G	G	A	rs6902415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	122	123	0	0.99187	0	G|0.789;A|0.211	0.211	strong	.	PREP	65	.	NM_002726	exon9	c.C1125T	p.F375F	GAGCGGGAAGGTC	.	PASS	Atlas-SNP
ZNF362	149076	hgsc.bcm.edu	37	1	33745781	33745781	+	Missense_Mutation	SNP	G	G	A	rs143005937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	81	103	0	0.591241	0	G|0.989;A|0.011	0.011	strong	.	ZNF362	31	.	NM_152493	exon5	c.G406A	p.A136T	GCGGGCGCGGGCA	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47506874	47506874	+	Silent	SNP	G	G	T	rs16951352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	60	139	0	0.447761	0	G|0.993;T|0.007	0.007	strong	.	MYO5B	178	.	NM_001080467	exon9	c.C996A	p.I332I	GTGCAAGATAGAA	.	PASS	Atlas-SNP
IDS	3423	hgsc.bcm.edu	37	X	148582549	148582549	+	Silent	SNP	G	G	A	rs1141608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	26	62	0	0.351351	0	G|0.703;0|0.015	.	strong	.	IDS	46	.	NM_006123	exon4	c.C438T	p.T146T	ATCATCGGTATGG	.	PASS	Atlas-SNP
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117553	46117553	+	Missense_Mutation	SNP	C	C	A	rs35076450	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	136	221	1	0.513208	0.00452489	C|0.995;A|0.005	0.005	strong	.	KRTAP10-12	21	.	NM_198699	exon1	c.C437A	p.P146Q	CCTCCCCGTGTCA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464755	10464755	+	Missense_Mutation	SNP	C	C	T	rs55642448	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	96	0	1	0	C|0.574;T|0.426	0.426	strong	RP1L1,NS,carcinoma,0,2	RP1L1	453	2	NM_178857	exon4	c.G6853A	p.G2285R	TGTCTCCACCTGG	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102269085	102269085	+	Missense_Mutation	SNP	C	C	A	rs3793706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	61	132	0	0.480315	0	C|0.796;A|0.204	0.204	strong	.	SEC31B	84	.	NM_015490	exon4	c.G387T	p.L129F	AGGATTCAAGTCG	.	PASS	Atlas-SNP
ITGA7	3679	hgsc.bcm.edu	37	12	56089357	56089357	+	Missense_Mutation	SNP	C	C	T	rs1800974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	109	208	0	0.493213	0	C|0.489;T|0.511	0.511	strong	.	ITGA7	194	.	NM_001144996	exon14	c.G1964A	p.R655H	CGGGCGCGGACCA	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	617573	617573	+	Missense_Mutation	SNP	G	G	A	rs142850300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	25	37	0	0.657895	0	G|0.995;A|0.005	0.005	strong	.	POLRMT	91	.	NM_005035	exon19	c.C3578T	p.S1193F	TACTCAGAGCAGA	.	PASS	Atlas-SNP
C2orf43	60526	hgsc.bcm.edu	37	2	20886706	20886706	+	Missense_Mutation	SNP	T	T	C	rs147773589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	89	191	0	0.532934	0	T|0.998;C|0.002	0.002	strong	.	C2orf43	28	.	NM_021925	exon7	c.A935G	p.D312G	ATCATGTCTGCCA	.	PASS	Atlas-SNP
KIF1C	10749	hgsc.bcm.edu	37	17	4918122	4918122	+	Silent	SNP	A	A	G	rs57144955	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	30	76	0	0.47619	0	A|0.964;G|0.036	0.036	strong	.	KIF1C	70	.	NM_006612	exon18	c.A1656G	p.P552P	CCAGCCAGATGGA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144852477	144852477	+	Missense_Mutation	SNP	G	G	A	rs148370554	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	6	83	0	0.0508475	0	.	.	weak	.	PDE4DIP	817	.	NM_014644	exon44	c.C7022T	p.P2341L	GTACATGGCAGAG	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893904	123893904	+	Missense_Mutation	SNP	C	C	T	rs75423810		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	685	327	708	2	0.477372	0.00282486	T|1.000;|0.000	1.000	weak	OR10G9,NS,carcinoma,0,1	OR10G9	80	1	NM_001001953	exon1	c.C185T	p.T62I	TCCTCACCAACCT	.	scavenged	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77476809	77476809	+	Silent	SNP	T	T	C	rs75039400	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	40	64	0	0.421053	0	T|0.980;C|0.020	0.020	strong	.	SHROOM3	134	.	NM_020859	exon2	c.T216C	p.A72A	GCAGGCTGGGGAT	.	PASS	Atlas-SNP
ECHDC3	79746	hgsc.bcm.edu	37	10	11805249	11805249	+	Silent	SNP	T	T	C	rs61739577	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	22	36	0	0.44	0	T|0.807;C|0.193	0.193	strong	.	ECHDC3	12	.	NM_024693	exon5	c.T618C	p.G206G	TACTGGTGAGCCC	.	PASS	Atlas-SNP
IL31	386653	hgsc.bcm.edu	37	12	122658492	122658492	+	Silent	SNP	G	G	A	rs56719421	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	76	129	0	0.520548	0	G|0.928;A|0.072	0.072	strong	IL31,colon,carcinoma,+1,1	IL31	23	1	NM_001014336	exon2	c.C64T	p.L22L	AGGCCAGCCAGCC	.	PASS	Atlas-SNP
ADD2	119	hgsc.bcm.edu	37	2	70933494	70933494	+	Missense_Mutation	SNP	T	T	C	rs201443444	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	111	0	0.486486	0	T|0.978;C|0.022	0.022	strong	.	ADD2	261	.	NM_001185055	exon2	c.A95G	p.Q32R	TGCCCCTGCGGGG	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	284477	284477	+	Missense_Mutation	SNP	T	T	C	rs74044411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	30	87	0	0.379747	0	T|0.940;C|0.060	0.060	strong	.	NLRP6	4	.	NM_138329	exon7	c.T2375C	p.V792A	ACAGGGTACAGCT	.	PASS	Atlas-SNP
TMEFF2	23671	hgsc.bcm.edu	37	2	192922499	192922499	+	Missense_Mutation	SNP	G	G	A	rs61744272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	68	130	0	0.53125	0	G|0.982;A|0.018	0.018	strong	.	TMEFF2	54	.	NM_016192	exon5	c.C442T	p.H148Y	CTTCATGGACTGT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057343	46057343	+	Silent	SNP	C	C	A	rs76468958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	103	192	0	0.47032	0	C|0.960;A|0.040	0.040	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C9A	p.A3A	GGCCGCCTCCACC	.	PASS	Atlas-SNP
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	56	75	0	0.543689	0	A|0.760;G|0.240	0.240	strong	.	OR4C15	145	.	NM_001001920	exon1	c.A429G	p.K143K	GACAAAAACCATC	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12924826	12924826	+	Missense_Mutation	SNP	A	A	G	rs3764880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	133	275	0	0.460208	0	A|0.639;0|0.017	.	strong	.	TLR8	134	.	NM_138636	exon1	c.A1G	p.M1V	AGAAACATGGTAA	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122354796	122354796	+	Missense_Mutation	SNP	G	G	C	rs145474072	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	58	127	0	0.504348	0	G|0.995;C|0.005	0.005	strong	.	PARP15	115	.	NM_001113523	exon12	c.G1886C	p.R629P	AGGGACGTGCAGG	.	PASS	Atlas-SNP
GIMAP1-GIMAP5	0	hgsc.bcm.edu	37	7	150439500	150439500	+	Silent	SNP	C	C	T	rs759011	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	91	0	1	0	T|0.385;G|0.004	0.385	strong	GIMAP5,NS,carcinoma,0,1	.	.	1	NM_001199577	exon6	c.C885T	p.A295A	ACAGGCCGATACC	.	PASS	Atlas-SNP
QRFPR	84109	hgsc.bcm.edu	37	4	122254014	122254014	+	Silent	SNP	A	A	G	rs55975435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	114	240	0	0.452381	0	A|0.909;G|0.091	0.091	strong	.	QRFPR	65	.	NM_198179	exon4	c.T759C	p.L253L	AGTTCGAAGCACT	.	PASS	Atlas-SNP
TTC23	64927	hgsc.bcm.edu	37	15	99678257	99678257	+	Silent	SNP	G	G	A	rs28617660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	35	92	0	0.416667	0	G|0.888;A|0.112	0.112	strong	.	TTC23	33	.	NM_001040657	exon12	c.C1302T	p.D434D	CAGGGTGTCCTGA	.	PASS	Atlas-SNP
CUL5	8065	hgsc.bcm.edu	37	11	107943124	107943124	+	Silent	SNP	T	T	C	rs111339569	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	28	81	0	0.451613	0	T|0.987;C|0.013	0.013	strong	.	CUL5	71	.	NM_003478	exon9	c.T940C	p.L314L	AAAGACTTGGAGG	.	PASS	Atlas-SNP
UNC5D	137970	hgsc.bcm.edu	37	8	35606168	35606168	+	Silent	SNP	T	T	C	rs1436615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	63	155	1	0.431507	0.00645161	T|0.896;C|0.104	0.104	strong	UNC5D_ENST00000404895,caecum,carcinoma,-2,3	UNC5D	393	3	NM_080872	exon12	c.T1890C	p.H630H	TGAGCATTGGAAT	.	scavenged	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587865	39587865	+	Silent	SNP	A	A	C	rs3751378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	70	126	0	0.460526	0	A|0.810;C|0.190	0.190	strong	C13orf23,NS,carcinoma,-1,1	.	.	1	NM_025138	exon11	c.T1524G	p.S508S	AGAGTCAGAGTTC	.	PASS	Atlas-SNP
OR5AK2	390181	hgsc.bcm.edu	37	11	56756565	56756565	+	Silent	SNP	G	G	A	rs62001001	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	116	247	0	0.462151	0	G|0.987;A|0.013	0.013	strong	OR5AK2,NS,carcinoma,0,1	OR5AK2	45	1	NM_001005323	exon1	c.G177A	p.T59T	ACTCACGTACTTT	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220347907	220347907	+	Missense_Mutation	SNP	A	A	G	rs200747365	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	42	88	0	0.5	0	A|1.000;G|0.000	0.000	strong	.	SPEG	272	.	NM_005876	exon30	c.A5722G	p.M1908V	GTGACCATGCCCA	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45755646	45755646	+	Silent	SNP	C	C	T	rs146104157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	79	140	0	0.44382	0	C|0.997;T|0.003	0.003	strong	.	C21orf2	10	.	NM_004928	exon3	c.G138A	p.T46T	CCTGAGCGTGATC	.	PASS	Atlas-SNP
ZMIZ2	83637	hgsc.bcm.edu	37	7	44804989	44804989	+	Missense_Mutation	SNP	G	G	A	rs114574038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	34	68	0	0.441558	0	G|0.990;A|0.010	0.010	strong	.	ZMIZ2	82	.	NM_031449	exon16	c.G2053A	p.V685M	GTGCCCGTGAAGC	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	35	227	14	0.118644	0.061674	.	.	none	KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.T258C	p.G86G	CTTGGAACCCCCA	.	scavenged	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84228770	84228770	+	Missense_Mutation	SNP	G	G	C	rs11149631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	117	0	1	0	G|0.680;C|0.320	0.320	strong	.	ADAD2	46	.	NM_139174	exon5	c.G919C	p.G307R	TGTAAGGGGACTG	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	37	17	39084504	39084504	+	Missense_Mutation	SNP	T	T	C	rs9257	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	189	180	0	0.989529	0	T|0.485;C|0.515	0.515	strong	.	KRT23	59	.	NM_015515	exon6	c.A907G	p.T303A	ACTGTGTCTGCAG	.	PASS	Atlas-SNP
ARHGEF2	9181	hgsc.bcm.edu	37	1	155935158	155935158	+	Silent	SNP	T	T	C	rs149517516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	87	158	0	0.511765	0	T|0.995;C|0.005	0.005	strong	.	ARHGEF2	81	.	NM_001162383	exon6	c.A516G	p.S172S	GGACTGTGAGAGG	.	PASS	Atlas-SNP
TSTD2	158427	hgsc.bcm.edu	37	9	100388119	100388119	+	Missense_Mutation	SNP	G	G	T	rs10817858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	85	159	0	0.607143	0	G|0.832;T|0.168	0.168	strong	TSTD2,NS,carcinoma,0,1	TSTD2	42	1	NM_139246	exon3	c.C326A	p.A109D	ATAGAAGCTGTCT	.	PASS	Atlas-SNP
ATG4B	23192	hgsc.bcm.edu	37	2	242610172	242610172	+	Missense_Mutation	SNP	A	A	G	rs138274580	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	56	85	0	0.486957	0	A|0.945;G|0.055	0.055	strong	.	ATG4B	35	.	NM_178326	exon11	c.A989G	p.N330S	ACTTCAATGATTG	.	PASS	Atlas-SNP
STK32C	282974	hgsc.bcm.edu	37	10	134038817	134038817	+	Missense_Mutation	SNP	C	C	T	rs148669059	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	54	137	0	0.529412	0	C|0.996;T|0.004	0.004	strong	.	STK32C	61	.	NM_173575	exon7	c.G796A	p.V266I	CGTTGACAAAAGA	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109629457	109629457	+	Silent	SNP	C	C	T	rs7135947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	141	278	0	0.526119	0	C|0.587;T|0.413	0.413	strong	.	ACACB	330	.	NM_001093	exon13	c.C2184T	p.G728G	CCGAGGCGACTTT	.	PASS	Atlas-SNP
CST4	1472	hgsc.bcm.edu	37	20	23669598	23669598	+	Silent	SNP	C	C	T	rs73902132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	40	93	0	0.366972	0	C|0.964;T|0.036	0.036	strong	.	CST4	37	.	NM_001899	exon1	c.G9A	p.R3R	CAGAGGCCGGGCC	.	PASS	Atlas-SNP
LUZP6	767558	hgsc.bcm.edu	37	7	135612057	135612057	+	Missense_Mutation	SNP	G	G	C	rs78834486	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	33	80	0	0.540984	0	G|0.993;C|0.007	0.007	strong	.	.	.	.	NM_001128619	exon4	c.C142G	p.P48A	TACTTGGGATATT	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	81	65	0	1	0	T|0.908;C|0.092	0.092	strong	ZNF93,NS,carcinoma,0,1	ZNF93	81	1	NM_031218	exon4	c.T1122C	p.C374C	AGAATGTGGCAAA	.	PASS	Atlas-SNP
FAM151A	338094	hgsc.bcm.edu	37	1	55075452	55075452	+	Missense_Mutation	SNP	G	G	A	rs1368883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	132	0	1	0	G|0.630;A|0.370	0.370	strong	.	FAM151A	58	.	NM_176782	exon8	c.C1247T	p.A416V	GGCTCCGCTATTT	.	PASS	Atlas-SNP
ITGB3	3690	hgsc.bcm.edu	37	17	45369789	45369789	+	Silent	SNP	G	G	A	rs4634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	42	75	0	0.545455	0	G|0.717;A|0.283	0.283	strong	ITGB3_ENST00000435993,colon,carcinoma,0,2	ITGB3	157	2	NM_000212	exon10	c.G1545A	p.R515R	CCCCCGGGAGGGT	.	PASS	Atlas-SNP
NCKAP5L	57701	hgsc.bcm.edu	37	12	50190653	50190653	+	Silent	SNP	C	C	T	rs3741555	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	32	46	0	0.561404	0	C|0.733;T|0.267	0.267	strong	NCKAP5L_ENST00000335999,rectum,carcinoma,0,2	NCKAP5L	142	2	NM_001037806	exon8	c.G990A	p.Q330Q	AAGGAGCTGGCCC	.	PASS	Atlas-SNP
SLC33A1	9197	hgsc.bcm.edu	37	3	155571275	155571275	+	Missense_Mutation	SNP	T	T	C	rs3804769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	44	106	0	0.52381	0	T|0.919;C|0.081	0.081	strong	.	SLC33A1	57	.	NM_004733	exon1	c.A512G	p.D171G	GTTCTGTCATCGG	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42442546	42442546	+	Missense_Mutation	SNP	A	A	G	rs3742262	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	95	202	0	0.524862	0	A|0.760;G|0.240	0.240	strong	.	.	.	.	NM_015058	exon10	c.T1148C	p.M383T	TTTTCCATCATCT	.	PASS	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65298657	65298657	+	Missense_Mutation	SNP	A	A	G	rs13389745	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	101	163	0	0.5	0	A|0.929;G|0.071	0.071	strong	.	CEP68	69	.	NM_015147	exon3	c.A427G	p.I143V	ACAACTATTTGCT	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	155	335	0	0.45858	0	G|0.822;T|0.178	0.178	strong	ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	NM_032828	exon3	c.G1494T	p.G498G	ATGTGGGAAATCA	.	PASS	Atlas-SNP
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	61	124	0	0.525862	0	C|0.728;T|0.272	0.272	strong	.	CTNND1	203	.	NM_001085461	exon6	c.C483T	p.D161D	ACCAGACGGGTTG	.	PASS	Atlas-SNP
APBA2	321	hgsc.bcm.edu	37	15	29398914	29398914	+	Silent	SNP	C	C	T	rs8032178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	107	231	0	0.481982	0	C|0.932;T|0.068	0.068	strong	.	APBA2	132	.	NM_005503	exon11	c.C1809T	p.G603G	GAATGGCGGCCCG	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25319977	25319977	+	Missense_Mutation	SNP	C	C	T	rs11904930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	126	0	0.444444	0	C|0.993;T|0.007	0.007	strong	.	ABHD12	46	.	NM_001042472	exon2	c.G202A	p.V68M	ACCACACGCCCTT	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208207839	208207839	+	Silent	SNP	G	G	A	rs3736963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	58	0	1	0	G|0.471;A|0.529	0.529	strong	.	PLXNA2	178	.	NM_025179	exon27	c.C4863T	p.Y1621Y	CTCACCGTATCTG	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74006079	74006079	+	Silent	SNP	G	G	A	rs79450818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	70	107	0	0.608696	0	G|0.987;A|0.013	0.013	strong	.	EVPL	155	.	NM_001988	exon22	c.C3207T	p.D1069D	CTTCACGTCCACC	.	PASS	Atlas-SNP
THOC6	79228	hgsc.bcm.edu	37	16	3076393	3076393	+	Silent	SNP	C	C	T	rs8057262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	56	121	0	0.486957	0	C|0.955;T|0.045	0.045	strong	.	THOC6	40	.	NM_001142350	exon6	c.C390T	p.N130N	GATCAACGCTTTG	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183720831	183720831	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	8	3	0	0.8	0	.	.	none	.	.	.	.	NM_001080477	exon27	c.G7427A	p.S2476N	AGGTGAGCCGGCG	.	PASS	Atlas-SNP
INTS4	92105	hgsc.bcm.edu	37	11	77635882	77635882	+	Silent	SNP	A	A	C	rs7119720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	401	168	372	1	0.418953	0.00268817	A|0.818;C|0.182	0.182	strong	.	INTS4	89	.	NM_033547	exon12	c.T1428G	p.V476V	GGTTGAAACATTA	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47863757	47863757	+	Missense_Mutation	SNP	A	A	C	rs2073380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	43	90	0	0.438776	0	A|0.810;C|0.190	0.190	strong	.	PCNT	283	.	NM_006031	exon45	c.A9735C	p.R3245S	ACCCAGAACCAGA	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90016763	90016763	+	Missense_Mutation	SNP	T	T	C	rs199833843	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	124	0	0.463636	0	.	.	weak	.	GPR98	605	.	NM_032119	exon45	c.T9635C	p.I3212T	CCTCCATAGACAT	.	PASS	Atlas-SNP
SLC2A7	155184	hgsc.bcm.edu	37	1	9083094	9083094	+	Missense_Mutation	SNP	G	G	T	rs61744620	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	77	0	0.542169	0	G|0.974;T|0.026	0.026	strong	SLC2A7,rectum,carcinoma,-1,2	SLC2A7	56	2	NM_207420	exon3	c.C194A	p.A65E	AATGTTGCGTGTC	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	131	0	1	0	C|0.837;T|0.163	0.163	strong	.	ELSPBP1	29	.	NM_022142	exon4	c.C217T	p.R73C	TACCCACGCTGTA	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27777751	27777751	+	Silent	SNP	T	T	C	rs16950126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	75	99	0	0.510204	0	T|0.932;C|0.068	0.068	strong	.	GABRG3	115	.	NM_033223	exon10	c.T1128C	p.Y376Y	GAACTATTCCCTC	.	PASS	Atlas-SNP
SNTG2	54221	hgsc.bcm.edu	37	2	1204796	1204796	+	Missense_Mutation	SNP	C	C	T	rs6751090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	43	74	0	0.589041	0	C|0.811;T|0.189	0.189	strong	SNTG2,colon,carcinoma,0,4	SNTG2	125	4	NM_018968	exon9	c.C599T	p.S200L	CCCCATCGTCACC	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060248	16060248	+	Missense_Mutation	SNP	A	A	G	rs16980822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	273	240	1	0.99635	0.00416667	A|0.724;G|0.276	0.276	strong	OR10H4,NS,carcinoma,+1,1	OR10H4	48	1	NM_001004465	exon1	c.A431G	p.H144R	GTGCCCATCTTGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509611	195509611	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	3	292	2	0.014218	0.00684932	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.T8840A	p.V2947D	TCGGTGACAGGAA	.	scavenged	Atlas-SNP
CHRM1	1128	hgsc.bcm.edu	37	11	62677529	62677529	+	Silent	SNP	C	C	T	rs2067478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	57	0	0.517857	0	C|0.938;T|0.062	0.062	strong	.	CHRM1	29	.	NM_000738	exon2	c.G1044A	p.Q348Q	GGCCAGCTGCTCC	.	PASS	Atlas-SNP
FAM90A1	55138	hgsc.bcm.edu	37	12	8375112	8375112	+	Missense_Mutation	SNP	G	G	T	rs9668582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	302	249	1	1	0.00401606	G|0.793;T|0.207	0.207	strong	.	FAM90A1	68	.	NM_018088	exon7	c.C701A	p.A234E	CCACCCGCAGGGC	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220421417	220421417	+	Missense_Mutation	SNP	C	C	G	rs1983210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	146	231	0	0.528986	0	C|0.289;G|0.711	0.711	strong	OBSL1_ENST00000404537,NS,carcinoma,0,1	OBSL1	120	1	NM_001173431	exon13	c.G4095C	p.E1365D	TGTCAGCTCCGAG	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361642	107361642	+	Missense_Mutation	SNP	G	G	A	rs41430948	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	489	234	478	1	0.478528	0.00209205	G|1.000;|0.000	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.C53T	p.S18F	TGACCAGAAAGTC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	37	104	0	0.430233	0	T|0.601;G|0.399	0.399	strong	CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	NM_015692	exon14	c.A1665C	p.R555R	CTTGCTTCGCTGC	.	PASS	Atlas-SNP
IPO13	9670	hgsc.bcm.edu	37	1	44433055	44433055	+	Silent	SNP	G	G	A	rs34392712	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	59	98	0	0.504274	0	G|0.989;A|0.011	0.011	strong	.	IPO13	86	.	NM_014652	exon19	c.G2682A	p.K894K	GAACAAGCACTGC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411096	105411096	+	Missense_Mutation	SNP	T	T	G	rs146355838	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	252	238	2	0.992126	0.00840336	T|0.971;G|0.029	0.029	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A10692C	p.L3564F	CGTCTTTAAACTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511781	195511781	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	47	404	1	0.251337	0.00247525	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	NM_018406	exon2	c.C6670T	p.P2224S	GAAGAGGGATGGC	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62886706	62886706	+	Missense_Mutation	SNP	C	C	T	rs116063135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	84	165	0	0.518519	0	C|0.988;T|0.012	0.012	strong	.	SLC22A24	31	.	NM_001136506	exon3	c.G608A	p.R203H	AAGAAGCGCAGTA	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196529982	196529982	+	Missense_Mutation	SNP	A	A	G	rs78043821	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	13	130	1	0.0833333	0.00769231	A|0.915;G|0.084	0.084	strong	PAK2_ENST00000327134,NS,lymphoid_neoplasm,0,2	PAK2	113	2	NM_002577	exon4	c.A383G	p.K128R	TCCTAAAGTTCTA	.	scavenged	Atlas-SNP
XKR3	150165	hgsc.bcm.edu	37	22	17280822	17280822	+	Missense_Mutation	SNP	G	G	A	rs5748648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	340	159	314	0	0.467647	0	G|0.881;A|0.119	0.119	strong	.	XKR3	51	.	NM_175878	exon3	c.C428T	p.T143M	AGCATCGTGTTTC	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178257364	178257364	+	Missense_Mutation	SNP	G	G	C	rs17064658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	41	95	0	0.465909	0	G|0.975;C|0.025	0.025	strong	.	NEIL3	89	.	NM_018248	exon4	c.G516C	p.Q172H	AAAACAGAAAGGC	.	PASS	Atlas-SNP
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387344	46387344	+	Silent	SNP	G	G	A	rs11550348	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	65	71	0	0.984848	0	G|0.836;A|0.164	0.164	strong	.	IRF2BP1	23	.	NM_015649	exon1	c.C1689T	p.F563F	CTGCATGAAGGCC	.	PASS	Atlas-SNP
DNMT3B	1789	hgsc.bcm.edu	37	20	31388080	31388080	+	Silent	SNP	C	C	T	rs17123657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	56	94	0	0.528302	0	C|0.944;T|0.056	0.056	strong	DNMT3B_ENST00000201963,NS,carcinoma,+2,4	DNMT3B	196	4	NM_006892	exon17	c.C1881T	p.D627D	GAACGACGTGAGG	.	PASS	Atlas-SNP
TNFRSF25	8718	hgsc.bcm.edu	37	1	6525257	6525257	+	Silent	SNP	C	C	T	rs45438594	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	49	115	0	0.556818	0	C|0.965;T|0.035	0.035	strong	.	TNFRSF25	22	.	NM_148966	exon3	c.G186A	p.T62T	GGGCTCCGTGCAA	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	109	93	0	0.981982	0	G|0.878;A|0.122	0.122	strong	.	SEC16B	92	.	NM_033127	exon22	c.C2784T	p.P928P	TCCAGCGGGGGAT	.	PASS	Atlas-SNP
SLMAP	7871	hgsc.bcm.edu	37	3	57743531	57743531	+	Silent	SNP	A	A	G	rs147270008		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	106	224	0	0.475336	0	A|1.000;G|0.000	0.000	weak	.	SLMAP	46	.	NM_007159	exon1	c.A153G	p.L51L	AGTGCTATCAAGG	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6639981	6639981	+	Missense_Mutation	SNP	C	C	G	rs2240871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	28	64	0	0.363636	0	C|0.834;G|0.166	0.166	strong	.	NCAPD2	99	.	NM_014865	exon30	c.C3962G	p.T1321S	CATCCACTGGTAC	.	PASS	Atlas-SNP
AURKC	6795	hgsc.bcm.edu	37	19	57743518	57743518	+	Silent	SNP	C	C	T	rs142351971	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	19	68	0	0.287879	0	C|0.999;T|0.001	0.001	strong	AURKC_ENST00000302804,colon,carcinoma,+2,2	AURKC	97	2	NM_001015878	exon3	c.C222T	p.L74L	GGTTCTCTTCAAG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	90	148	0	0.511364	0	C|0.719;T|0.281	0.281	strong	.	ACACB	330	.	NM_001093	exon44	c.C6204T	p.H2068H	TGACCACGGCAGT	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36841536	36841536	+	Missense_Mutation	SNP	G	G	A	rs142596886	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	23	72	0	0.410714	0	G|0.999;A|0.001	0.001	strong	.	KIAA1755	145	.	NM_001029864	exon14	c.C3511T	p.R1171C	TGAGGCGAGGGAC	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62200738	62200738	+	Missense_Mutation	SNP	G	G	A	rs6089924	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	35	39	0	0.625	0	G|0.836;A|0.164	0.164	strong	.	.	.	.	NM_001037335	exon5	c.C851T	p.A284V	CCGAGCGCCAGAT	.	PASS	Atlas-SNP
ZNF22	7570	hgsc.bcm.edu	37	10	45499272	45499272	+	Silent	SNP	C	C	G	rs3740092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	30	53	0	0.517241	0	C|0.960;G|0.040	0.040	strong	ZNF22,colon,carcinoma,0,1	ZNF22	28	1	NM_006963	exon2	c.C456G	p.S152S	GAGCTCCCACCTT	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	114186003	114186003	+	Missense_Mutation	SNP	T	T	C	rs2219898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	61	177	0	0.38125	0	T|0.622;C|0.378	0.378	strong	.	CSMD3	2325	.	NM_052900	exon4	c.A657G	p.I219M	ATTGGCTATGCAG	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77738664	77738664	+	Silent	SNP	A	A	G	rs2274547	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	56	117	0	0.466667	0	A|0.832;G|0.168	0.168	strong	.	MYCBP2	1029	.	NM_015057	exon43	c.T6472C	p.L2158L	TTTCCAATTGGAT	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89839752	89839752	+	Silent	SNP	C	C	T	rs17232917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	52	90	0	0.553191	0	C|0.960;T|0.040	0.040	strong	.	FANCA	99	.	NM_000135	exon22	c.G1941A	p.E647E	GGGCTCCTCAGCA	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327918	16327918	+	Missense_Mutation	SNP	C	C	A	rs28555263		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	7	68	1	0.107692	0.0147059	C|0.500;A|0.500	0.500	weak	ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.G624T	p.Q208H	CTGATGCTGCTGC	.	scavenged	Atlas-SNP
EFCAB13	124989	hgsc.bcm.edu	37	17	45471443	45471443	+	Silent	SNP	G	G	A	rs7217678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	68	162	0	0.427673	0	G|0.977;A|0.023	0.023	strong	C17orf57,NS,carcinoma,+1,1	.	.	1	NM_152347	exon16	c.G1779A	p.T593T	CAACACGGAATGC	.	PASS	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47575291	47575291	+	Silent	SNP	A	A	G	rs79459609	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	50	117	0	0.515464	0	A|0.983;G|0.017	0.017	strong	.	ZC3H4	96	.	NM_015168	exon13	c.T1890C	p.P630P	CATGTCAGGATGC	.	PASS	Atlas-SNP
RAD21	5885	hgsc.bcm.edu	37	8	117864867	117864867	+	Missense_Mutation	SNP	A	A	C	rs75160167	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	86	197	0	0.423645	0	A|0.992;C|0.008	0.008	strong	.	RAD21	95	.	NM_006265	exon10	c.T1242G	p.D414E	GAATTCATCCAAA	.	PASS	Atlas-SNP
CXXC1	30827	hgsc.bcm.edu	37	18	47809710	47809710	+	Silent	SNP	A	A	G	rs150530383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	74	108	0	0.503401	0	A|0.999;G|0.001	0.001	strong	.	CXXC1	50	.	NM_001101654	exon13	c.T1608C	p.D536D	ATACACATCACAG	.	PASS	Atlas-SNP
UBXN4	23190	hgsc.bcm.edu	37	2	136511817	136511817	+	Silent	SNP	A	A	G	rs1050115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	139	0	0.567568	0	A|0.774;G|0.226	0.226	strong	UBXN4,NS,carcinoma,0,1	UBXN4	54	1	NM_014607	exon4	c.A303G	p.E101E	AGATGAACTTGTT	.	PASS	Atlas-SNP
ZNF263	10127	hgsc.bcm.edu	37	16	3339435	3339435	+	Missense_Mutation	SNP	G	G	C	rs220379	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	56	137	0	0.543689	0	G|0.701;C|0.299	0.299	strong	.	ZNF263	58	.	NM_005741	exon6	c.G929C	p.C310S	CTGTATGCTCTGA	.	PASS	Atlas-SNP
ARHGAP20	57569	hgsc.bcm.edu	37	11	110451470	110451470	+	Missense_Mutation	SNP	T	T	C	rs151169911	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	58	164	0	0.456693	0	T|0.999;C|0.001	0.001	strong	.	ARHGAP20	150	.	NM_020809	exon16	c.A2200G	p.I734V	AAAGAATTGCATC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26699033	26699033	+	Silent	SNP	G	G	A	rs73920285	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	85	0	0.417582	0	G|0.953;A|0.047	0.047	strong	OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	NM_194248	exon23	c.C2829T	p.G943G	ATGCAGGCCCAGG	.	PASS	Atlas-SNP
CASP5	838	hgsc.bcm.edu	37	11	104871193	104871193	+	Silent	SNP	A	A	G	rs45501691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	68	139	0	0.576271	0	A|0.954;G|0.046	0.046	strong	.	CASP5	213	.	NM_001136112	exon6	c.T786C	p.A262A	TCTGGCAGCAAAT	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57060136	57060136	+	Missense_Mutation	SNP	G	G	T	rs149735722	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	19	44	1	0.413043	0.0227273	G|0.998;T|0.002	0.002	strong	NLRC5,NS,carcinoma,+1,1	NLRC5	186	1	NM_032206	exon5	c.G1281T	p.Q427H	AGGCCAGTCTGTG	.	scavenged	Atlas-SNP
MAT1A	4143	hgsc.bcm.edu	37	10	82034842	82034842	+	Silent	SNP	A	A	G	rs10887711	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	70	0	1	0	A|0.229;G|0.771	0.771	strong	MAT1A,NS,carcinoma,0,1	MAT1A	52	1	NM_000429	exon7	c.T882C	p.A294A	ATATGCAGCTGAG	.	PASS	Atlas-SNP
ZNF559	84527	hgsc.bcm.edu	37	19	9453160	9453160	+	Nonsense_Mutation	SNP	C	C	T	rs150358404	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	33	49	0	0.559322	0	C|0.999;T|0.001	0.001	strong	ZNF559,NS,carcinoma,-1,4	ZNF559	77	4	NM_001202406	exon6	c.C1225T	p.R409X	CACAGGCGAACTC	.	PASS	Atlas-SNP
ZNF330	27309	hgsc.bcm.edu	37	4	142155072	142155072	+	Missense_Mutation	SNP	T	T	A	rs34631212	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	74	131	0	0.451219	0	T|0.968;A|0.032	0.032	strong	.	ZNF330	31	.	NM_014487	exon10	c.T892A	p.L298M	TCAGATTTGTTTA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105409959	105409959	+	Silent	SNP	G	G	T	rs10152073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	317	326	0	0.996855	0	G|0.467;T|0.533	0.533	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C11829A	p.A3943A	CAGCTTGGCTCCT	.	PASS	Atlas-SNP
ABCB7	22	hgsc.bcm.edu	37	X	74284996	74284996	+	Silent	SNP	T	T	C	rs1340990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	121	248	0	0.484	0	T|0.867;0|0.003	.	strong	.	ABCB7	69	.	NM_004299	exon13	c.A1743G	p.A581A	TGCCACTGCATAC	.	PASS	Atlas-SNP
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358933	21358933	+	Missense_Mutation	SNP	G	G	C	rs59502379	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	55	156	0	0.366667	0	G|0.988;C|0.012	0.012	strong	.	SLCO1B1	151	.	NM_006446	exon11	c.G1463C	p.G488A	TAGCAGGTTGCAA	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Nonsense_Mutation	SNP	C	C	T	rs2294597	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	130	0	0.508065	0	C|0.774;T|0.226	0.226	strong	.	PLCB1	394	.	NM_182734	exon31	c.G3337T	p.G1113X	TTATAGCTAGAAG	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887282	52887282	+	Missense_Mutation	SNP	A	A	G	rs324125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	88	146	0	0.539877	0	A|0.833;G|0.167	0.167	strong	.	ZNF880	45	.	NM_001145434	exon4	c.A449G	p.Y150C	AAATTTATTCTAG	.	PASS	Atlas-SNP
TMEM176B	28959	hgsc.bcm.edu	37	7	150490376	150490376	+	Missense_Mutation	SNP	C	C	T	rs2072443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	31	69	0	0.492063	0	C|0.608;T|0.392	0.392	strong	.	TMEM176B	36	.	NM_014020	exon5	c.G400A	p.A134T	AGCCTGCCAGGGT	.	PASS	Atlas-SNP
PAG1	55824	hgsc.bcm.edu	37	8	81905397	81905397	+	Silent	SNP	A	A	G	rs2016465	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	48	0	1	0	A|0.513;G|0.487	0.487	strong	.	PAG1	39	.	NM_018440	exon4	c.T66C	p.A22A	GACAGCAGCCAGA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169519112	169519112	+	Missense_Mutation	SNP	C	C	T	rs6020	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	88	182	0	0.458333	0	C|0.805;T|0.195	0.195	strong	.	F5	301	.	NM_000130	exon10	c.G1538A	p.R513K	ATGTCTCTCATGA	.	PASS	Atlas-SNP
KITLG	4254	hgsc.bcm.edu	37	12	88912624	88912624	+	Silent	SNP	G	G	A	rs17015782	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	83	0	0.43617	0	G|0.988;A|0.012	0.012	strong	.	KITLG	26	.	NM_003994	exon4	c.C213T	p.S71S	CATCTCGCTTATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515093	195515093	+	Missense_Mutation	SNP	G	G	T	rs11916899	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	367	129	183	0	0.351499	0	A|0.002;G|0.995;T|0.004	0.004	strong	.	MUC4	1505	.	NM_018406	exon2	c.C3358A	p.P1120T	GAAGAGGGGTGGT	.	PASS	Atlas-SNP
HGF	3082	hgsc.bcm.edu	37	7	81388042	81388042	+	Silent	SNP	T	T	C	rs5745635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	159	0	1	0	T|0.896;C|0.104	0.104	strong	HGF,spleen,lymphoid_neoplasm,-2,1	HGF	171	1	NM_000601	exon3	c.A333G	p.E111E	GCCAAATTCTTTT	.	PASS	Atlas-SNP
RAPSN	5913	hgsc.bcm.edu	37	11	47463220	47463220	+	Silent	SNP	C	C	T	rs45603036	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	118	231	0	0.487603	0	C|0.891;T|0.109	0.109	strong	.	RAPSN	27	.	NM_005055	exon5	c.G855A	p.Q285Q	CTGCACCTGCCCC	.	PASS	Atlas-SNP
GJA4	2701	hgsc.bcm.edu	37	1	35259946	35259946	+	Silent	SNP	G	G	A	rs1764389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	162	189	0	1	0	G|0.731;A|0.269	0.269	strong	GJA4,NS,carcinoma,0,1	GJA4	25	1	NM_002060	exon2	c.G132A	p.V44V	GTCAGTGTGGGGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511310	195511310	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	29	517	1	0.221374	0.00193424	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7141G	p.H2381D	TGGTGTGACCTGA	.	PASS	Atlas-SNP
HSD17B11	51170	hgsc.bcm.edu	37	4	88278484	88278484	+	Silent	SNP	T	T	G	rs34025653	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	68	179	0	0.386364	0	T|0.938;G|0.062	0.062	strong	.	HSD17B11	28	.	NM_016245	exon5	c.A642C	p.T214T	CAGACATGTTGTT	.	PASS	Atlas-SNP
APOA4	337	hgsc.bcm.edu	37	11	116692558	116692558	+	Silent	SNP	G	G	A	rs5101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	31	92	0	0.364706	0	G|0.883;A|0.117	0.117	strong	.	APOA4	51	.	NM_000482	exon3	c.C216T	p.Y72Y	ACCTGCGTAAGTG	.	PASS	Atlas-SNP
SMTNL2	342527	hgsc.bcm.edu	37	17	4497137	4497137	+	Missense_Mutation	SNP	T	T	C	rs9916524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	45	129	0	0.381356	0	T|0.951;C|0.049	0.049	strong	.	SMTNL2	57	.	NM_001114974	exon4	c.T751C	p.W251R	TTCACGTGGTCTG	.	PASS	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	37	7	55433884	55433884	+	Missense_Mutation	SNP	A	A	C	rs2272263	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	9	35	0	0.230769	0	A|0.758;C|0.242	0.242	strong	.	LANCL2	54	.	NM_018697	exon1	c.A166C	p.T56P	GCGACCACGGATG	.	PASS	Atlas-SNP
LDB3	11155	hgsc.bcm.edu	37	10	88476458	88476458	+	Missense_Mutation	SNP	G	G	A	rs113817827	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	105	251	0	0.446809	0	G|0.998;A|0.002	0.002	strong	.	LDB3	164	.	NM_001171610	exon10	c.G1621A	p.V541I	GGGACCGTCCAGA	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114184477	114184477	+	Silent	SNP	C	C	T	rs868405	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	52	75	1	0.565217	0.0133333	C|0.909;T|0.091	0.091	strong	KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	NM_001080398	exon15	c.G1803A	p.R601R	TGGCATCCGACTG	.	scavenged	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	380390	380390	+	Silent	SNP	C	C	T	rs115057328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	64	73	0	0.615385	0	C|0.995;T|0.005	0.005	strong	.	B4GALNT4	83	.	NM_178537	exon18	c.C2814T	p.A938A	GCTGGCCTTCGCG	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6622139	6622139	+	Silent	SNP	G	G	T	rs148924682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	48	118	0	0.440367	0	G|0.990;T|0.010	0.010	strong	NSUN2,NS,carcinoma,-1,1	NSUN2	82	1	NM_017755	exon6	c.C612A	p.V204V	AAAGGGGACATTC	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs78240139		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	901	370	762	2	0.410655	0.00262467	C|0.500;G|0.500	0.500	weak	ZNF98_ENST00000357774,NS,carcinoma,0,4	ZNF98	230	4	NM_001098626	exon4	c.G1680C	p.K560N	GGAAATCTTTGCA	.	scavenged	Atlas-SNP
DEPDC4	120863	hgsc.bcm.edu	37	12	100657464	100657464	+	Missense_Mutation	SNP	T	T	C	rs7307415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	53	68	0	0.535354	0	T|0.876;C|0.124	0.124	strong	.	DEPDC4	34	.	NM_152317	exon2	c.A365G	p.H122R	CAAAGATGAACCC	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29840164	29840164	+	Silent	SNP	A	A	G	rs3740002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	23	53	0	0.425926	0	A|0.744;G|0.256	0.256	strong	.	SVIL	226	.	NM_003174	exon8	c.T189C	p.S63S	AGAATCAGAAGTT	.	PASS	Atlas-SNP
UPK3A	7380	hgsc.bcm.edu	37	22	45683309	45683309	+	Silent	SNP	C	C	T	rs62001037	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	30	67	0	0.447761	0	C|0.973;T|0.027	0.027	strong	.	UPK3A	14	.	NM_006953	exon3	c.C465T	p.P155P	CGCACCCCTGTCG	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31330280	31330280	+	Silent	SNP	A	A	G	rs2288242	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	61	0	1	0	A|0.207;G|0.793	0.793	strong	.	TRPM1	183	.	NM_001252020	exon18	c.T2457C	p.N819N	ATCCTCATTTTCC	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	66	137	0	0.496241	0	G|0.850;A|0.150	0.150	strong	.	MED24	89	.	NM_014815	exon26	c.C2886T	p.S962S	GGGGCTGGACATG	.	PASS	Atlas-SNP
LRRC24	441381	hgsc.bcm.edu	37	8	145748075	145748075	+	Silent	SNP	T	T	G	rs112652028	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	21	49	0	0.396226	0	T|0.986;G|0.014	0.014	strong	.	LRRC24	11	.	NM_001024678	exon5	c.A1326C	p.G442G	CAGCGCTCCCTCC	.	PASS	Atlas-SNP
OR2K2	26248	hgsc.bcm.edu	37	9	114090277	114090277	+	Missense_Mutation	SNP	G	G	A	rs73656223	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	44	85	0	0.564103	0	G|0.982;A|0.018	0.018	strong	.	OR2K2	77	.	NM_205859	exon1	c.C437T	p.T146M	GAGACCGTAGCCA	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22375868	22375868	+	Missense_Mutation	SNP	C	C	T	rs8104929	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	121	0	1	0	C|0.616;T|0.384	0.384	strong	.	ZNF676	146	.	NM_001001411	exon2	c.G80A	p.G27E	TCTTTTCCTTGCT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361439	107361439	+	Missense_Mutation	SNP	G	G	C	rs60573979	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	666	298	693	1	0.447447	0.001443	G|0.308;C|0.692	0.692	strong	.	OR13C5	60	.	NM_001004482	exon1	c.C256G	p.L86V	CTGAAAGGAAGCT	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5042715	5042715	+	Missense_Mutation	SNP	G	G	A	rs61740308	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	48	92	0	0.564706	0	G|0.881;A|0.119	0.119	strong	.	USP6	213	.	NM_004505	exon14	c.G1244A	p.C415Y	CGCCCTGTCCTGG	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801687	14801687	+	Silent	SNP	T	T	C	rs10738380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	322	135	252	0	0.419255	0	T|0.834;C|0.166	0.166	strong	.	FREM1	261	.	NM_144966	exon21	c.A3657G	p.A1219A	AACAGGTGCATGT	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109687288	109687288	+	Silent	SNP	T	T	C	rs1000152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	18	66	0	0.222222	0	T|0.801;C|0.199	0.199	strong	ZNF462,colon,carcinoma,0,1	ZNF462	322	1	NM_021224	exon3	c.T1095C	p.Y365Y	CCGTTATGGAATG	.	PASS	Atlas-SNP
PAPL	0	hgsc.bcm.edu	37	19	39575987	39575987	+	Silent	SNP	G	G	A	rs544041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	121	126	0	0.991803	0	G|0.870;A|0.130	0.130	strong	.	.	.	.	NM_001004318	exon2	c.G78A	p.G26G	CCTGGGGGCTCCC	.	PASS	Atlas-SNP
ETV7	51513	hgsc.bcm.edu	37	6	36343802	36343802	+	Silent	SNP	G	G	A	rs2234074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	9	29	0	0.391304	0	G|0.987;A|0.013	0.013	strong	.	ETV7	31	.	NM_001207035	exon3	c.C153T	p.P51P	CAGTGCGGGCTGG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281008	152281008	+	Silent	SNP	A	A	G	rs7512554	bycluster;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	969	500	480	2	0.515996	0.00416667	A|0.500;G|0.500	0.500	weak	.	FLG	900	.	NM_002016	exon3	c.T6354C	p.H2118H	ATCATAATGGGAT	.	PASS	Atlas-SNP
GMPPA	29926	hgsc.bcm.edu	37	2	220370746	220370746	+	Silent	SNP	G	G	A	rs13428617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	32	57	0	0.444444	0	G|0.979;A|0.021	0.021	strong	.	GMPPA	50	.	NM_205847	exon11	c.G945A	p.E315E	GGGTGAGGGTGTG	.	PASS	Atlas-SNP
FAM90A1	55138	hgsc.bcm.edu	37	12	8374812	8374812	+	Missense_Mutation	SNP	G	G	A	rs17855656	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	181	78	1	0.67037	0.0128205	G|0.833;A|0.167	0.167	strong	FAM90A1,caecum,carcinoma,0,1	FAM90A1	68	1	NM_018088	exon7	c.C1001T	p.P334L	GCTGGCGGAGGTT	.	scavenged	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	74	155	0	0.486842	0	G|0.840;A|0.159	0.159	strong	.	KANK3	35	.	NM_198471	exon10	c.C2310T	p.A770A	CTCCAGGGCGATG	.	PASS	Atlas-SNP
OR6N2	81442	hgsc.bcm.edu	37	1	158746678	158746678	+	Missense_Mutation	SNP	T	T	C	rs41273541	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	160	171	0	0.97561	0	T|0.900;C|0.100	0.100	strong	.	OR6N2	78	.	NM_001005278	exon1	c.A748G	p.I250V	AGAAGATGAGGAC	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45821582	45821582	+	Missense_Mutation	SNP	T	T	G	rs9974927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	46	97	0	0.511111	0	T|0.948;G|0.052	0.052	strong	.	TRPM2	196	.	NM_003307	exon16	c.T2340G	p.D780E	GCAGGATGTGGGC	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45750713	45750713	+	Missense_Mutation	SNP	C	C	T	rs62000360	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	80	157	0	0.516129	0	C|0.976;T|0.024	0.024	strong	.	C21orf2	10	.	NM_004928	exon6	c.G635A	p.R212K	CTGCCCCTGTGGC	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13715975	13715975	+	Silent	SNP	A	A	G	rs1805247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	42	78	0	0.488372	0	A|0.815;G|0.185	0.185	strong	GRIN2B,NS,carcinoma,-2,1	GRIN2B	303	1	NM_000834	exon13	c.T4197C	p.H1399H	GCTGCCATGGAGC	.	PASS	Atlas-SNP
PRR25	388199	hgsc.bcm.edu	37	16	863336	863336	+	Silent	SNP	T	T	C	rs11860086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	29	34	0	1	0	T|0.671;C|0.329	0.329	strong	.	PRR25	27	.	NM_001013638	exon3	c.T684C	p.A228A	CTCTGCTATTGCT	.	PASS	Atlas-SNP
PYROXD2	84795	hgsc.bcm.edu	37	10	100167396	100167396	+	Silent	SNP	G	G	A	rs12763326	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	28	62	0	0.5	0	G|0.643;A|0.356	0.356	strong	.	PYROXD2	43	.	NM_032709	exon4	c.C258T	p.R86R	GGACGCGCGGGAG	.	PASS	Atlas-SNP
POFUT2	23275	hgsc.bcm.edu	37	21	46685550	46685550	+	Silent	SNP	C	C	T	rs112907087	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	23	62	0	0.479167	0	C|0.992;T|0.008	0.008	strong	.	POFUT2	77	.	NM_133635	exon9	c.G1137A	p.R379R	AAAAAACCTGCAA	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7948175	7948175	+	Silent	SNP	C	C	T	rs6503070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	186	139	0	0.989362	0	A|0.000;C|0.449;T|0.551	0.551	strong	ALOX15B,NS,carcinoma,0,1	ALOX15B	66	1	NM_001141	exon6	c.C705T	p.D235D	GGAGGACGCCTTC	.	PASS	Atlas-SNP
NANOG	79923	hgsc.bcm.edu	37	12	7945757	7945757	+	Silent	SNP	C	C	T	rs78166980		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	77	136	0	0.44	0	.	.	weak	.	NANOG	30	.	NM_024865	exon2	c.C363T	p.S121S	CCTCAGCCTCCAG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46501268	46501268	+	Missense_Mutation	SNP	C	C	T	rs1126477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	107	189	2	0.521951	0.010582	C|0.578;T|0.421	0.421	strong	LTF,NS,carcinoma,+2,1	LTF	98	1	NM_002343	exon2	c.G85A	p.A29T	ATACGGCGCACCA	.	scavenged	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18368524	18368524	+	Silent	SNP	C	C	T	rs61740686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	93	56	0	0.978947	0	C|0.964;T|0.036	0.036	strong	.	KIAA1683	190	.	NM_001145304	exon4	c.G3570A	p.T1190T	CACCCACGTGACG	.	PASS	Atlas-SNP
DNAJC21	134218	hgsc.bcm.edu	37	5	34937649	34937649	+	Silent	SNP	G	G	A	rs77480286	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	108	257	1	0.473684	0.00389105	G|0.992;A|0.008	0.008	strong	DNAJC21,caecum,carcinoma,0,1	DNAJC21	54	1	NM_001012339	exon5	c.G657A	p.A219A	GCAGGCGCATCGA	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170965681	170965681	+	Silent	SNP	T	T	C	rs9427213	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	110	190	0	0.472103	0	T|0.882;C|0.118	0.118	strong	.	.	.	.	NM_025063	exon14	c.T1371C	p.N457N	GCTGAATTGTTCT	.	PASS	Atlas-SNP
CTRL	1506	hgsc.bcm.edu	37	16	67964203	67964203	+	Missense_Mutation	SNP	T	T	C	rs1134760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	53	112	0	0.456897	0	T|0.738;C|0.262	0.262	strong	.	CTRL	11	.	NM_001907	exon6	c.A518G	p.H173R	TGCAGATGTGCTG	.	PASS	Atlas-SNP
ADARB1	104	hgsc.bcm.edu	37	21	46641968	46641968	+	Silent	SNP	G	G	A	rs1051367	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	129	281	0	0.481343	0	G|0.494;A|0.506	0.506	strong	.	ADARB1	81	.	NM_015834	exon12	c.G2082A	p.K694K	TACCAAGCCCAAC	.	PASS	Atlas-SNP
GPR182	11318	hgsc.bcm.edu	37	12	57389536	57389536	+	Silent	SNP	G	G	A	rs61740222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	53	88	0	0.514563	0	G|0.987;A|0.013	0.013	strong	.	GPR182	35	.	NM_007264	exon2	c.G543A	p.S181S	CCTCTCGGCCATC	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	171969312	171969312	+	Silent	SNP	G	G	C	rs34553291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	17	29	0	0.435897	0	G|0.993;C|0.007	0.007	strong	FNDC3B,rectum,carcinoma,+1,1	FNDC3B	118	1	NM_001135095	exon6	c.G771C	p.S257S	AAAGTCGAATGAT	.	PASS	Atlas-SNP
INSL4	3641	hgsc.bcm.edu	37	9	5233664	5233664	+	Silent	SNP	A	A	G	rs7030463	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	33	55	0	0.540984	0	A|0.967;G|0.033	0.033	strong	INSL4,right_upper_lobe,carcinoma,+2,1	INSL4	20	1	NM_002195	exon2	c.A207G	p.S69S	GGTGTCAACCTCC	.	PASS	Atlas-SNP
NXN	64359	hgsc.bcm.edu	37	17	706933	706933	+	Missense_Mutation	SNP	C	C	T	rs61731770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	52	93	0	0.590909	0	C|0.977;T|0.023	0.023	strong	.	NXN	32	.	NM_022463	exon7	c.G1114A	p.V372I	CGGCTACGAAGAA	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118520170	118520170	+	Silent	SNP	G	G	A	rs7488309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	59	128	0	0.361963	0	G|0.506;A|0.494	0.494	strong	VSIG10,colon,carcinoma,0,1	VSIG10	41	1	NM_019086	exon3	c.C426T	p.Y142Y	GGCTGCGTAGAGG	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536357	1536357	+	Silent	SNP	G	G	A	rs112226694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	99	0	0.486842	0	G|0.979;A|0.021	0.021	strong	.	PTX4	46	.	NM_001013658	exon3	c.C1005T	p.F335F	GATCACGAAGTGG	.	PASS	Atlas-SNP
CALHM2	51063	hgsc.bcm.edu	37	10	105207176	105207176	+	Silent	SNP	G	G	A	rs2232663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	77	0	1	0	G|0.925;A|0.075	0.075	strong	.	CALHM2	30	.	NM_015916	exon4	c.C705T	p.A235A	CACCTCGGCCGTG	.	PASS	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	37	11	71725612	71725612	+	Silent	SNP	A	A	G	rs142372284	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	39	54	0	0.448276	0	A|0.995;G|0.005	0.005	strong	.	NUMA1	142	.	NM_006185	exon15	c.T2937C	p.N979N	CAGCTCATTGCCC	.	PASS	Atlas-SNP
SERPINB12	89777	hgsc.bcm.edu	37	18	61234091	61234091	+	Silent	SNP	C	C	T	rs35623491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	35	88	0	0.472973	0	C|0.962;T|0.038	0.038	strong	.	SERPINB12	55	.	NM_080474	exon7	c.C1065T	p.N355N	TGAAAACGGTACC	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7722048	7722048	+	Missense_Mutation	SNP	G	G	A	rs61743907	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	50	92	0	0.49505	0	G|0.989;A|0.011	0.011	strong	.	DNAH2	498	.	NM_020877	exon69	c.G10624A	p.A3542T	AACATCGCGGCTG	.	PASS	Atlas-SNP
ZACN	353174	hgsc.bcm.edu	37	17	74076504	74076504	+	Silent	SNP	G	G	A	rs8066946	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	45	74	0	0.56962	0	G|0.913;A|0.087	0.087	strong	.	ZACN	29	.	NM_180990	exon5	c.G543A	p.T181T	CAACACGGGTGCT	.	PASS	Atlas-SNP
CENPL	91687	hgsc.bcm.edu	37	1	173772506	173772506	+	Silent	SNP	T	T	G	rs16846420	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	85	176	0	0.497076	0	T|0.876;G|0.124	0.124	strong	.	CENPL	26	.	NM_001127181	exon6	c.A696C	p.A232A	TCCATTTGCAAGG	.	PASS	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681566	55681566	+	Missense_Mutation	SNP	G	G	A	rs61749302	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	33	69	0	0.37931	0	G|0.903;A|0.097	0.097	strong	OR5W2,NS,carcinoma,+1,5	OR5W2	112	5	NM_001001960	exon1	c.C493T	p.R165C	ATAGGCGGAAGGC	.	PASS	Atlas-SNP
TRMT6	51605	hgsc.bcm.edu	37	20	5923204	5923204	+	Missense_Mutation	SNP	T	T	C	rs451571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	342	341	360	2	0.997076	0.00555556	T|0.756;C|0.244	0.244	strong	.	TRMT6	28	.	NM_015939	exon7	c.A896G	p.E299G	TCTTGTTCAGAAG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110413806	110413806	+	Silent	SNP	G	G	A	rs200316129	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	136	0	0.523364	0	G|1.000;A|0.000	0.000	strong	PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	1	NM_177531	exon14	c.G1362A	p.Q454Q	TCTGCAGAAAGGA	.	PASS	Atlas-SNP
TSEN2	80746	hgsc.bcm.edu	37	3	12531421	12531421	+	Missense_Mutation	SNP	G	G	A	rs12495784	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	36	68	0	0.444444	0	A|0.068;G|0.932	0.068	strong	.	TSEN2	46	.	NM_001145394	exon2	c.G122A	p.R41H	TATTCCGTGCTGA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833369	82833369	+	Missense_Mutation	SNP	A	A	G	rs309559	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	29	88	0	0.508772	0	T|0.003;G|0.491	0.491	strong	.	VCAN	498	.	NM_004385	exon8	c.A4547G	p.K1516R	CAGCCAAAAAAGG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129910475	129910475	+	Missense_Mutation	SNP	T	T	G	rs997983	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	41	115	0	0.418367	0	T|0.906;G|0.094	0.094	strong	MKI67,rectum,carcinoma,0,2	MKI67	363	2	NM_002417	exon9	c.A1891C	p.I631L	GGCTGATAGACAC	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149323781	149323781	+	Silent	SNP	G	G	A	rs149256612	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	24	67	0	0.363636	0	G|1.000;A|0.000	0.000	strong	.	PDE6A	98	.	NM_000440	exon1	c.C456T	p.N152N	GGGGACGTTAGCA	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	37	19	42874900	42874900	+	Silent	SNP	C	C	T	rs28483598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	82	108	0	0.569444	0	C|0.981;T|0.019	0.019	strong	.	MEGF8	358	.	NM_001271938	exon40	c.C7053T	p.C2351C	CGTGTGCGTGAAC	.	PASS	Atlas-SNP
ZNF697	90874	hgsc.bcm.edu	37	1	120165412	120165412	+	Silent	SNP	G	G	A	rs61734323	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	72	154	0	0.470588	0	G|0.994;A|0.006	0.006	strong	.	ZNF697	26	.	NM_001080470	exon3	c.C1554T	p.N518N	CGGCTTGTTGCCC	.	PASS	Atlas-SNP
FBXO16	157574	hgsc.bcm.edu	37	8	28321153	28321153	+	Silent	SNP	A	A	G	rs7822086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	58	172	0	0.43609	0	A|0.932;G|0.068	0.068	strong	.	FBXO16	29	.	NM_172366	exon4	c.T318C	p.P106P	GCTCCGAGGGTCC	.	PASS	Atlas-SNP
VGLL2	245806	hgsc.bcm.edu	37	6	117591755	117591755	+	Silent	SNP	T	T	C	rs13194610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	7	24	0	0.212121	0	T|0.831;C|0.169	0.169	strong	.	VGLL2	18	.	NM_182645	exon3	c.T441C	p.N147N	CTGGAATAGCGCG	.	PASS	Atlas-SNP
CELA2B	51032	hgsc.bcm.edu	37	1	15808872	15808872	+	Missense_Mutation	SNP	G	G	A	rs3766160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	96	232	1	0.5	0.00431034	G|0.715;A|0.285	0.285	strong	.	CELA2B	37	.	NM_015849	exon4	c.G340A	p.D114N	AACTCCGACCAGG	.	PASS	Atlas-SNP
CLEC1A	51267	hgsc.bcm.edu	37	12	10224073	10224073	+	Missense_Mutation	SNP	T	T	G	rs77910243	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	31	78	0	0.326316	0	T|0.983;G|0.017	0.017	strong	.	CLEC1A	48	.	NM_016511	exon6	c.A702C	p.R234S	ACAGTCTCTGCTT	.	PASS	Atlas-SNP
ZNF684	127396	hgsc.bcm.edu	37	1	41006341	41006341	+	Silent	SNP	T	T	C	rs74575870	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	133	287	0	0.427653	0	T|0.973;C|0.027	0.027	strong	.	ZNF684	37	.	NM_152373	exon3	c.T99C	p.Y33Y	CCTGTATTGGGAT	.	PASS	Atlas-SNP
CHSY3	337876	hgsc.bcm.edu	37	5	129520932	129520932	+	Silent	SNP	T	T	G	rs73788438	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	55	122	0	0.462185	0	T|0.966;G|0.034	0.034	strong	CHSY3,colon,carcinoma,+2,2	CHSY3	92	2	NM_175856	exon3	c.T2097G	p.L699L	AGGTCTTGGTCTT	.	PASS	Atlas-SNP
COMMD2	51122	hgsc.bcm.edu	37	3	149459413	149459413	+	Silent	SNP	C	C	T	rs11549572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	147	234	0	0.517606	0	C|0.755;T|0.245	0.245	strong	.	COMMD2	21	.	NM_016094	exon5	c.G495A	p.L165L	TGTCTGCAGAACT	.	PASS	Atlas-SNP
C11orf85	283129	hgsc.bcm.edu	37	11	64714908	64714908	+	Silent	SNP	A	A	G	rs75184517	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	20	33	0	0.487805	0	A|0.982;G|0.018	0.018	strong	.	C11orf85	20	.	NM_001037225	exon7	c.T411C	p.A137A	CATCACAGCTCCT	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	37	20	47588949	47588949	+	Silent	SNP	G	G	A	rs116550473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	64	0	0.477612	0	G|0.996;A|0.004	0.004	strong	.	ARFGEF2	160	.	NM_006420	exon11	c.G1512A	p.T504T	TCTGACGAGGATC	.	PASS	Atlas-SNP
PRKAG2	51422	hgsc.bcm.edu	37	7	151257665	151257665	+	Silent	SNP	A	A	G	rs28763998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	45	119	0	0.45	0	A|0.955;G|0.045	0.045	strong	.	PRKAG2	86	.	NM_016203	exon15	c.T1623C	p.I541I	ACCCACAATACTA	.	PASS	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120384162	120384162	+	Missense_Mutation	SNP	G	G	A	rs78204967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	99	245	2	0.485294	0.00816326	G|0.983;A|0.017	0.017	strong	NBPF7,NS,carcinoma,0,1	NBPF7	46	1	NM_001047980	exon3	c.C400T	p.R134W	CTTCCCGTAACTT	.	scavenged	Atlas-SNP
CD180	4064	hgsc.bcm.edu	37	5	66479189	66479189	+	Silent	SNP	G	G	A	rs3733910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	57	132	0	0.504425	0	G|0.912;A|0.088	0.088	strong	.	CD180	78	.	NM_005582	exon3	c.C1482T	p.T494T	GCCCACGGTCTGA	.	PASS	Atlas-SNP
OR2H1	26716	hgsc.bcm.edu	37	6	29430356	29430356	+	Missense_Mutation	SNP	G	G	C	rs148433584	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	453	227	464	0	0.501104	0	G|0.995;C|0.005	0.005	strong	.	OR2H1	38	.	NM_030883	exon3	c.G810C	p.K270N	GGGCAAGTTCTTT	.	PASS	Atlas-SNP
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	352	6	310	4	0.0170455	0.0129032	.	.	none	HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	NM_002156	exon2	c.G39A	p.P13P	GGACACCGGTCTC	.	scavenged	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475763	140475763	+	Silent	SNP	C	C	G	rs61742867	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	14	175	0	0.0714286	0	C|0.029;G|0.971	0.971	strong	PCDHB2,NS,carcinoma,+2,2	PCDHB2	163	2	NM_018936	exon1	c.C1389G	p.R463R	CGTCCGCGAGAAC	.	scavenged	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71101206	71101206	+	Silent	SNP	A	A	G	rs75778420	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	70	0	0.407407	0	A|0.919;G|0.081	0.081	strong	.	HYDIN	788	.	NM_001198542	exon15	c.T2143C	p.L715L	TAATTAAGAGCGC	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54755923	54755923	+	Silent	SNP	A	A	G	rs12976868	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	110	268	0	0.514019	0	A|0.786;G|0.214	0.214	strong	.	LILRB5	176	.	NM_001081442	exon12	c.T1623C	p.D541D	CCGAGCATCCATC	.	PASS	Atlas-SNP
ARHGEF4	50649	hgsc.bcm.edu	37	2	131802045	131802045	+	Silent	SNP	C	C	T	rs10928515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	40	74	0	0.493827	0	A|0.000;C|0.838;G|0.000;T|0.161	0.161	strong	ARHGEF4,NS,carcinoma,0,1	ARHGEF4	89	1	NM_032995	exon12	c.C1773T	p.P591P	GAAGCCCGAGCAG	.	PASS	Atlas-SNP
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357581	39357581	+	Silent	SNP	C	C	T	rs72487648	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	67	81	0	0.465278	0	C|0.803;T|0.197	0.197	strong	.	APOBEC3A	20	.	NM_145699	exon3	c.C364T	p.L122L	GTGAGACTGCGTA	.	PASS	Atlas-SNP
C8orf44	56260	hgsc.bcm.edu	37	8	67592152	67592152	+	Missense_Mutation	SNP	T	T	C	rs1057463	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	56	0	0.5	0	T|0.781;C|0.219	0.219	strong	.	C8orf44	18	.	NM_019607	exon3	c.T443C	p.F148S	AAGGCTTCTGGAG	.	PASS	Atlas-SNP
CACNA2D3	55799	hgsc.bcm.edu	37	3	55108188	55108188	+	Silent	SNP	A	A	G	rs35471424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	62	163	0	0.512397	0	A|0.903;G|0.097	0.097	strong	.	CACNA2D3	159	.	NM_018398	exon38	c.A3231G	p.T1077T	CCAGACAGTCCTC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124265687	124265687	+	Missense_Mutation	SNP	T	T	C	rs11057353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	74	153	0	0.486842	0	T|0.310;C|0.690	0.690	strong	.	DNAH10	888	.	NM_207437	exon6	c.T499C	p.S167P	GTCACATCTGGAG	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167167186	167167186	+	Silent	SNP	T	T	A	rs6770577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	50	101	0	0.45045	0	T|0.632;A|0.368	0.368	strong	.	SERPINI2	85	.	NM_001012303	exon8	c.A999T	p.S333S	TTCAGATGAATCT	.	PASS	Atlas-SNP
SSFA2	6744	hgsc.bcm.edu	37	2	182780817	182780817	+	Missense_Mutation	SNP	C	C	T	rs16867510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	92	191	1	0.489362	0.0052356	C|0.965;T|0.035	0.035	strong	SSFA2,colon,carcinoma,0,1	SSFA2	130	1	NM_001130445	exon11	c.C2450T	p.A817V	GTGAGGCGCCGCG	.	scavenged	Atlas-SNP
PRAME	23532	hgsc.bcm.edu	37	22	22899234	22899234	+	Missense_Mutation	SNP	A	A	G	rs1129172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	88	123	0	0.988764	0	G|0.653;N|0.000	0.653	strong	PRAME,NS,carcinoma,0,4	PRAME	78	4	NM_206954	exon3	c.T19C	p.W7R	TTACCCACAAACG	.	PASS	Atlas-SNP
ADCY3	109	hgsc.bcm.edu	37	2	25046090	25046090	+	Silent	SNP	T	T	C	rs1127568	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	47	83	0	0.54023	0	T|0.344;C|0.656	0.656	strong	.	ADCY3	114	.	NM_004036	exon17	c.A2871G	p.S957S	AAAATCTGAGATG	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44559578	44559578	+	Silent	SNP	G	G	A	rs149717505	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	77	170	0	0.5	0	G|0.998;A|0.002	0.002	strong	.	TCEB3B	141	.	NM_016427	exon1	c.C2058T	p.S686S	CTGGCTGGAGGGA	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39180100	39180100	+	Missense_Mutation	SNP	G	G	A	rs80238762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	111	236	1	0.470339	0.00423729	G|0.989;A|0.011	0.011	strong	.	TTC21A	96	.	NM_145755	exon28	c.G3871A	p.E1291K	GCCATTGAAATCT	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	65	106	0	0.590909	0	C|0.651;T|0.349	0.349	strong	.	AKR1B15	105	.	NM_001080538	exon12	c.C1020T	p.F340F	TCCCTTCGATGCA	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	37	20	47626847	47626847	+	Silent	SNP	T	T	C	rs2295580	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	113	0	1	0	A|0.003;C|0.372;G|0.003;T|0.622	0.372	strong	ARFGEF2,colon,carcinoma,0,1	ARFGEF2	160	1	NM_006420	exon27	c.T3663C	p.G1221G	CTCAGGTTGGAAG	.	PASS	Atlas-SNP
ARVCF	421	hgsc.bcm.edu	37	22	19960666	19960666	+	Missense_Mutation	SNP	G	G	A	rs115736959	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	19	24	0	0.5	0	G|0.985;A|0.015	0.015	strong	.	ARVCF	54	.	NM_001670	exon14	c.C2414T	p.A805V	ACCAACGCTGGCA	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558528	140558528	+	Missense_Mutation	SNP	A	A	G	rs3733694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	74	304	0	0.490066	0	G|0.146;N|0.001	0.146	strong	.	PCDHB8	199	.	NM_019120	exon1	c.A913G	p.K305E	CGACTAAAGAAAC	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3627619	3627619	+	Silent	SNP	C	C	T	rs1185511	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	5	0	0	0.714286	.	C|0.779;T|0.221	0.221	strong	.	GSG2	48	.	NM_031965	exon1	c.C390T	p.C130C	ACCCTGCGGCCCG	.	PASS	Atlas-SNP
BTNL9	153579	hgsc.bcm.edu	37	5	180485374	180485374	+	Silent	SNP	T	T	C	rs60738644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	141	281	0	0.465347	0	T|0.963;C|0.037	0.037	strong	.	BTNL9	58	.	NM_152547	exon10	c.T978C	p.Y326Y	AAAATATGCAGGT	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122515924	122515924	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	4	144	0	0.028169	0	.	.	none	PRDM6,colon,carcinoma,+1,1	PRDM6	26	1	NM_001136239	exon7	c.G1580A	p.R527Q	GTGACCGGCCTTT	.	scavenged	Atlas-SNP
TMEM64	169200	hgsc.bcm.edu	37	8	91637929	91637929	+	Silent	SNP	T	T	C	rs75193995	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	77	207	0	0.442529	0	T|0.995;C|0.005	0.005	strong	.	TMEM64	31	.	NM_001008495	exon3	c.A1113G	p.T371T	AGAAAATGTTAGG	.	PASS	Atlas-SNP
ZNFX1	57169	hgsc.bcm.edu	37	20	47874005	47874005	+	Silent	SNP	A	A	G	rs3021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	79	227	0	0.446328	0	A|0.821;G|0.179;T|0.000	0.179	strong	.	ZNFX1	194	.	NM_021035	exon8	c.T2613C	p.H871H	GCCACAATGGTCT	.	PASS	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	37	22	26688401	26688401	+	Silent	SNP	T	T	C	rs16981666	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	32	62	0	0.533333	0	T|0.927;C|0.073	0.073	strong	.	SEZ6L	174	.	NM_001184777	exon2	c.T124C	p.L42L	AGCCCTTTGGGTC	.	PASS	Atlas-SNP
FPR1	2357	hgsc.bcm.edu	37	19	52250216	52250216	+	Missense_Mutation	SNP	A	A	G	rs5030878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	117	247	0	0.515419	0	A|0.201;G|0.799	0.799	strong	.	FPR1	64	.	NM_001193306	exon3	c.T32C	p.I11T	CCAGAGATGTTCG	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804327	804327	+	Silent	SNP	C	C	T	rs10420953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	22	34	0	0.458333	0	C|0.916;T|0.084	0.084	strong	.	PTBP1	43	.	NM_031990	exon5	c.C324T	p.N108N	TGCCAACACCATG	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862845	5862845	+	Missense_Mutation	SNP	A	A	G	rs4592451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	74	135	0	0.510345	0	A|0.608;G|0.392	0.392	strong	.	OR52E6	70	.	NM_001005167	exon1	c.T283C	p.S95P	CAAAAGATATTTC	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11991328	11991328	+	Missense_Mutation	SNP	G	G	A	rs144333235	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	18	51	0	0.276923	0	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_001256869	exon1	c.C191T	p.P64L	TCCCTGGGAGCAA	.	PASS	Atlas-SNP
B9D2	80776	hgsc.bcm.edu	37	19	41869392	41869392	+	Missense_Mutation	SNP	T	T	C	rs2241714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	122	117	0	0.99187	0	T|0.311;C|0.689	0.689	strong	.	B9D2	9	.	NM_030578	exon2	c.A33G	p.I11M	GGCCCCTATGATC	.	PASS	Atlas-SNP
UGGT2	55757	hgsc.bcm.edu	37	13	96648384	96648384	+	Missense_Mutation	SNP	T	T	C	rs73562939	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	98	212	0	0.455814	0	T|0.976;C|0.024	0.024	strong	.	UGGT2	127	.	NM_020121	exon7	c.A763G	p.T255A	TATTAGTCACAGC	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1057738	1057738	+	Silent	SNP	G	G	A	rs60281693	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	15	40	0	0.483871	0	G|0.931;A|0.069	0.069	strong	.	SLC12A7	97	.	NM_006598	exon22	c.C2874T	p.T958T	GGACGCGGTGTTC	.	PASS	Atlas-SNP
ITGB5	3693	hgsc.bcm.edu	37	3	124515509	124515509	+	Silent	SNP	G	G	A	rs2291088	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	67	128	0	0.531746	0	G|0.851;A|0.149	0.149	strong	.	ITGB5	66	.	NM_002213	exon10	c.C1419T	p.S473S	CCTGGCGCTGTTG	.	PASS	Atlas-SNP
PRSS1	5644	hgsc.bcm.edu	37	7	142460744	142460744	+	Missense_Mutation	SNP	G	G	C	rs150930992	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	420	10	382	2	0.0238095	0.0052356	G|0.582;C|0.418	0.418	strong	PRSS1,NS,carcinoma,0,1	PRSS1	68	1	NM_002769	exon5	c.G617C	p.C206S	TGGTCTGCAATGG	.	scavenged	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122392038	122392038	+	Missense_Mutation	SNP	C	C	T	rs11043265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	69	105	1	0.985714	0.00952381	C|0.752;T|0.248	0.248	strong	.	WDR66	143	.	NM_001178003	exon10	c.C1333T	p.L445F	AACAAGCTTGTGG	.	PASS	Atlas-SNP
NYNRIN	57523	hgsc.bcm.edu	37	14	24877699	24877699	+	Missense_Mutation	SNP	A	A	G	rs74036628	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	20	41	0	0.454545	0	A|0.934;G|0.066	0.066	strong	.	NYNRIN	120	.	NM_025081	exon3	c.A823G	p.S275G	GCCCAGAGCACAC	.	PASS	Atlas-SNP
GGH	8836	hgsc.bcm.edu	37	8	63938764	63938764	+	Missense_Mutation	SNP	G	G	A	rs11545078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	58	117	0	0.487395	0	G|0.919;A|0.081	0.081	strong	GGH,NS,carcinoma,0,1	GGH	32	1	NM_003878	exon5	c.C452T	p.T151I	GTGGCAGTTAATA	.	PASS	Atlas-SNP
ORM2	5005	hgsc.bcm.edu	37	9	117094119	117094119	+	Silent	SNP	G	G	A	rs148394636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	46	176	0	0.252747	0	G|0.931;A|0.069	0.069	strong	.	ORM2	13	.	NM_000608	exon5	c.G450A	p.E150E	GCCAGAGACGACC	.	PASS	Atlas-SNP
OAS2	4939	hgsc.bcm.edu	37	12	113435450	113435450	+	Silent	SNP	A	A	T	rs1293755	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	108	0	1	0	A|0.208;T|0.792	0.792	strong	.	OAS2	86	.	NM_002535	exon4	c.A753T	p.V251V	AACCGTACTGGAG	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38568308	38568308	+	Silent	SNP	C	C	T	rs6579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	62	105	0	0.521008	0	C|0.476;T|0.524	0.524	strong	TTC3,NS,carcinoma,+1,1	TTC3	182	1	NM_001001894	exon42	c.C5550T	p.H1850H	TGAGCACCTGTCA	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	95	209	0	0.43379	0	G|0.912;A|0.088	0.088	strong	.	RUFY1	101	.	NM_025158	exon14	c.G1728A	p.R576R	ACTCAGGATGGAG	.	PASS	Atlas-SNP
EIF4G2	1982	hgsc.bcm.edu	37	11	10821185	10821185	+	Silent	SNP	G	G	A	rs11542384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	86	191	0	0.434343	0	T|0.000;G|0.885;C|0.000;A|0.115	0.115	strong	.	EIF4G2	89	.	NM_001172705	exon19	c.C2238T	p.S746S	TTGAGGGGATGGA	.	PASS	Atlas-SNP
KDM1B	221656	hgsc.bcm.edu	37	6	18213988	18213988	+	Silent	SNP	C	C	T	rs6903583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	107	240	0	0.442149	0	C|0.808;T|0.192	0.192	strong	.	KDM1B	58	.	NM_153042	exon15	c.C1389T	p.A463A	TTTTGCCGTGTTC	.	PASS	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51783820	51783820	+	Silent	SNP	T	T	C	rs10851500	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	49	87	0	0.445455	0	T|0.514;C|0.486	0.486	strong	DMXL2,NS,carcinoma,0,1	DMXL2	262	1	NM_001174116	exon20	c.A4908G	p.G1636G	CCACCATCCTATG	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86591141	86591141	+	Missense_Mutation	SNP	A	A	G	rs17128866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	64	98	0	0.547009	0	A|0.915;G|0.085	0.085	strong	COL24A1,NS,carcinoma,+1,2	COL24A1	202	2	NM_152890	exon3	c.T878C	p.I293T	TTTATGATATTTG	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51917735	51917735	+	Silent	SNP	G	G	A	rs1974821	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	66	113	1	0.673469	0.00884956	G|0.795;A|0.205	0.205	strong	SIGLEC12_ENST00000439889,NS,carcinoma,0,2	SIGLEC10	112	2	NM_033130	exon9	c.C1650T	p.N550N	CGCTCCGTTGGAG	.	scavenged	Atlas-SNP
PVR	5817	hgsc.bcm.edu	37	19	45150763	45150763	+	Silent	SNP	G	G	A	rs10421291	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	86	0	0.43617	0	G|0.937;A|0.063	0.063	strong	.	PVR	23	.	NM_001135769	exon2	c.G348A	p.E116E	CGTAGAGGATGAA	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	75	173	0	0.572519	0	T|0.747;C|0.253	0.253	strong	ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	NM_025003	exon36	c.A5352G	p.R1784R	TTCCCTTCTACTC	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39180099	39180099	+	Silent	SNP	T	T	C	rs784498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	229	234	0	1	0	T|0.306;C|0.694	0.694	strong	.	TTC21A	96	.	NM_145755	exon28	c.T3870C	p.I1290I	GGCCATTGAAATC	.	PASS	Atlas-SNP
CYLD	1540	hgsc.bcm.edu	37	16	50783696	50783696	+	Silent	SNP	C	C	T	rs34564491	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	26	50	0	0.433333	0	C|0.991;T|0.009	0.009	strong	.	CYLD	150	.	NM_001042355	exon3	c.C87T	p.S29S	ATGCAGCGTTACA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82835852	82835852	+	Missense_Mutation	SNP	C	C	T	rs61733401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	80	166	0	0.457143	0	C|0.965;T|0.035	0.035	strong	.	VCAN	498	.	NM_004385	exon8	c.C7030T	p.P2344S	GAAGGACCCACGG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537306	88537306	+	Silent	SNP	T	T	C	rs374381786		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	402	36	183	3	0.0895522	0.0163934	.	.	weak	DSPP,rectum,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.T3492C	p.D1164D	CAGCGATAGCAGC	.	scavenged	Atlas-SNP
ITGA9	3680	hgsc.bcm.edu	37	3	37536020	37536020	+	Silent	SNP	C	C	T	rs62001860	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	312	150	326	1	0.480769	0.00306748	C|0.994;T|0.006	0.006	strong	.	ITGA9	98	.	NM_002207	exon5	c.C573T	p.H191H	GGAACACGGCTCC	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7229346	7229346	+	Silent	SNP	T	T	C	rs2714315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	89	96	0	0.988889	0	T|0.555;C|0.445	0.445	strong	.	RREB1	242	.	NM_001003700	exon10	c.T1014C	p.H338H	GACCCATGTGGCG	.	PASS	Atlas-SNP
GPSM2	29899	hgsc.bcm.edu	37	1	109465084	109465084	+	Missense_Mutation	SNP	T	T	A	rs61758992	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	78	197	0	0.438202	0	T|1.000;A|0.000	0.000	weak	.	GPSM2	56	.	NM_013296	exon13	c.T1486A	p.L496I	GACTTATTAAGCC	.	PASS	Atlas-SNP
WFIKKN2	124857	hgsc.bcm.edu	37	17	48913352	48913352	+	Silent	SNP	G	G	A	rs117494161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	63	110	0	0.588785	0	G|0.982;A|0.018	0.018	strong	.	WFIKKN2	69	.	NM_175575	exon1	c.G54A	p.A18A	GGCAGCGCTGCTG	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	24	92	0	0.45283	0	C|0.748;T|0.252	0.252	strong	LMF1,NS,carcinoma,0,1	LMF1	42	1	NM_022773	exon4	c.G543A	p.G181G	CAGGAACCCCGTC	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32184785	32184785	+	Missense_Mutation	SNP	C	C	G	rs11963697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	95	178	0	0.452381	0	C|0.989;G|0.011;T|0.000	0.011	strong	.	NOTCH4	201	.	NM_004557	exon11	c.G1798C	p.V600L	CTCCAACGGGACA	.	PASS	Atlas-SNP
PREB	10113	hgsc.bcm.edu	37	2	27354306	27354306	+	Silent	SNP	C	C	T	rs61276776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	38	96	0	0.436782	0	C|0.989;T|0.011	0.011	strong	.	PREB	37	.	NM_013388	exon9	c.G1230A	p.Q410Q	GGCACTCTGGAGC	.	PASS	Atlas-SNP
DCAF15	90379	hgsc.bcm.edu	37	19	14066772	14066772	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	5	87	0	0.0442478	0	.	.	none	.	DCAF15	30	.	NM_138353	exon4	c.T415C	p.Y139H	GACCTGTACCTGA	.	PASS	Atlas-SNP
VTN	7448	hgsc.bcm.edu	37	17	26694861	26694861	+	Missense_Mutation	SNP	G	G	A	rs704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	47	84	0	0.566265	0	G|0.469;A|0.531	0.531	strong	.	VTN	45	.	NM_000638	exon7	c.C1199T	p.T400M	AGCCACGTGGCGC	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276909	71276909	+	Silent	SNP	G	G	A	rs12289712	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	34	149	0	0.19209	0	A|0.153;G|0.847	0.153	strong	KRTAP5-10,rectum,carcinoma,0,3	KRTAP5-10	37	3	NM_001012710	exon1	c.G276A	p.G92G	CAAGGGGGGCTGT	.	scavenged	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	100226883	100226883	+	Missense_Mutation	SNP	T	T	A	rs1216183	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	54	117	0	0.568421	0	T|0.706;A|0.294	0.294	strong	CNTN5_ENST00000524871,colon,carcinoma,-2,2	CNTN5	324	2	NM_001243270	exon24	c.T3235A	p.S1079T	CTTCACTCTCTCT	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135359073	135359073	+	Silent	SNP	G	G	A	rs115458424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	70	115	0	0.555556	0	G|0.979;A|0.021	0.021	strong	.	HBS1L	75	.	NM_001145207	exon5	c.C522T	p.P174P	ATCAAAGGGTTTG	.	PASS	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107450525	107450525	+	Missense_Mutation	SNP	T	T	C	rs12615112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	89	183	1	0.445	0.00546448	T|0.811;C|0.189	0.189	strong	ST6GAL2,NS,carcinoma,0,1	ST6GAL2	159	1	NM_032528	exon3	c.A1021G	p.I341V	TGCGTATGGTGGT	.	scavenged	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43650915	43650915	+	Silent	SNP	C	C	T	rs41298781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	59	112	0	0.508621	0	C|0.955;T|0.045	0.045	strong	CSGALNACT2,NS,carcinoma,+2,1	CSGALNACT2	67	1	NM_018590	exon2	c.C318T	p.G106G	TAATGGCATAGGC	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047322	46047322	+	Silent	SNP	G	G	A	rs74337742		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	76	135	0	0.452381	0	.	.	weak	.	KRTAP10-9	24	.	NM_198690	exon1	c.G234A	p.S78S	GCCCTCGTGCTGC	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6981353	6981353	+	Silent	SNP	G	G	C	rs732828	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	80	158	0	0.467836	0	G|0.584;C|0.416	0.416	strong	.	CLEC10A	40	.	NM_182906	exon3	c.C147G	p.L49L	CAGCAGGAGGCCG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47754576	47754576	+	Missense_Mutation	SNP	A	A	C	rs200285580	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	333	48	293	0	0.144144	0	A|0.999;G|0.001	.	alt	.	PCNT	283	.	NM_006031	exon3	c.A533C	p.Q178P	ACCACCAACCGGA	.	PASS	Atlas-SNP
GPR150	285601	hgsc.bcm.edu	37	5	94957071	94957071	+	Silent	SNP	A	A	T	rs375018988		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	14	21	0	0.666667	0	.	.	weak	.	GPR150	7	.	NM_199243	exon1	c.A1092T	p.R364R	CCGGCGACAGCTG	.	PASS	Atlas-SNP
AGO1	26523	hgsc.bcm.edu	37	1	36359669	36359669	+	Silent	SNP	A	A	G	rs2296470	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	35	75	0	0.479452	0	A|0.788;G|0.212	0.212	strong	.	.	.	.	NM_012199	exon6	c.A681G	p.P227P	ACAGCCAGTGATT	.	PASS	Atlas-SNP
PLA1A	51365	hgsc.bcm.edu	37	3	119327653	119327653	+	Silent	SNP	T	T	C	rs1723969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	193	158	0	1	0	T|0.678;C|0.322	0.322	strong	.	PLA1A	65	.	NM_001206960	exon3	c.T312C	p.F104F	CACATTTATTAGA	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	120989335	120989335	+	Missense_Mutation	SNP	A	A	G	rs612969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	129	0	1	0	A|0.525;G|0.475	0.475	strong	.	TECTA	329	.	NM_005422	exon6	c.A1111G	p.R371G	CACCGCAGAGGTT	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57829301	57829301	+	Missense_Mutation	SNP	T	T	C	rs259956	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	66	109	1	0.485294	0.00917431	T|0.411;C|0.589	0.589	strong	ZNF831,caecum,carcinoma,0,1	ZNF831	287	1	NM_178457	exon5	c.T4537C	p.S1513P	GCTGAATCACGAG	.	scavenged	Atlas-SNP
GFRA2	2675	hgsc.bcm.edu	37	8	21608105	21608105	+	Silent	SNP	C	C	G	rs2229903	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	81	135	0	0.543624	0	C|0.935;G|0.065	0.065	strong	.	GFRA2	23	.	NM_001495	exon4	c.G789C	p.L263L	CCGACACAGGTGG	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123152019	123152019	+	Missense_Mutation	SNP	C	C	T	rs10255061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	112	1	1	0.00892857	C|0.741;T|0.259	0.259	strong	IQUB,NS,adenoma,0,2	IQUB	117	2	NM_178827	exon2	c.G376A	p.V126M	CTTCCACTGATTC	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	137	268	0	0.462838	0	G|0.472;A|0.528	0.528	strong	.	RHBG	133	.	NM_020407	exon6	c.G943A	p.G315R	TTGGCTGGGACTG	.	PASS	Atlas-SNP
GCAT	23464	hgsc.bcm.edu	37	22	38211728	38211728	+	Silent	SNP	A	A	G	rs34340481	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	119	214	0	0.452471	0	A|0.958;G|0.042	0.042	strong	.	GCAT	27	.	NM_001171690	exon7	c.A951G	p.P317P	CCGGCCATACCTC	.	PASS	Atlas-SNP
ARSF	416	hgsc.bcm.edu	37	X	3028260	3028260	+	Silent	SNP	C	C	T	rs17051478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	110	183	0	0.547264	0	C|0.873;0|0.002	.	strong	.	ARSF	97	.	NM_004042	exon10	c.C1357T	p.L453L	TCCTACCTGCACG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160738803	160738803	+	Missense_Mutation	SNP	G	G	A	rs35675007	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	27	77	0	0.350649	0	G|0.996;A|0.004	0.004	strong	LY75,NS,carcinoma,+1,1	LY75	151	1	NM_002349	exon7	c.C1078T	p.R360C	CACAGCGGGTATC	.	PASS	Atlas-SNP
CCRL2	9034	hgsc.bcm.edu	37	3	46449864	46449864	+	Silent	SNP	G	G	T	rs6808835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	131	257	0	0.530364	0	G|0.831;T|0.169	0.169	strong	.	CCRL2	23	.	NM_001130910	exon2	c.G330T	p.G110G	TGCTGGGGGCGAT	.	PASS	Atlas-SNP
PPARGC1B	133522	hgsc.bcm.edu	37	5	149200008	149200008	+	Missense_Mutation	SNP	G	G	A	rs45518035	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	28	30	0	0.622222	0	G|0.994;A|0.006	0.006	strong	.	PPARGC1B	74	.	NM_133263	exon2	c.G91A	p.G31R	GGGTCCGGGGAGG	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44084739	44084739	+	Silent	SNP	C	C	T	rs1143701	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	116	86	0	0.966667	0	A|0.000;C|0.209;T|0.790	0.790	strong	.	PTPRF	172	.	NM_002840	exon27	c.C4512T	p.R1504R	GAAGCGCGAGCTG	.	PASS	Atlas-SNP
ERBB2	2064	hgsc.bcm.edu	37	17	37863268	37863268	+	Silent	SNP	G	G	A	rs4252610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	63	128	0	0.459854	0	G|0.982;A|0.018	0.018	strong	.	ERBB2	429	.	NM_004448	exon2	c.G99A	p.L33L	GAAGCTGCGGCTC	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346670	140346670	+	Silent	SNP	C	C	A	rs155809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	11	28	0	0.392857	0	C|0.979;A|0.021	0.021	strong	.	PCDHAC2	142	.	NM_031883	exon1	c.C319A	p.R107R	ATTGATCGGGAGG	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	26	63	0	0.440678	0	G|0.286;A|0.714	0.714	strong	GOT2,NS,carcinoma,0,1	GOT2	42	1	NM_002080	exon7	c.C816T	p.C272C	GCAGAGGCAAACA	.	PASS	Atlas-SNP
OAS2	4939	hgsc.bcm.edu	37	12	113444285	113444285	+	Silent	SNP	C	C	T	rs16942424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	54	70	0	0.509434	0	C|0.957;T|0.043	0.043	strong	.	OAS2	86	.	NM_002535	exon8	c.C1536T	p.S512S	TAAATCCTCGGAC	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11252	11252	+	Missense_Mutation	SNP	A	A	G	rs3915952	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	13	12	0	1	0	A|0.936;G|0.064	0.064	strong	.	.	.	.	ENST00000361381	exon1	c.A493G	p.I165V	GCACTAATTTACA	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617413	183617413	+	Silent	SNP	T	T	C	rs12045762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	26	86	0	0.371429	0	T|0.934;C|0.066	0.066	strong	.	APOBEC4	45	.	NM_203454	exon2	c.A504G	p.A168A	GTTCCATGCTGAG	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	35	68	0	0.5	0	G|0.862;A|0.138	0.138	strong	.	ATP9B	96	.	NM_198531	exon3	c.G336A	p.E112E	GAAAGAGCTGAAA	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039779	239039779	+	Silent	SNP	G	G	A	rs73102306	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	4	8	0	0.5	0	G|0.922;A|0.078	0.078	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2424A	p.L808L	CCTGCTGGGCAAC	.	PASS	Atlas-SNP
CDH13	1012	hgsc.bcm.edu	37	16	82892037	82892037	+	Missense_Mutation	SNP	A	A	G	rs72807847	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	64	165	0	0.361582	0	A|0.972;G|0.028	0.028	strong	.	CDH13	97	.	NM_001220488	exon3	c.A257G	p.N86S	ATATCAATCAGCC	.	PASS	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	37	14	69259662	69259662	+	Silent	SNP	C	C	A	rs1051533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	72	0	0.451613	0	C|0.791;A|0.209	0.209	strong	.	ZFP36L1	47	.	NM_001244701	exon2	c.G201T	p.T67T	CCTGTGCGTTCGC	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104117191	104117191	+	Silent	SNP	A	A	G	rs2290943	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	38	69	0	0.513514	0	A|0.848;G|0.152	0.152	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon4	c.T243C	p.T81T	AAATATAGTACCT	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1110829	1110829	+	Silent	SNP	G	G	A	rs2302109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	194	208	0	1	0	G|0.461;A|0.539	0.539	strong	.	SBNO2	112	.	NM_014963	exon26	c.C2943T	p.N981N	CAGGGCGTTCTGC	.	PASS	Atlas-SNP
SLC25A37	51312	hgsc.bcm.edu	37	8	23429093	23429093	+	Missense_Mutation	SNP	G	G	T	rs116050502	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	40	50	0	0.615385	0	G|0.994;T|0.006	0.006	strong	.	SLC25A37	27	.	NM_016612	exon4	c.G742T	p.A248S	GCCCTCGCCGCGG	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	6995438	6995438	+	Silent	SNP	C	C	T	rs1803675	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	91	160	0	0.52907	0	C|0.723;T|0.277	0.277	strong	.	HDHD1	21	.	NM_001135565	exon4	c.G402A	p.L134L	GGTGGCCAGTGCA	.	PASS	Atlas-SNP
MTO1	25821	hgsc.bcm.edu	37	6	74190448	74190448	+	Silent	SNP	T	T	C	rs2036039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	99	198	0	0.532258	0	T|0.668;G|0.032;C|0.170;N|0.000;A|0.130	0.170	strong	MTO1,NS,carcinoma,0,1	MTO1	59	1	NM_133645	exon8	c.T1255C	p.L419L	CCTTCCTTGGAGA	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048663	33048663	+	Missense_Mutation	SNP	G	G	A	rs1042153	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	18	33	9	0.580645	0.272727	G|0.755;A|0.245	0.245	strong	HLA-DPB1,NS,lymphoid_neoplasm,+2,1	HLA-DPB1	28	1	NM_002121	exon2	c.G315A	p.M105I	CAGGATGTGCAGA	.	scavenged	Atlas-SNP
SP100	6672	hgsc.bcm.edu	37	2	231380146	231380146	+	Missense_Mutation	SNP	G	G	A	rs61733089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	40	80	0	0.512821	0	G|0.991;A|0.009	0.009	strong	.	SP100	167	.	NM_003113	exon25	c.G2431A	p.A811T	AACACCGCTGCAG	.	PASS	Atlas-SNP
TSPAN8	7103	hgsc.bcm.edu	37	12	71523134	71523134	+	Missense_Mutation	SNP	A	A	C	rs1051334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	76	142	0	0.493506	0	A|0.689;C|0.311	0.311	strong	.	TSPAN8	30	.	NM_004616	exon8	c.T637G	p.S213A	CAAATGATATTCC	.	PASS	Atlas-SNP
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	405	220	301	0	0.54321	0	C|0.751;G|0.249	0.249	strong	.	OR6B3	37	.	NM_173351	exon1	c.G657C	p.A219A	GATGTGCGCATAT	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103205949	103205949	+	Silent	SNP	G	G	C	rs78221963	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	31	70	0	0.476923	0	G|0.993;C|0.007	0.007	strong	.	RELN	593	.	NM_173054	exon34	c.C4986G	p.T1662T	CAAAAAGGTAGAT	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1537693	1537693	+	Missense_Mutation	SNP	C	C	A	rs61734779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	77	72	0	0.987179	0	C|0.868;A|0.132	0.132	strong	.	PTX4	46	.	NM_001013658	exon2	c.G405T	p.R135S	TGCCTTCCTTTCC	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6303354	6303354	+	Missense_Mutation	SNP	G	G	A	rs734312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	98	145	0	0.518519	0	G|0.550;A|0.450	0.450	strong	WFS1,NS,carcinoma,+1,2	WFS1	71	2	NM_001145853	exon8	c.G1832A	p.R611H	TGTTGCGCTGGTG	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3576475	3576475	+	Missense_Mutation	SNP	A	A	C	rs35603863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	55	97	0	0.514019	0	A|0.981;C|0.019	0.019	strong	.	CLUAP1	32	.	NM_015041	exon9	c.A919C	p.K307Q	CTGCTCAAGAGTG	.	PASS	Atlas-SNP
WHSC1L1	54904	hgsc.bcm.edu	37	8	38205133	38205133	+	Missense_Mutation	SNP	G	G	A	rs13034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	86	224	0	0.455026	0	G|0.983;A|0.017	0.017	strong	.	WHSC1L1	137	.	NM_017778	exon2	c.C557T	p.T186M	GATTTCGTGTGCT	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107084716	107084716	+	Missense_Mutation	SNP	C	C	T	rs190902687	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	437	193	341	0	0.441648	0	C|0.992;T|0.008	0.008	strong	.	RGPD3	316	.	NM_001144013	exon1	c.G29A	p.R10Q	ACGTACCGCTCCC	.	PASS	Atlas-SNP
ITGAD	3681	hgsc.bcm.edu	37	16	31422531	31422531	+	Silent	SNP	T	T	C	rs368058587		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	104	179	0	0.454148	0	.	.	weak	.	ITGAD	154	.	NM_005353	exon13	c.T1491C	p.P497P	CTTGCCTAGGGGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149522163	149522163	+	Missense_Mutation	SNP	C	C	G	rs73727642	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	23	85	0	0.348485	0	C|0.974;G|0.026	0.026	strong	.	.	.	.	NM_198455	exon96	c.C13950G	p.C4650W	AGGCTGCCGGGAG	.	PASS	Atlas-SNP
JPH2	57158	hgsc.bcm.edu	37	20	42744587	42744587	+	Silent	SNP	G	G	C	rs74352869	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	21	0	0	1	.	G|0.824;C|0.176	0.176	strong	JPH2,NS,carcinoma,0,1	JPH2	86	1	NM_020433	exon4	c.C1728G	p.P576P	GGGCTCGGGCGGC	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135370639	135370639	+	Missense_Mutation	SNP	C	C	A	rs8181357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	89	157	0	0.511494	0	C|0.892;A|0.108	0.108	strong	SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	NM_001143763	exon7	c.G396T	p.E132D	CTTGCACTCCTGC	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	37	6	84925636	84925636	+	Silent	SNP	A	A	C	rs9449840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	31	74	0	0.5	0	A|0.936;C|0.064	0.064	strong	.	KIAA1009	119	.	NM_014895	exon4	c.T177G	p.L59L	TCCAAGAAGTCCT	.	PASS	Atlas-SNP
SIPA1	6494	hgsc.bcm.edu	37	11	65418048	65418048	+	Silent	SNP	G	G	A	rs76089059	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	105	210	0	0.435685	0	G|0.964;A|0.036	0.036	strong	SIPA1,colon,carcinoma,+1,1	SIPA1	45	1	NM_006747	exon16	c.G2991A	p.A997A	GAAGGCGGACAGG	.	PASS	Atlas-SNP
SLC24A4	123041	hgsc.bcm.edu	37	14	92922900	92922900	+	Silent	SNP	G	G	A	rs77671856	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	34	69	1	0.485714	0.0144928	G|0.792;A|0.208	0.208	strong	SLC24A4,colon,carcinoma,0,1	SLC24A4	112	1	NM_153646	exon12	c.G1203A	p.P401P	ACCACCGCCAGAG	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678372	100678372	+	Silent	SNP	T	T	G	rs11769823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	39	116	0	0.209677	0	T|0.914;G|0.086	0.086	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3675G	p.P1225P	TATGCCTGTCAGA	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2820043	2820043	+	Silent	SNP	G	G	T	rs4876056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	49	118	0	0.569767	0	G|0.871;T|0.129	0.129	strong	CSMD1_ENST00000318252,NS,carcinoma,-1,1	CSMD1	1469	1	NM_033225	exon61	c.C9573A	p.S3191S	TCTTCTGGAGGAT	.	PASS	Atlas-SNP
C2orf43	60526	hgsc.bcm.edu	37	2	21001192	21001192	+	Missense_Mutation	SNP	A	A	G	rs139472393	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	34	112	0	0.373626	0	A|0.999;G|0.001	0.001	strong	.	C2orf43	28	.	NM_021925	exon2	c.T32C	p.V11A	TCATGCACAGGAA	.	PASS	Atlas-SNP
GPR85	54329	hgsc.bcm.edu	37	7	112724147	112724147	+	Silent	SNP	G	G	A	rs28392728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	39	91	0	0.414894	0	G|0.978;A|0.022	0.022	strong	.	GPR85	49	.	NM_001146265	exon3	c.C630T	p.H210H	TCGATCGTGGACG	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145639681	145639681	+	Missense_Mutation	SNP	G	G	C	rs1871534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	315	136	262	0	0.431746	0	G|0.744;C|0.256	0.256	strong	.	SLC39A4	54	.	NM_130849	exon6	c.C1114G	p.L372V	CAGTGAGTGCACC	.	PASS	Atlas-SNP
ZNF567	163081	hgsc.bcm.edu	37	19	37210529	37210529	+	Silent	SNP	A	A	G	rs3108200	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	184	144	0	1	0	A|0.701;G|0.299	0.299	strong	.	ZNF567	61	.	NM_152603	exon4	c.A810G	p.R270R	TCAGAGAACTCAC	.	PASS	Atlas-SNP
HAS1	3036	hgsc.bcm.edu	37	19	52223026	52223026	+	Silent	SNP	C	C	A	rs61736497	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	16	20	0	0.592593	0	C|0.947;A|0.053	0.053	strong	.	HAS1	61	.	NM_001523	exon2	c.G135T	p.P45P	GGCCAGCGGCACC	.	PASS	Atlas-SNP
UBE4B	10277	hgsc.bcm.edu	37	1	10211588	10211588	+	Silent	SNP	G	G	A	rs149899336	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	86	179	0	0.480447	0	G|0.999;A|0.001	0.001	strong	.	UBE4B	233	.	NM_001105562	exon21	c.G2895A	p.L965L	CAAGTTGTTGGTA	.	PASS	Atlas-SNP
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	77	116	0	0.516779	0	A|0.954;G|0.046	0.046	strong	.	FNDC3A	93	.	NM_001079673	exon24	c.A3049G	p.T1017A	GAGTCAACATCCT	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6302707	6302707	+	Silent	SNP	C	C	T	rs1801206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	207	224	0	1	0	C|0.405;T|0.595	0.595	strong	.	WFS1	71	.	NM_001145853	exon8	c.C1185T	p.V395V	CGAGGTCAACTTC	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935258	4935258	+	Missense_Mutation	SNP	A	A	T	rs145318499		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	54	151	0	0.362416	0	.	.	weak	.	PPL	168	.	NM_002705	exon22	c.T3398A	p.L1133H	CGGGTGAGATCGC	.	PASS	Atlas-SNP
CIZ1	25792	hgsc.bcm.edu	37	9	130938650	130938650	+	Silent	SNP	G	G	A	rs45475893	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	86	102	0	0.722689	0	G|0.994;A|0.006	0.006	strong	.	CIZ1	75	.	NM_001257975	exon11	c.C2013T	p.D671D	CAGGACGTCCCGG	.	PASS	Atlas-SNP
OR8U1	219417	hgsc.bcm.edu	37	11	56143113	56143113	+	Missense_Mutation	SNP	A	A	G	rs116344671	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	99	156	0	0.502538	0	A|0.974;G|0.026	0.026	strong	.	OR8U1	59	.	NM_001005204	exon1	c.A14G	p.N5S	ACATCAATTGCAC	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4869792	4869792	+	Missense_Mutation	SNP	A	A	G	rs57238061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	77	0	0.542169	0	A|0.944;G|0.056	0.056	strong	.	OR51S1	83	.	NM_001004758	exon1	c.T647C	p.L216S	GGGTCCAAACCCA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62259637	62259637	+	Missense_Mutation	SNP	C	C	T	rs3784634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	136	0	1	0	C|0.293;T|0.707	0.707	strong	.	VPS13C	506	.	NM_020821	exon29	c.G2921A	p.R974K	GGCTTCCTTTTGG	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808526	18808526	+	Missense_Mutation	SNP	A	A	C	rs2992752	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	50	54	1	1	0.0185185	A|0.310;C|0.690	0.690	strong	KLHDC7A,NS,carcinoma,0,1	KLHDC7A	60	1	NM_152375	exon1	c.A1051C	p.T351P	CCGCAGACAGGGC	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677405	100677405	+	Missense_Mutation	SNP	G	G	A	rs141963257		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	34	102	0	0.21118	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.G2708A	p.R903H	AAGCCCGTTCGTC	.	PASS	Atlas-SNP
DMP1	1758	hgsc.bcm.edu	37	4	88584160	88584160	+	Silent	SNP	G	G	A	rs2615497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	62	142	0	0.455882	0	G|0.715;A|0.285	0.285	strong	DMP1,caecum,carcinoma,0,1	DMP1	72	1	NM_004407	exon6	c.G1230A	p.E410E	CAGTGAGAGCCTC	.	PASS	Atlas-SNP
PIN4	5303	hgsc.bcm.edu	37	X	71416721	71416721	+	Silent	SNP	C	C	T	rs11415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	234	259	0	0.991525	0	C|0.810;0|0.003	.	strong	.	PIN4	8	.	NM_001170747	exon3	c.C279T	p.A93A	AGTGGCCGCACAG	.	PASS	Atlas-SNP
ZNF292	23036	hgsc.bcm.edu	37	6	87969480	87969480	+	Missense_Mutation	SNP	G	G	A	rs6910541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	93	185	0	0.484375	0	G|0.875;A|0.125	0.125	strong	.	ZNF292	479	.	NM_015021	exon8	c.G6133A	p.V2045I	CAACTTGTAGAAA	.	PASS	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078424	2078424	+	Silent	SNP	G	G	T	rs34059622	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	65	0	0.509091	0	G|0.982;T|0.018	0.018	strong	.	.	.	.	NM_130807	exon3	c.C136A	p.R46R	CCAGCCGCAGGTC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179611680	179611680	+	Silent	SNP	G	G	A	rs72648911	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	99	181	0	0.521053	0	G|0.954;A|0.046	0.046	strong	.	TTN	18412	.	NM_133379	exon46	c.C15447T	p.Y5149Y	AGGTGTGTAGAAA	.	PASS	Atlas-SNP
GAPDH	2597	hgsc.bcm.edu	37	12	6646320	6646320	+	Silent	SNP	T	T	C	rs1065691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	13	32	0	0.464286	0	T|0.687;C|0.313	0.313	strong	.	GAPDH	20	.	NM_002046	exon6	c.T381C	p.D127D	TGCTGATGCCCCC	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14766	14766	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	122	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.C20T	p.T7I	GCAAAACTAACCC	.	PASS	Atlas-SNP
CAPN9	10753	hgsc.bcm.edu	37	1	230910339	230910339	+	Silent	SNP	G	G	A	rs7517389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	157	289	0	0.523333	0	G|0.936;A|0.064	0.064	strong	.	CAPN9	116	.	NM_006615	exon8	c.G915A	p.K305K	GCAGAAGCGTCTG	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921110	12921110	+	Missense_Mutation	SNP	A	A	G	rs12139546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	82	166	0	0.398058	0	A|0.887;G|0.113	0.113	strong	PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	NM_023014	exon4	c.A901G	p.T301A	GAATTAACTTGTG	.	PASS	Atlas-SNP
OBP2B	29989	hgsc.bcm.edu	37	9	136083580	136083580	+	Silent	SNP	T	T	G	rs2073870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	131	125	0	1	0	T|0.223;G|0.777	0.777	strong	.	OBP2B	20	.	NM_014581	exon3	c.A217C	p.R73R	TGCACCTATCCTC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47955167	47955167	+	Silent	SNP	A	A	G	rs17131941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	24	46	0	0.55814	0	A|0.981;G|0.019	0.019	strong	.	PKD1L1	328	.	NM_138295	exon8	c.T1090C	p.L364L	TATCCAACTGAAA	.	PASS	Atlas-SNP
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	34	65	0	0.523077	0	T|0.829;G|0.171	0.171	strong	.	NCOA7	92	.	NM_001199619	exon17	c.T2826G	p.D942E	ATTTGATTGAAAT	.	PASS	Atlas-SNP
HIP1	3092	hgsc.bcm.edu	37	7	75221693	75221693	+	Silent	SNP	C	C	T	rs144446822	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	35	49	0	0.648148	0	C|0.999;T|0.001	0.001	strong	.	HIP1	91	.	NM_005338	exon3	c.G324A	p.P108P	CACGTTCGGGTGT	.	PASS	Atlas-SNP
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	54	0	1	0	T|0.791;C|0.209	0.209	strong	CAV3,NS,carcinoma,0,1	CAV3	20	1	NM_033337	exon2	c.T123C	p.F41F	GGATTTTGAAGAC	.	PASS	Atlas-SNP
OR2T6	254879	hgsc.bcm.edu	37	1	248551636	248551636	+	Missense_Mutation	SNP	T	T	G	rs954475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	123	267	0	0.514644	0	T|0.707;G|0.293	0.293	strong	.	OR2T6	101	.	NM_001005471	exon1	c.T727G	p.S243A	TGCTCTTCACACA	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17270751	17270751	+	Silent	SNP	G	G	A	rs12025984	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	5	10	0	0.277778	0	G|0.762;A|0.238	0.238	strong	.	CROCC	185	.	NM_014675	exon14	c.G1965A	p.A655A	TGGCGCGCGGGTG	.	PASS	Atlas-SNP
PNPLA5	150379	hgsc.bcm.edu	37	22	44287062	44287062	+	Silent	SNP	A	A	G	rs2071884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	109	165	0	0.509346	0	A|0.657;G|0.343	0.343	strong	PNPLA5,NS,carcinoma,0,3	PNPLA5	46	3	NM_138814	exon2	c.T306C	p.D102D	CAGAGCATCCTGC	.	PASS	Atlas-SNP
CASP4	837	hgsc.bcm.edu	37	11	104825597	104825597	+	Missense_Mutation	SNP	C	C	T	rs56226603	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	60	181	0	0.333333	0	C|0.969;T|0.031	0.031	strong	.	CASP4	57	.	NM_001225	exon2	c.G139A	p.D47N	TAGCATCGTAATA	.	PASS	Atlas-SNP
TMEM41B	440026	hgsc.bcm.edu	37	11	9305136	9305136	+	Silent	SNP	G	G	A	rs77349011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	33	58	0	1	0	G|0.941;A|0.059	0.059	strong	TMEM41B,NS,haematopoietic_neoplasm,0,1	TMEM41B	22	1	NM_015012	exon7	c.C711T	p.V237V	AGGTGCGACACCT	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32032756	32032756	+	Missense_Mutation	SNP	A	A	T	rs3749960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	65	130	0	0.515873	0	A|0.947;T|0.053	0.053	strong	.	TNXB	553	.	NM_019105	exon19	c.T6683A	p.F2228Y	TTCTTAAACTGGA	.	PASS	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	37	4	9784642	9784642	+	Missense_Mutation	SNP	C	C	A	rs1800762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	61	72	0	0.586538	0	C|0.986;A|0.014	0.014	strong	DRD5,NS,carcinoma,0,1	DRD5	119	1	NM_000798	exon1	c.C989A	p.P330Q	GCCCTCCGGCCGG	.	PASS	Atlas-SNP
GRB10	2887	hgsc.bcm.edu	37	7	50742326	50742326	+	Missense_Mutation	SNP	T	T	C	rs185094083	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	26	66	0	0.38806	0	T|0.999;C|0.001	0.001	strong	.	GRB10	155	.	NM_005311	exon3	c.A169G	p.N57D	TATCGTTCACCAG	.	PASS	Atlas-SNP
TMEM45B	120224	hgsc.bcm.edu	37	11	129722512	129722512	+	Silent	SNP	C	C	T	rs115605173	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	132	235	0	0.532258	0	C|0.991;T|0.009	0.009	strong	.	TMEM45B	25	.	NM_138788	exon2	c.C135T	p.L45L	GCGTCTCGAGATC	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15713446	15713446	+	Silent	SNP	C	C	T	rs2302463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	76	137	0	0.496732	0	C|0.946;T|0.054	0.054	strong	BST1,NS,carcinoma,0,1	BST1	30	1	NM_004334	exon4	c.C468T	p.S156S	CCAATCCTGCCCT	.	PASS	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462885	37462885	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	3	195	1	0.0157068	0.00512821	.	.	none	TMPRSS6,NS,neuroblastoma,+1,1	TMPRSS6	99	1	NM_153609	exon17	c.G2258A	p.G753D	TTCTTGCCCTTGC	.	scavenged	Atlas-SNP
GTPBP2	54676	hgsc.bcm.edu	37	6	43590408	43590408	+	Silent	SNP	G	G	A	rs16896609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	121	0	1	0	G|0.812;A|0.188	0.188	strong	.	GTPBP2	39	.	NM_019096	exon10	c.C1429T	p.L477L	GCGCCAGTGTAGC	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41552840	41552840	+	Silent	SNP	G	G	A	rs34969689	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	85	173	0	0.472222	0	G|0.987;A|0.013	0.013	strong	.	ANK1	497	.	NM_001142446	exon28	c.C3093T	p.I1031I	CTCCACGATTACA	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52198619	52198619	+	Silent	SNP	C	C	A	rs78786003	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	52	118	0	0.468468	0	C|0.985;A|0.015	0.015	strong	.	ZNF217	227	.	NM_006526	exon1	c.G747T	p.A249A	TGTCTGCGCGCTG	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234394569	234394569	+	Silent	SNP	A	A	G	rs2603547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	51	119	0	0.435897	0	A|0.749;G|0.251	0.251	strong	.	USP40	174	.	NM_018218	exon28	c.T3285C	p.Y1095Y	AGGGGCATAGGTC	.	PASS	Atlas-SNP
MGAT4A	11320	hgsc.bcm.edu	37	2	99256447	99256447	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	42	78	0	0.512195	0	.	.	none	.	MGAT4A	51	.	NM_012214	exon12	c.A1146T	p.K382N	TAATGGTTTCATA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9080462	9080462	+	Missense_Mutation	SNP	C	C	G	rs2547065	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	42	71	0	0.415842	0	C|0.370;G|0.630	0.630	strong	.	MUC16	4315	.	NM_024690	exon2	c.G9569C	p.S3190T	GGACTGCTCCCCG	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	37	15	50534789	50534789	+	Missense_Mutation	SNP	A	A	G	rs16963486	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	65	135	0	0.528455	0	A|0.975;G|0.025	0.025	strong	.	HDC	86	.	NM_002112	exon12	c.T1657C	p.F553L	CTGAAAAGCAGTC	.	PASS	Atlas-SNP
MDH2	4191	hgsc.bcm.edu	37	7	75684273	75684273	+	Silent	SNP	G	G	A	rs77424348	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	54	69	0	0.701299	0	G|0.984;A|0.016	0.016	strong	.	MDH2	35	.	NM_005918	exon2	c.G192A	p.V64V	CGGAGTGGCCGCA	.	PASS	Atlas-SNP
SF3B3	23450	hgsc.bcm.edu	37	16	70602221	70602221	+	Silent	SNP	C	C	T	rs12909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	220	255	0	1	0	C|0.569;T|0.431	0.431	strong	SF3B3,NS,carcinoma,0,1	SF3B3	99	1	NM_012426	exon22	c.C2988T	p.I996I	GACTATCGGACAT	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187524176	187524176	+	Missense_Mutation	SNP	G	G	A	rs200262460	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	71	122	0	0.577236	0	G|1.000;A|0.000	0.000	strong	.	FAT1	500	.	NM_005245	exon20	c.C11363T	p.P3788L	ACAGGTGGGCACC	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140589334	140589334	+	Silent	SNP	A	A	G	rs149716951	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	64	138	0	0.528926	0	A|0.994;G|0.006	0.006	strong	.	PCDHB12	179	.	NM_018932	exon1	c.A855G	p.S285S	TGCCTCAGAAGAT	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3850910	3850910	+	Silent	SNP	A	A	G	rs55837933	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	26	38	0	0.604651	0	A|0.928;G|0.072	0.072	strong	.	ATP2A3	148	.	NM_174956	exon8	c.T870C	p.R290R	AGCGCCACGCAGC	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120054215	120054215	+	Missense_Mutation	SNP	A	A	G	rs6201	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	103	203	0	0.507389	0	A|0.902;G|0.098	0.098	strong	.	HSD3B1	53	.	NM_000862	exon3	c.A235G	p.I79V	TCGGTCATCATCC	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247013733	247013733	+	Missense_Mutation	SNP	T	T	C	rs79472697		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	408	167	406	0	0.409314	0	.	.	weak	.	AHCTF1	187	.	NM_015446	exon33	c.A5602G	p.K1868E	CTTTTTTAGTAGT	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242063448	242063448	+	Silent	SNP	G	G	A	rs2302052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	66	135	0	0.488889	0	G|0.898;A|0.102	0.102	strong	.	PASK	230	.	NM_015148	exon11	c.C2820T	p.A940A	CCTGGCGGCTGAG	.	PASS	Atlas-SNP
SLC22A5	6584	hgsc.bcm.edu	37	5	131705949	131705949	+	Silent	SNP	T	T	C	rs61742215	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	58	108	0	0.483333	0	T|0.732;C|0.268	0.268	strong	.	SLC22A5	34	.	NM_003060	exon1	c.T285C	p.L95L	GGCGCTTGGGCTG	.	PASS	Atlas-SNP
UPK3A	7380	hgsc.bcm.edu	37	22	45691594	45691594	+	Silent	SNP	A	A	G	rs1057356	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	33	55	0	0.6	0	A|0.474;G|0.526	0.526	strong	.	UPK3A	14	.	NM_006953	exon6	c.A858G	p.Q286Q	GCTCCAAGACTGA	.	PASS	Atlas-SNP
CEACAM1	634	hgsc.bcm.edu	37	19	43031514	43031514	+	Missense_Mutation	SNP	G	G	T	rs8111171	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	124	214	0	0.56621	0	G|0.888;T|0.112	0.112	strong	.	CEACAM1	43	.	NM_001184816	exon2	c.C103A	p.Q35K	TGAGCTGGGCAGT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23915089	23915089	+	Missense_Mutation	SNP	G	G	T	rs139993038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	71	190	1	0.387978	0.00526316	A|0.000;G|0.999;T|0.001	0.001	strong	SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	NM_014363	exon10	c.C2926A	p.R976S	CCAGACGAATAGT	.	scavenged	Atlas-SNP
LRFN2	57497	hgsc.bcm.edu	37	6	40400823	40400823	+	Silent	SNP	C	C	T	rs61731039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	35	69	0	0.507246	0	C|0.950;T|0.050	0.050	strong	LRFN2,NS,carcinoma,-1,1	LRFN2	133	1	NM_020737	exon2	c.G30A	p.A10A	GCCAAACGCTAGC	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231248261	231248261	+	Missense_Mutation	SNP	C	C	T	rs28497362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	132	239	0	0.487085	0	C|0.819;T|0.181	0.181	strong	.	SP140L	68	.	NM_138402	exon8	c.C674T	p.T225M	TGGGAACGAGAAC	.	PASS	Atlas-SNP
S100A5	6276	hgsc.bcm.edu	37	1	153509892	153509892	+	Silent	SNP	A	A	G	rs2248745	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	81	150	0	0.460227	0	A|0.877;G|0.123	0.123	strong	S100A5,NS,carcinoma,-2,1	S100A5	10	1	NM_002962	exon4	c.T159C	p.D53D	CAAGTCATCGATG	.	PASS	Atlas-SNP
SERPINF2	5345	hgsc.bcm.edu	37	17	1648502	1648502	+	Missense_Mutation	SNP	C	C	T	rs2070863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	38	64	0	0.5	0	C|0.794;T|0.206	0.206	strong	.	SERPINF2	33	.	NM_000934	exon3	c.C97T	p.R33W	TTGGGCCGGCAGG	.	PASS	Atlas-SNP
OAS1	4938	hgsc.bcm.edu	37	12	113357193	113357193	+	Splice_Site	SNP	G	G	A	rs10774671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	64	0	0.477612	0	G|0.396;A|0.604	0.604	strong	.	OAS1	128	.	NM_016816	exon6	c.1039-1G>A	.	CTTTCAGGCTGAA	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71495320	71495320	+	Silent	SNP	G	G	A	rs115914542	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	87	122	0	0.533742	0	G|0.999;A|0.001	0.001	strong	MAP1B,rectum,carcinoma,0,2	MAP1B	243	2	NM_005909	exon5	c.G6138A	p.E2046E	TGCAGAGAAAATC	.	PASS	Atlas-SNP
PLB1	151056	hgsc.bcm.edu	37	2	28855840	28855840	+	Silent	SNP	C	C	T	rs3752902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	66	115	0	0.507692	0	C|0.881;T|0.119	0.119	strong	PLB1_ENST00000422425,NS,carcinoma,+1,2	PLB1	255	2	NM_153021	exon56	c.C4032T	p.S1344S	CTTCTCCGAGGAC	.	PASS	Atlas-SNP
CRELD2	79174	hgsc.bcm.edu	37	22	50315363	50315363	+	Missense_Mutation	SNP	C	C	A	rs8139422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	118	0	1	0	C|0.811;A|0.189	0.189	strong	CRELD2_ENST00000404488,NS,lymphoid_neoplasm,+2,6	CRELD2	57	6	NM_024324	exon5	c.C546A	p.D182E	CATGGACGGCTAC	.	PASS	Atlas-SNP
HSD3B2	3284	hgsc.bcm.edu	37	1	119962118	119962118	+	Missense_Mutation	SNP	G	G	A	rs4986954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	88	161	0	0.44898	0	G|0.996;A|0.004	0.004	strong	.	HSD3B2	48	.	NM_001166120	exon3	c.G220A	p.D74N	TGCCAGGACGTCT	.	PASS	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	107002806	107002806	+	Missense_Mutation	SNP	A	A	G	rs2269970	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	238	194	0	0.995816	0	A|0.339;G|0.661	0.661	strong	COG5,NS,carcinoma,0,1	COG5	78	1	NM_006348	exon9	c.T988C	p.F330L	TCCAGAATGAGGC	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57732012	57732012	+	Missense_Mutation	SNP	G	G	A	rs55645458	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	110	0	0.523364	0	G|0.971;A|0.029	0.029	strong	.	CCDC135	97	.	NM_032269	exon2	c.G151A	p.D51N	CTCAGAGACCTGG	.	PASS	Atlas-SNP
PROKR2	128674	hgsc.bcm.edu	37	20	5283051	5283051	+	Missense_Mutation	SNP	G	G	A	rs148868355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	37	74	0	0.474359	0	G|0.999;A|0.001	0.001	strong	.	PROKR2	90	.	NM_144773	exon2	c.C790T	p.R264C	GCTTGCGAATCTG	.	PASS	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109661359	109661359	+	Missense_Mutation	SNP	C	C	G	rs3825491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	48	65	0	0.489796	0	C|0.610;G|0.390	0.390	strong	.	MYO16	285	.	NM_001198950	exon22	c.C2557G	p.P853A	TATTCTCCTGGTA	.	PASS	Atlas-SNP
KCNK10	54207	hgsc.bcm.edu	37	14	88693725	88693725	+	Silent	SNP	G	G	C	rs2277524	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	47	84	0	0.435185	0	G|0.690;C|0.310	0.310	strong	.	KCNK10	273	.	NM_138318	exon4	c.C675G	p.V225V	TCGAAAGACCTTC	.	PASS	Atlas-SNP
AKR1C2	1646	hgsc.bcm.edu	37	10	5043749	5043749	+	Missense_Mutation	SNP	G	G	A	rs147648222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	172	297	0	0.52439	0	G|0.998;A|0.002	0.002	strong	.	AKR1C2	68	.	NM_001354	exon4	c.C209T	p.A70V	CCATCTGCAATCT	.	PASS	Atlas-SNP
HIP1R	9026	hgsc.bcm.edu	37	12	123341199	123341199	+	Missense_Mutation	SNP	A	A	C	rs7972242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	42	108	0	0.477273	0	A|0.954;C|0.046	0.046	strong	.	HIP1R	68	.	NM_003959	exon17	c.A1546C	p.K516Q	CTGGAGAAGCTCA	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140590766	140590766	+	Missense_Mutation	SNP	A	A	G	rs2910006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	82	0	1	0	A|0.559;G|0.441	0.441	strong	PCDHB12,tonsil,carcinoma,0,1	PCDHB12	179	1	NM_018932	exon1	c.A2287G	p.K763E	TCAAATAAGTTCA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101727766	101727766	+	Silent	SNP	T	T	C	rs201406152		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	6	102	0	0.0434783	0	T|0.998;C|0.002	0.002	weak	PABPC1,colon,carcinoma,-2,6	PABPC1	76	6	NM_002568	exon4	c.A567G	p.E189E	GGTGAATTCTTTT	.	scavenged	Atlas-SNP
METTL21B	25895	hgsc.bcm.edu	37	12	58174306	58174306	+	Silent	SNP	T	T	C	rs923829	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	36	96	0	0.553846	0	T|0.672;C|0.328	0.328	strong	.	METTL21B	16	.	NM_015433	exon3	c.T558C	p.H186H	GGAGCATGGGACA	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14316642	14316642	+	Silent	SNP	G	G	A	rs55920001	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	116	243	0	0.464	0	G|0.957;A|0.043	0.043	strong	.	TRIO	305	.	NM_007118	exon9	c.G1521A	p.S507S	GAAGTCGCTCCTT	.	PASS	Atlas-SNP
FILIP1	27145	hgsc.bcm.edu	37	6	76022541	76022541	+	Missense_Mutation	SNP	G	G	A	rs34807169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	109	241	1	0.459916	0.00414938	G|0.973;A|0.027	0.027	strong	.	FILIP1	173	.	NM_015687	exon5	c.C3007T	p.P1003S	ATGTGGGCCTGTC	.	PASS	Atlas-SNP
GNG8	94235	hgsc.bcm.edu	37	19	47137459	47137459	+	Silent	SNP	C	C	T	rs12974613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	84	0	1	0	C|0.728;T|0.272	0.272	strong	.	GNG8	2	.	NM_033258	exon2	c.G87A	p.V29V	CTGCGACACCTGC	.	PASS	Atlas-SNP
KIAA1024	23251	hgsc.bcm.edu	37	15	79748603	79748603	+	Silent	SNP	C	C	T	rs7183867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	142	143	0	0.986111	0	C|0.813;T|0.187	0.187	strong	.	KIAA1024	146	.	NM_015206	exon2	c.C114T	p.F38F	CCGGTTCGACCTG	.	PASS	Atlas-SNP
FAM186B	84070	hgsc.bcm.edu	37	12	49993678	49993678	+	Missense_Mutation	SNP	C	C	T	rs52824916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	64	165	0	0.42953	0	C|0.886;T|0.114	0.114	strong	.	FAM186B	72	.	NM_032130	exon4	c.G1745A	p.R582Q	TGGGTCCGGCTTG	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587889	39587889	+	Silent	SNP	T	T	C	rs3751377	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	53	105	0	0.452991	0	T|0.809;C|0.191	0.191	strong	.	.	.	.	NM_025138	exon11	c.A1500G	p.L500L	AGAAGATAGTGAA	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	37	12	94976159	94976159	+	Silent	SNP	T	T	C	rs3747551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	68	84	0	0.561983	0	T|0.673;C|0.327	0.327	strong	.	TMCC3	63	.	NM_020698	exon2	c.A234G	p.V78V	CTCTGTTACCTTT	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52486850	52486850	+	Silent	SNP	G	G	A	rs8007166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	60	111	0	0.521739	0	G|0.971;A|0.029	0.029	strong	.	NID2	201	.	NM_007361	exon13	c.C2721T	p.C907C	ATTGTAGCAGGTA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110492328	110492328	+	Missense_Mutation	SNP	A	A	C	rs140472257	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	58	149	0	0.42029	0	A|0.993;C|0.007	0.007	strong	.	PKHD1L1	522	.	NM_177531	exon55	c.A9287C	p.Y3096S	CTTCTTACAGAGA	.	PASS	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110831	33110831	+	Missense_Mutation	SNP	C	C	T	rs149614093	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	184	0	0.442708	0	C|0.998;T|0.002	0.002	strong	.	N4BP2L2	90	.	NM_014887	exon2	c.G334A	p.A112T	CGTCTGCGGATAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413790	105413790	+	Silent	SNP	G	G	A	rs11848564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	392	391	337	0	0.997449	0	G|0.610;A|0.390	0.390	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C7998T	p.S2666S	CTCGATGGACTCG	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1614097	1614097	+	Silent	SNP	A	A	G	rs8048410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	115	215	0	0.469388	0	A|0.566;G|0.434	0.434	strong	.	IFT140	128	.	NM_014714	exon17	c.T1968C	p.S656S	GGGCTCACTCTGG	.	PASS	Atlas-SNP
KIAA1024	23251	hgsc.bcm.edu	37	15	79755604	79755604	+	Missense_Mutation	SNP	A	A	G	rs2297773	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	58	130	0	0.464	0	A|0.733;G|0.267	0.267	strong	.	KIAA1024	146	.	NM_015206	exon3	c.A2494G	p.I832V	TGGACCATTGAGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677995	100677995	+	Missense_Mutation	SNP	A	A	G	rs149287079	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	385	54	159	0	0.14026	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.A3298G	p.S1100G	GAAGGAAGCACTC	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	90	184	0	0.471204	0	C|0.567;T|0.433	0.433	strong	SYNE2,NS,carcinoma,0,1	SYNE2	577	1	NM_182914	exon84	c.C15543T	p.I5181I	ACAGATCTTGAAC	.	PASS	Atlas-SNP
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959279	45959279	+	Missense_Mutation	SNP	C	C	T	rs28644341	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	42	89	0	0.518519	0	C|0.991;T|0.009	0.009	strong	.	KRTAP10-1	34	.	NM_198691	exon1	c.G755A	p.C252Y	GGGGCACAGCAGG	.	PASS	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	33	61	0	0.428571	0	T|0.695;C|0.305	0.305	strong	BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	NM_001170794	exon5	c.A1506G	p.V502V	GATTGGTACCGGG	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1542814	1542814	+	Silent	SNP	T	T	C	rs3752715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	136	131	0	0.992701	0	T|0.412;C|0.588	0.588	strong	INTS1,colon,carcinoma,-1,1	INTS1	145	1	NM_001080453	exon3	c.A72G	p.P24P	GTCTCCTGGGGGA	.	PASS	Atlas-SNP
DSCR3	10311	hgsc.bcm.edu	37	21	38605694	38605694	+	Missense_Mutation	SNP	G	G	A	rs145630556	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	33	73	0	0.445946	0	G|0.998;A|0.002	0.002	strong	.	DSCR3	21	.	NM_006052	exon4	c.C401T	p.T134I	GTCTTTGTCAAGT	.	PASS	Atlas-SNP
PPP1R12C	54776	hgsc.bcm.edu	37	19	55606944	55606944	+	Missense_Mutation	SNP	G	G	A	rs35849605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	39	56	0	0.513158	0	G|0.958;A|0.042	0.042	strong	.	PPP1R12C	46	.	NM_017607	exon10	c.C1255T	p.R419C	CAAAGCGCCTGGA	.	PASS	Atlas-SNP
NAPRT1	93100	hgsc.bcm.edu	37	8	144658711	144658711	+	Silent	SNP	G	G	A	rs872935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	28	59	0	0.538462	0	G|0.525;C|0.000;A|0.475	0.475	strong	.	NAPRT1	47	.	NM_145201	exon7	c.C913T	p.L305L	GGGCCAGGGCGAC	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121652964	121652964	+	Silent	SNP	T	T	C	rs139671030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	116	0	0.45614	0	T|0.997;C|0.003	0.003	strong	.	PTPRZ1	605	.	NM_002851	exon12	c.T3864C	p.S1288S	GTACAGTAATGAT	.	PASS	Atlas-SNP
METTL15	196074	hgsc.bcm.edu	37	11	28351963	28351963	+	Missense_Mutation	SNP	A	A	T	rs11030280	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	117	229	1	0.483471	0.00436681	A|0.993;T|0.007	0.007	strong	.	METTL15	63	.	NM_001113528	exon7	c.A799T	p.I267F	TCTGCTATTTATA	.	PASS	Atlas-SNP
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	37	88	0	0.4625	0	T|0.867;C|0.133	0.133	strong	KRIT1,NS,carcinoma,0,1	KRIT1	66	1	NM_194456	exon18	c.A1980G	p.V660V	CACTCCTACATAC	.	PASS	Atlas-SNP
FAM26F	441168	hgsc.bcm.edu	37	6	116783585	116783585	+	Missense_Mutation	SNP	G	G	C	rs76716752	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	33	15	0	1	0	G|0.954;C|0.046	0.046	strong	.	FAM26F	12	.	NM_001010919	exon2	c.T493C	p.S165P	GTGCAGGACCTCC	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs7655494	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	91	88	0	0.98913	0	T|0.732;C|0.268	0.268	strong	.	PALLD	179	.	NM_001166108	exon2	c.T671C	p.M224T	GCCCTATGGAAGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679390	100679390	+	Missense_Mutation	SNP	A	A	G	rs150982179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	13	170	0	0.0687831	0	.	.	weak	MUC17,NS,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.A4693G	p.T1565A	ATGCAAACCTCAA	.	scavenged	Atlas-SNP
FCRL6	343413	hgsc.bcm.edu	37	1	159778910	159778910	+	Missense_Mutation	SNP	G	G	A	rs72700615	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	113	149	0	0.545894	0	G|0.901;A|0.099	0.099	strong	.	FCRL6	61	.	NM_001004310	exon4	c.G479A	p.G160D	ACAGGGGCCCTCA	.	PASS	Atlas-SNP
TMEM131	23505	hgsc.bcm.edu	37	2	98611994	98611994	+	Silent	SNP	G	G	T	rs2279824	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	6	0	0	0.666667	.	G|0.352;T|0.648	0.648	strong	.	TMEM131	258	.	NM_015348	exon1	c.C132A	p.G44G	CAGCGCGCCTAGG	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	68968171	68968171	+	Silent	SNP	G	G	A	rs1434775	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	25	82	0	0.308642	0	G|0.421;A|0.579	0.579	strong	.	PREX2	614	.	NM_025170	exon10	c.G1200A	p.K400K	CCGAAAGAGAAAA	.	PASS	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68934515	68934515	+	Silent	SNP	A	A	G	rs35687346	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	61	129	0	0.462121	0	A|0.955;G|0.045	0.045	strong	.	TMPRSS11F	79	.	NM_207407	exon7	c.T576C	p.S192S	GTTTGAAGATGTC	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161132146	161132146	+	Silent	SNP	C	C	T	rs4757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	265	289	1	0.988806	0.00346021	C|0.671;T|0.329	0.329	strong	.	PLG	150	.	NM_001168338	exon4	c.C330T	p.N110N	AAAGAACTACAGA	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	62	96	0	0.574074	0	A|0.879;T|0.121	0.121	strong	.	ZC3H3	75	.	NM_015117	exon11	c.T2638A	p.S880T	GGGATGAGGAGGA	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	37	11	118770054	118770054	+	Silent	SNP	G	G	A	rs12277303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	55	112	0	0.578947	0	G|0.948;A|0.052	0.052	strong	.	BCL9L	254	.	NM_182557	exon8	c.C3570T	p.N1190N	CTGTGCGTTGGGA	.	PASS	Atlas-SNP
ZNF540	163255	hgsc.bcm.edu	37	19	38102955	38102955	+	Silent	SNP	T	T	C	rs115588579	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	26	68	0	0.509804	0	T|0.992;C|0.008	0.008	strong	.	ZNF540	75	.	NM_152606	exon5	c.T774C	p.L258L	ACAACTTAATCGA	.	PASS	Atlas-SNP
CHD3	1107	hgsc.bcm.edu	37	17	7792326	7792326	+	Missense_Mutation	SNP	C	C	T	rs931543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	47	102	0	0.47	0	C|0.915;T|0.085	0.085	strong	.	CHD3	169	.	NM_001005273	exon1	c.C8T	p.A3V	TGAAGGCGGCAGA	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10446568	10446568	+	Missense_Mutation	SNP	T	T	C	rs2304237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	32	36	0	1	0	T|0.817;C|0.183	0.183	strong	.	ICAM3	29	.	NM_002162	exon3	c.A428G	p.D143G	GACCCATCCTCCA	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	88	0	1	0	C|0.483;N|0.000	0.483	strong	DDX20,NS,carcinoma,+1,1	DDX20	50	1	NM_007204	exon11	c.T1907C	p.I636T	AAGTTATTGAACA	.	PASS	Atlas-SNP
DNAJB13	374407	hgsc.bcm.edu	37	11	73670645	73670645	+	Silent	SNP	T	T	C	rs653263	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	99	0	1	0	T|0.418;C|0.582	0.582	strong	.	DNAJB13	28	.	NM_153614	exon3	c.T279C	p.H93H	CTTCCATGGCAAA	.	PASS	Atlas-SNP
LAMA3	3909	hgsc.bcm.edu	37	18	21447864	21447864	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	2	98	0	0.0186916	0	.	.	none	LAMA3,NS,carcinoma,-1,2	LAMA3	397	2	NM_001127717	exon37	c.C4750T	p.R1584X	CATGGACGAGTGC	.	scavenged	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16386065	16386065	+	Silent	SNP	T	T	A	rs61769893	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	456	89	221	0	0.195175	0	T|0.958;A|0.042	0.042	strong	FAM131C,caecum,carcinoma,0,1	FAM131C	21	1	NM_182623	exon6	c.A486T	p.T162T	GCTCAGTGTGGCC	.	PASS	Atlas-SNP
GPR26	2849	hgsc.bcm.edu	37	10	125447511	125447511	+	Silent	SNP	G	G	A	rs62640899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	31	58	0	0.462687	0	G|0.970;A|0.030	0.030	strong	.	GPR26	47	.	NM_153442	exon3	c.G849A	p.A283A	CTTGGCGTACAGC	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9987324	9987324	+	Silent	SNP	G	G	A	rs3733589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	103	207	0	0.490476	0	G|0.895;A|0.105	0.105	strong	.	SLC2A9	158	.	NM_020041	exon4	c.C504T	p.I168I	TCCCACGATGAGC	.	PASS	Atlas-SNP
PFAS	5198	hgsc.bcm.edu	37	17	8172141	8172141	+	Missense_Mutation	SNP	G	G	A	rs73975814	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	10	17	0	0.555556	0	G|0.994;A|0.006	0.006	strong	.	PFAS	91	.	NM_012393	exon27	c.G3673A	p.A1225T	GAGGGCGCCGTGC	.	PASS	Atlas-SNP
HECW2	57520	hgsc.bcm.edu	37	2	197208397	197208397	+	Silent	SNP	C	C	T	rs61741962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	117	0	0.5	0	C|0.984;T|0.016	0.016	strong	.	HECW2	239	.	NM_020760	exon3	c.G384A	p.G128G	ATAGGGCCCAGGC	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2554807	2554807	+	Missense_Mutation	SNP	T	T	G	rs34143130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	54	123	0	0.453782	0	T|0.889;G|0.111	0.111	strong	.	METTL4	40	.	NM_022840	exon4	c.A690C	p.E230D	ATCCTGTTCTGTA	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	108	218	0	0.467532	0	C|0.767;T|0.233	0.233	strong	.	SPATA22	49	.	NM_032598	exon6	c.G442A	p.V148M	AACTCACTGGACA	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262091	39262091	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	64	126	0	0.344086	0	.	.	none	.	KRTAP4-9	110	.	NM_001146041	exon1	c.C451T	p.R151C	TGCTGCCGCCCCA	.	PASS	Atlas-SNP
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329890	24329890	+	Missense_Mutation	SNP	G	G	C	rs150066125	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	138	212	1	0.492857	0.00471698	G|0.925;C|0.075	0.075	strong	.	.	.	.	NM_001136233	exon1	c.C1543G	p.P515A	AAGCAGGAGCAGC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79026360	79026360	+	Missense_Mutation	SNP	G	G	A	rs16877124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	176	169	0	1	0	G|0.704;A|0.296	0.296	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.G1772A	p.G591D	CTACTGGTTCTGC	.	PASS	Atlas-SNP
SORD	6652	hgsc.bcm.edu	37	15	45361180	45361180	+	Missense_Mutation	SNP	A	A	T	rs55739437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	305	291	0	0.993485	0	A|0.734;T|0.266	0.266	strong	.	SORD	24	.	NM_003104	exon7	c.A716T	p.Q239L	AAGGTCAGCTGGG	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31610701	31610701	+	Silent	SNP	C	C	T	rs45575032	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	15	38	0	0.357143	0	C|0.972;T|0.028	0.028	strong	.	XDH	191	.	NM_000379	exon8	c.G627A	p.E209E	AATGGGCTCCTGG	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119449159	119449159	+	Missense_Mutation	SNP	G	G	A	rs61742290	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	69	108	0	0.526718	0	G|0.995;A|0.005	0.005	strong	C3orf15,NS,carcinoma,+1,2	.	.	2	NM_033364	exon8	c.G953A	p.R318Q	ATGCCCGGTGGTC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	717523	717523	+	Silent	SNP	G	G	T	rs3752493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	37	78	0	0.474359	0	G|0.369;T|0.631	0.631	strong	WDR90,colon,carcinoma,0,2	WDR90	107	2	NM_145294	exon41	c.G5181T	p.P1727P	TACACCGTCCGCC	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43020983	43020983	+	Missense_Mutation	SNP	G	G	A	rs8023524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	87	195	0	0.465241	0	G|0.749;A|0.251	0.251	strong	.	CDAN1	70	.	NM_138477	exon20	c.C2671T	p.R891C	CCTGGCGCACCAG	.	PASS	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107076783	107076783	+	Silent	SNP	A	A	T	rs1987623	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	53	182	0	0.401515	0	A|0.608;T|0.392	0.392	strong	.	RTN4IP1	31	.	NM_032730	exon1	c.T114A	p.P38P	GCTCCTAGGAGAG	.	PASS	Atlas-SNP
HSPA1L	3305	hgsc.bcm.edu	37	6	31778529	31778529	+	Silent	SNP	C	C	T	rs2075799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	81	158	0	0.487952	0	C|0.854;T|0.146	0.146	strong	HSPA1L,caecum,carcinoma,0,1	HSPA1L	185	1	NM_005527	exon2	c.G1221A	p.T407T	CCCAGCCGTCTCC	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27374400	27374400	+	Missense_Mutation	SNP	A	A	G	rs1801275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	43	86	0	0.632353	0	A|0.641;G|0.358	0.358	strong	.	IL4R	70	.	NM_000418	exon11	c.A1727G	p.Q576R	GCTATCAGGAGTT	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32077653	32077653	+	Missense_Mutation	SNP	G	G	A	rs61745726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	121	106	0	1	0	G|0.913;A|0.087	0.087	strong	.	PDZD2	306	.	NM_178140	exon18	c.G3623A	p.S1208N	ATGCCAGCCACCT	.	PASS	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44179112	44179112	+	Missense_Mutation	SNP	C	C	G	rs146382324	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	71	99	0	0.533835	0	C|0.999;G|0.001	0.001	strong	.	PDE9A	69	.	NM_002606	exon11	c.C814G	p.L272V	CAGATGCTGAGCT	.	PASS	Atlas-SNP
TRPC5	7224	hgsc.bcm.edu	37	X	111020096	111020096	+	Silent	SNP	C	C	A	rs141761268	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	101	177	0	0.63125	0	C|0.998;A|0.002	0.002	strong	.	TRPC5	142	.	NM_012471	exon11	c.G2367T	p.G789G	CCGAGCCCCACCA	.	PASS	Atlas-SNP
SNX30	401548	hgsc.bcm.edu	37	9	115567184	115567184	+	Silent	SNP	T	T	C	rs1891402	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	175	179	1	0.994318	0.00558659	T|0.054;C|0.946	0.946	strong	.	SNX30	32	.	NM_001012994	exon2	c.T285C	p.V95V	TATAGTTGATGAT	.	PASS	Atlas-SNP
GPR68	8111	hgsc.bcm.edu	37	14	91700846	91700846	+	Silent	SNP	G	G	A	rs2540862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	39	95	0	0.393939	0	G|0.874;A|0.126	0.126	strong	GPR68,colon,carcinoma,-2,1	GPR68	32	1	NM_001177676	exon2	c.C549T	p.R183R	GATGGCGCGCTGC	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5417093	5417093	+	Silent	SNP	G	G	T	rs60530083	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	32	28	0	0.603774	0	G|0.985;T|0.015	0.015	strong	.	TNRC18	311	.	NM_001080495	exon7	c.C2370A	p.R790R	AGACCAGCGACCT	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109941887	109941887	+	Missense_Mutation	SNP	C	C	T	rs73224392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	98	238	0	0.451613	0	C|0.965;T|0.035	0.035	strong	.	TMEM232	57	.	NM_001039763	exon9	c.G1004A	p.S335N	ATAATGCTTGAAA	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113352628	113352628	+	Missense_Mutation	SNP	A	A	G	rs13148353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	128	99	0	0.992248	0	A|0.320;G|0.679	0.679	strong	.	ALPK1	125	.	NM_001102406	exon11	c.A1925G	p.H642R	CATTGCATTCACA	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	50	105	0	0.480769	0	G|0.899;A|0.101	0.101	strong	.	BRD1	144	.	NM_014577	exon1	c.C579T	p.F193F	CTTCTCGAAGCGG	.	PASS	Atlas-SNP
OR10K1	391109	hgsc.bcm.edu	37	1	158436201	158436201	+	Silent	SNP	T	T	C	rs76117330	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	62	131	0	0.446043	0	T|0.963;C|0.037	0.037	strong	.	OR10K1	80	.	NM_001004473	exon1	c.T850C	p.L284L	ACCCCATTGTTCA	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	37	3	145809622	145809622	+	Missense_Mutation	SNP	A	A	G	rs138948307	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	53	115	0	0.389706	0	A|0.999;G|0.001	0.001	strong	.	PLOD2	81	.	NM_182943	exon8	c.T844C	p.C282R	ATTCACAAAGAGT	.	PASS	Atlas-SNP
SSPN	8082	hgsc.bcm.edu	37	12	26383959	26383959	+	Missense_Mutation	SNP	G	G	A	rs12313736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	83	0	0.451613	0	G|0.913;A|0.087	0.087	strong	.	SSPN	19	.	NM_005086	exon3	c.G682A	p.V228I	GTGGGTGTCAGGA	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs28583670		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	520	16	575	5	0.0307692	0.00869565	.	.	weak	ENSG00000188219,NS,carcinoma,-1,1	.	.	1	NM_001083538	exon15	c.C2656A	p.P886T	GAACTGCCTGACT	.	scavenged	Atlas-SNP
KIAA0141	9812	hgsc.bcm.edu	37	5	141313888	141313888	+	Silent	SNP	A	A	C	rs115183657	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	61	88	0	0.472868	0	A|0.991;C|0.009	0.009	strong	.	KIAA0141	44	.	NM_001142603	exon9	c.A981C	p.P327P	AGACCCAGCCTCT	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135745722	135745722	+	Silent	SNP	A	A	G	rs10928526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	18	68	0	0.352941	0	A|0.687;G|0.313	0.313	strong	.	.	.	.	NM_025052	exon7	c.T720C	p.S240S	TGTGAGACTTGGA	.	PASS	Atlas-SNP
PEX16	9409	hgsc.bcm.edu	37	11	45932458	45932458	+	Silent	SNP	G	G	A	rs150774189	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	60	91	0	0.540541	0	G|0.995;A|0.005	0.005	strong	.	PEX16	24	.	NM_004813	exon10	c.C943T	p.L315L	TGACCAGGCCAAC	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61528074	61528074	+	Silent	SNP	T	T	C	rs910149	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	95	70	0	0.989583	0	T|0.366;C|0.634	0.634	strong	.	DIDO1	321	.	NM_080797	exon7	c.A1863G	p.A621A	AGCCGTTGCCGCT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1255773	1255773	+	Silent	SNP	C	C	T	rs7116614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	87	186	0	0.467742	0	C|0.647;T|0.353	0.353	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon21	c.C2493T	p.C831C	ACACTGCGTGTCC	.	PASS	Atlas-SNP
ERN1	2081	hgsc.bcm.edu	37	17	62149423	62149423	+	Silent	SNP	G	G	A	rs374999844		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	29	72	0	0.453125	0	.	.	weak	.	ERN1	102	.	NM_001433	exon6	c.C396T	p.T132T	CTCTCCGGTCAGG	.	PASS	Atlas-SNP
HCST	10870	hgsc.bcm.edu	37	19	36394272	36394272	+	Silent	SNP	T	T	C	rs33964243	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	60	58	0	1	0	T|0.876;C|0.124	0.124	strong	.	HCST	10	.	NM_001007469	exon2	c.T63C	p.T21T	GACGACTCCAGGA	.	PASS	Atlas-SNP
LILRA2	11027	hgsc.bcm.edu	37	19	55098736	55098736	+	Missense_Mutation	SNP	G	G	C	rs73939007	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	115	228	1	0.447471	0.00438596	G|0.991;C|0.009	0.009	strong	.	LILRA2	99	.	NM_001130917	exon8	c.G1375C	p.V459L	GGCTTGGTCCTGG	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	66	141	0	0.55	0	G|0.633;A|0.367	0.367	strong	.	MYOM3	131	.	NM_152372	exon9	c.C797T	p.T266M	CCAAACGTCGATC	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78399121	78399121	+	Silent	SNP	G	G	A	rs1792148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	65	104	0	0.532787	0	G|0.864;A|0.136	0.136	strong	ODZ4_ENST00000278550,colon,carcinoma,-2,1	.	.	1	NM_001098816	exon29	c.C5238T	p.G1746G	GAAGGCGCCTGAG	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104014294	104014294	+	Missense_Mutation	SNP	C	C	T	rs150189813	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	107	195	0	0.511962	0	C|1.000;T|0.000	0.000	strong	.	STAB2	370	.	NM_017564	exon4	c.C380T	p.A127V	GTTGTGCTGAAGG	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	52	98	0	0.444444	0	C|0.585;T|0.415	0.415	strong	FUCA2,NS,carcinoma,0,1	FUCA2	28	1	NM_032020	exon7	c.G1389A	p.L463L	ATTAGTCAGGGCT	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29839787	29839787	+	Missense_Mutation	SNP	A	A	G	rs10160013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	53	88	0	0.490741	0	A|0.692;G|0.308	0.308	strong	SVIL,NS,carcinoma,0,1	SVIL	226	1	NM_003174	exon8	c.T566C	p.V189A	TCACCCACATGGA	.	PASS	Atlas-SNP
SEPT8	23176	hgsc.bcm.edu	37	5	132099999	132099999	+	Silent	SNP	A	A	G	rs30507	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	256	231	2	0.988417	0.00865801	G|0.438;N|0.000	0.438	strong	.	SEPT8	28	.	NM_015146	exon3	c.T264C	p.Y88Y	GAGGTCATAGGTC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8150428	8150428	+	Silent	SNP	G	G	A	rs34514496	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	40	0	0.490566	0	G|0.956;A|0.044	0.044	strong	.	FBN3	300	.	NM_032447	exon55	c.C6906T	p.A2302A	CACCTCGGCAAAG	.	PASS	Atlas-SNP
MMP17	4326	hgsc.bcm.edu	37	12	132326298	132326298	+	Missense_Mutation	SNP	G	G	A	rs35466884	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	40	81	0	0.412371	0	G|0.780;A|0.220	0.220	strong	.	MMP17	77	.	NM_016155	exon5	c.G836A	p.R279H	CGCTGCGCTACGG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531907	50531907	+	Silent	SNP	C	C	T	rs74528495	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	42	97	0	0.428571	0	C|0.994;T|0.006	0.006	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C1317T	p.P439P	TGATCCCCCCTTT	.	PASS	Atlas-SNP
VARS	7407	hgsc.bcm.edu	37	6	31747833	31747833	+	Missense_Mutation	SNP	G	G	A	rs1076827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	37	82	0	0.5	0	G|0.978;A|0.022	0.022	strong	.	VARS	76	.	NM_006295	exon26	c.C3023T	p.P1008L	ACGGCCGGGAAGT	.	PASS	Atlas-SNP
SSUH2	51066	hgsc.bcm.edu	37	3	8675539	8675539	+	Missense_Mutation	SNP	G	G	A	rs2276800	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	93	119	0	0.958763	0	G|0.689;A|0.311	0.311	strong	C3orf32,NS,carcinoma,0,2	.	.	2	NM_015931	exon4	c.C86T	p.P29L	TCACGCGGGCCAG	.	PASS	Atlas-SNP
TAS2R16	50833	hgsc.bcm.edu	37	7	122635389	122635389	+	Silent	SNP	G	G	A	rs2233988	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	53	131	0	0.410853	0	G|0.917;A|0.083	0.083	strong	.	TAS2R16	57	.	NM_016945	exon1	c.C300T	p.T100T	GAACACGGTAAGC	.	PASS	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156745224	156745224	+	Silent	SNP	G	G	A	rs59371845	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	81	170	0	0.487952	0	G|0.950;A|0.050	0.050	strong	.	NOM1	73	.	NM_138400	exon2	c.G1044A	p.E348E	TGAGGAGACAGTG	.	PASS	Atlas-SNP
ARID3C	138715	hgsc.bcm.edu	37	9	34625800	34625800	+	Silent	SNP	G	G	A	rs144207435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	80	142	0	0.547945	0	G|0.997;A|0.003	0.003	strong	ARID3C,NS,carcinoma,0,2	ARID3C	33	2	NM_001017363	exon2	c.C330T	p.L110L	TGCATCGAGCTCA	.	PASS	Atlas-SNP
LZTR1	8216	hgsc.bcm.edu	37	22	21348914	21348914	+	Silent	SNP	C	C	T	rs4822790	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	85	83	0	0.977012	0	C|0.855;T|0.145	0.145	strong	.	LZTR1	99	.	NM_006767	exon15	c.C1683T	p.R561R	GTGCCGCCTGGAG	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62173927	62173927	+	Missense_Mutation	SNP	G	G	A	rs378483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	136	0	1	0	G|0.845;A|0.155	0.155	strong	SRMS,NS,lymphoid_neoplasm,0,1	SRMS	48	1	NM_080823	exon4	c.C653T	p.P218L	TGCCTCGGGGCCT	.	PASS	Atlas-SNP
ZNF236	7776	hgsc.bcm.edu	37	18	74640002	74640002	+	Missense_Mutation	SNP	G	G	A	rs76679748	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	99	180	0	0.495	0	G|0.996;A|0.004	0.004	strong	.	ZNF236	325	.	NM_007345	exon25	c.G4528A	p.A1510T	CAGGCCGCTGGGC	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33574784	33574784	+	Missense_Mutation	SNP	G	G	A	rs115275866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	50	66	0	0.537634	0	G|0.993;A|0.007	0.007	strong	MYH7B,colon,carcinoma,0,1	MYH7B	145	1	NM_020884	exon15	c.G1126A	p.A376T	CTCATCGCCACCG	.	PASS	Atlas-SNP
KLHL2	11275	hgsc.bcm.edu	37	4	166149999	166149999	+	Missense_Mutation	SNP	A	A	G	rs80341433	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	576	285	736	0	0.494792	0	A|0.994;G|0.006	0.006	strong	.	KLHL2	42	.	NM_001161521	exon3	c.A205G	p.M69V	GAAGACATGGAAA	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48701800	48701800	+	Silent	SNP	C	C	T	rs2301835	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	340	174	345	0	0.511765	0	C|0.878;T|0.122	0.122	strong	.	CACNA1G	659	.	NM_018896	exon37	c.C6309T	p.L2103L	TCTGCTCCAGCCC	.	PASS	Atlas-SNP
C14orf159	80017	hgsc.bcm.edu	37	14	91666248	91666248	+	Silent	SNP	T	T	C	rs28715808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	86	135	0	0.554839	0	T|0.967;C|0.033	0.033	strong	.	C14orf159	57	.	NM_001102368	exon11	c.T1443C	p.T481T	ATCAACTGGTAAG	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587677	39587677	+	Missense_Mutation	SNP	A	A	G	rs3751379	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	55	110	0	0.555556	0	G|0.254;N|0.000	0.254	strong	.	.	.	.	NM_025138	exon11	c.T1712C	p.V571A	ACTGGCACTGACG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414312	105414312	+	Silent	SNP	T	T	C	rs79130434	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	126	298	1	0.484615	0.0033557	T|0.964;C|0.036	0.036	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A7476G	p.S2492S	CCCGAATGACGGC	.	PASS	Atlas-SNP
PELP1	27043	hgsc.bcm.edu	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	94	162	0	0.5	0	C|0.892;T|0.108	0.108	strong	.	PELP1	102	.	NM_014389	exon15	c.G1770A	p.P590P	AGGAGACGGGGCC	.	PASS	Atlas-SNP
NAT8	9027	hgsc.bcm.edu	37	2	73868446	73868446	+	Missense_Mutation	SNP	C	C	T	rs13424561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	83	139	0	0.506098	0	C|0.956;T|0.044	0.044	strong	.	NAT8	26	.	NM_003960	exon2	c.G310A	p.E104K	CACGCTCACTCAG	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	21581805	21581805	+	Silent	SNP	C	C	T	rs8176789	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	83	183	0	0.448649	0	C|0.342;T|0.658	0.658	strong	.	NELL1	179	.	NM_006157	exon17	c.C1857T	p.G619G	AGGGGGCTTTGAC	.	PASS	Atlas-SNP
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	21	44	0	0.567568	0	C|0.895;A|0.105	0.105	strong	.	FAM162B	19	.	NM_001085480	exon2	c.G213T	p.Q71H	GTCGAACTGCGAA	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	T	rs2228411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	38	64	0	0.5	0	C|0.590;T|0.410	0.410	strong	AOAH,NS,carcinoma,0,2	AOAH	79	2	NM_001177507	exon1	c.G66A	p.S22S	AGAGGCCGAGGAC	.	PASS	Atlas-SNP
SERPINB3	6317	hgsc.bcm.edu	37	18	61322998	61322998	+	Missense_Mutation	SNP	G	G	A	rs73962331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	71	215	0	0.349754	0	G|0.948;A|0.052	0.052	strong	.	SERPINB3	90	.	NM_006919	exon8	c.C1066T	p.P356S	AAGTAGGTGATGA	.	PASS	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	13	22	0	0.5	0	A|0.893;G|0.106;T|0.000	0.106	strong	.	GPR146	20	.	NM_138445	exon1	c.A744G	p.P248P	GACGCCACACTAT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13931340	13931340	+	Missense_Mutation	SNP	C	C	T	rs1530496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	83	0	1	0	C|0.571;T|0.429	0.429	strong	.	DNAH5	868	.	NM_001369	exon2	c.G71A	p.G24E	TTCTCTCCCTTCA	.	PASS	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	107204371	107204371	+	Missense_Mutation	SNP	C	C	T	rs73419464	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	64	93	0	0.571429	0	C|0.970;T|0.030	0.030	strong	.	COG5	78	.	NM_006348	exon1	c.G64A	p.A22T	CGTCAGCAGCAGA	.	PASS	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	37	12	7015707	7015707	+	Missense_Mutation	SNP	G	G	T	rs2071073	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	69	125	0	0.539062	0	G|0.920;N|0.000	.	strong	LRRC23,NS,carcinoma,0,2	LRRC23	46	2	NM_001135217	exon4	c.G371T	p.R124L	GCAATCGGCTGCG	.	PASS	Atlas-SNP
MMP17	4326	hgsc.bcm.edu	37	12	132329666	132329666	+	Silent	SNP	C	C	T	rs36031288	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	58	102	0	0.491525	0	C|0.961;T|0.039	0.039	strong	.	MMP17	77	.	NM_016155	exon7	c.C972T	p.P324P	CAGGCCCAGGAAG	.	PASS	Atlas-SNP
EYA2	2139	hgsc.bcm.edu	37	20	45816757	45816757	+	Silent	SNP	C	C	T	rs3818015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	96	0	1	0	C|0.904;T|0.096	0.096	strong	.	EYA2	85	.	NM_005244	exon16	c.C1593T	p.H531H	GAGGCACGCCCTG	.	PASS	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35223303	35223303	+	Silent	SNP	G	G	A	rs11033026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	160	170	0	0.993789	0	G|0.883;A|0.117	0.117	strong	.	CD44	48	.	NM_000610	exon9	c.G1122A	p.E374E	TCATGAGGAAGAA	.	PASS	Atlas-SNP
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	39	79	0	0.5	0	G|0.745;A|0.255	0.255	strong	.	FAM178B	35	.	NM_001122646	exon14	c.C1680T	p.L560L	CCTCATGAGGCCC	.	PASS	Atlas-SNP
SLC25A26	115286	hgsc.bcm.edu	37	3	66293688	66293688	+	Silent	SNP	A	A	G	rs3772197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	61	98	0	0.54955	0	A|0.941;G|0.059	0.059	strong	SLC25A26,NS,carcinoma,0,1	SLC25A26	12	1	NM_173471	exon4	c.A252G	p.S84S	ATCTTCATATTTG	.	PASS	Atlas-SNP
ADTRP	84830	hgsc.bcm.edu	37	6	11723636	11723636	+	Missense_Mutation	SNP	C	C	T	rs2076185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	46	94	0	0.560976	0	C|0.890;T|0.110	0.110	strong	.	ADTRP	3	.	NM_001143948	exon6	c.G658A	p.V220I	TGAAGACGTAGCT	.	PASS	Atlas-SNP
SSTR1	6751	hgsc.bcm.edu	37	14	38679473	38679473	+	Silent	SNP	C	C	T	rs2228497	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	62	89	0	0.521008	0	C|0.772;T|0.228	0.228	strong	.	SSTR1	66	.	NM_001049	exon3	c.C879T	p.V293V	GCTGGTCAACGTG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124436234	124436234	+	Splice_Site	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	2	70	0	0.0253165	0	.	.	none	TRAD,colon,carcinoma,0,2	KALRN	556	2	NM_001024660	exon59	c.8415+2T>C	.	TAAAGGTAATAAG	.	scavenged	Atlas-SNP
PMS2	5395	hgsc.bcm.edu	37	7	6026864	6026864	+	Missense_Mutation	SNP	G	G	A	rs74902811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	30	73	0	0.422535	0	G|0.973;A|0.026	0.026	strong	.	PMS2	88	.	NM_000535	exon11	c.C1532T	p.T511M	CTGCCCGTGTCTG	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43455432	43455432	+	Silent	SNP	G	G	A	rs5759125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	45	109	0	0.412844	0	G|0.704;A|0.296	0.296	strong	TTLL1,NS,carcinoma,0,1	TTLL1	41	1	NM_012263	exon8	c.C849T	p.D283D	GATCTCGTCGAAC	.	PASS	Atlas-SNP
PASD1	139135	hgsc.bcm.edu	37	X	150840690	150840690	+	Missense_Mutation	SNP	G	G	T	rs370395923		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	48	84	0	0.417391	0	.	.	weak	.	PASD1	286	.	NM_173493	exon14	c.G1473T	p.E491D	GAAGGAGCAGCAG	.	PASS	Atlas-SNP
TIMP3	7078	hgsc.bcm.edu	37	22	33253280	33253280	+	Silent	SNP	T	T	C	rs9862	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	235	164	1	1	0.00609756	T|0.372;C|0.628	0.628	strong	.	TIMP3	31	.	NM_000362	exon3	c.T249C	p.H83H	CATCCATACGGAA	.	PASS	Atlas-SNP
IL25	64806	hgsc.bcm.edu	37	14	23845061	23845061	+	Missense_Mutation	SNP	T	T	C	rs149802556	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	105	254	1	0.400763	0.00393701	T|1.000;C|0.000	0.000	strong	.	IL25	21	.	NM_022789	exon2	c.T506C	p.V169A	CTTGTGTGTGTGT	.	PASS	Atlas-SNP
EPHA4	2043	hgsc.bcm.edu	37	2	222308226	222308226	+	Silent	SNP	T	T	C	rs10498111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	98	209	0	0.451613	0	T|0.936;C|0.064	0.064	strong	.	EPHA4	263	.	NM_004438	exon10	c.A1875G	p.K625K	TATAACTTTTTCA	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175049405	175049405	+	Silent	SNP	C	C	A	rs61742080	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	57	117	0	0.416058	0	C|0.931;A|0.069	0.069	strong	.	TNN	297	.	NM_022093	exon4	c.C891A	p.P297P	CTACCCCCTGGGG	.	PASS	Atlas-SNP
PTCD2	79810	hgsc.bcm.edu	37	5	71618069	71618069	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	24	86	0	0.32	0	.	.	none	.	PTCD2	31	.	NM_024754	exon2	c.A198G	p.A66A	TGTTGCATGTAAT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38130459	38130459	+	Missense_Mutation	SNP	G	G	T	rs8140207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	85	199	0	0.488506	0	G|0.726;T|0.274	0.274	strong	.	TRIOBP	262	.	NM_001039141	exon9	c.G4116T	p.E1372D	AGCAGAGCCCCCT	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88407959	88407959	+	Silent	SNP	T	T	C	rs2970918	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	89	0	1	0	T|0.711;G|0.000;C|0.288;A|0.000	0.288	strong	.	SMYD1	95	.	NM_198274	exon9	c.T1215C	p.H405H	CTGGCATGCTGGT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283367	152283367	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	622	48	509	0	0.0771704	0	.	.	none	.	FLG	900	.	NM_002016	exon3	c.A3995G	p.H1332R	GTGTGATGAGTGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179398509	179398509	+	Missense_Mutation	SNP	C	C	A	rs3731752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	67	108	0	0.5	0	C|0.922;A|0.078	0.078	strong	.	TTN	18412	.	NM_001267550	exon358	c.G102833T	p.G34278V	GTTACTCCAAACC	.	PASS	Atlas-SNP
LARS2	23395	hgsc.bcm.edu	37	3	45459030	45459030	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	29	143	0	0.29	0	.	.	none	.	LARS2	48	.	NM_015340	exon5	c.C420T	p.V140V	CGCAGTCGAGAGG	.	PASS	Atlas-SNP
AP5M1	55745	hgsc.bcm.edu	37	14	57741550	57741550	+	Silent	SNP	A	A	G	rs1189899	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	67	87	0	0.54918	0	A|0.764;G|0.236	0.236	strong	.	.	.	.	NM_018229	exon2	c.A663G	p.Q221Q	CATGCAATATGAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179441917	179441917	+	Missense_Mutation	SNP	T	T	C	rs72646881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	56	112	0	0.482759	0	T|0.967;C|0.033	0.033	strong	TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	NM_001267550	exon324	c.A69145G	p.I23049V	TACTGATTTCAAC	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639350	84639350	+	Missense_Mutation	SNP	C	C	T	rs2277849	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	45	96	0	0.412844	0	C|0.712;T|0.288	0.288	strong	ADAMTSL3,NS,carcinoma,0,1	ADAMTSL3	290	1	NM_207517	exon20	c.C2605T	p.L869F	CCAGGGCTCCCTC	.	PASS	Atlas-SNP
CSH2	1443	hgsc.bcm.edu	37	17	61950694	61950694	+	Missense_Mutation	SNP	G	G	A	rs61763993	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	55	248	0	0.234043	0	G|0.980;A|0.020	0.020	strong	.	CSH2	37	.	NM_022645	exon2	c.C16T	p.R6W	ACGTCCGGGAGCC	.	PASS	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	72	158	1	0.455696	0.00632911	A|0.634;C|0.366	0.366	strong	ZNF879,NS,carcinoma,0,2	ZNF879	41	2	NM_001136116	exon5	c.A477C	p.E159D	TGTTGAATTTGGG	.	scavenged	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41386033	41386033	+	Missense_Mutation	SNP	T	T	C	rs73032311	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	116	200	0	0.489451	0	T|0.862;C|0.138	0.138	strong	.	CYP2A7	71	.	NM_000764	exon4	c.A610G	p.M204V	GCATCATGCTCAG	.	PASS	Atlas-SNP
KIAA0895L	653319	hgsc.bcm.edu	37	16	67214346	67214346	+	Silent	SNP	C	C	T	rs7186508	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	67	103	0	0.523438	0	C|0.864;T|0.136	0.136	strong	.	KIAA0895L	32	.	NM_001040715	exon2	c.G168A	p.A56A	CTGCAGCGCTGGG	.	PASS	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	37	11	120811161	120811161	+	Missense_Mutation	SNP	G	G	A	rs2230298	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	30	103	0	0.461538	0	G|0.964;A|0.036	0.036	strong	.	GRIK4	149	.	NM_014619	exon12	c.G1582A	p.V528I	TACCGCGTTCATA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511889	195511889	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	11	489	2	0.026764	0.00408998	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	NM_018406	exon2	c.G6562A	p.G2188S	CGTGACCTGTGGA	.	scavenged	Atlas-SNP
SRGAP2D	100996712	hgsc.bcm.edu	37	1	206566947	206566947	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	647	99	553	0	0.153014	0	.	.	none	.	.	.	.	NM_001271887	exon3	c.C289T	p.Q97X	AAAGCCCGGAATG	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175335162	175335162	+	Silent	SNP	T	T	C	rs7516376	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	114	228	0	0.473029	0	T|0.929;C|0.071	0.071	strong	TNR,NS,carcinoma,-1,2	TNR	399	2	NM_003285	exon11	c.A2166G	p.P722P	AGAGGATGGGGTA	.	PASS	Atlas-SNP
TACR2	6865	hgsc.bcm.edu	37	10	71167027	71167027	+	Missense_Mutation	SNP	T	T	C	rs142415572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	87	117	0	0.511765	0	T|0.979;C|0.021	0.021	strong	.	TACR2	37	.	NM_001057	exon4	c.A751G	p.T251A	CCATGGTCTTCAC	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62288730	62288730	+	Missense_Mutation	SNP	G	G	C	rs1286812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	111	223	0	0.506849	0	G|0.992;C|0.008	0.008	strong	.	INADL	179	.	NM_176877	exon15	c.G1797C	p.Q599H	CCTACAGCCAGAA	.	PASS	Atlas-SNP
PRSS21	10942	hgsc.bcm.edu	37	16	2868783	2868783	+	Silent	SNP	A	A	G	rs2074906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	185	179	1	0.994624	0.00558659	A|0.944;G|0.056	0.056	strong	PRSS21,NS,carcinoma,+1,1	PRSS21	32	1	NM_144957	exon4	c.A363G	p.V121V	CTTCGTATCGAAT	.	PASS	Atlas-SNP
KRBA2	124751	hgsc.bcm.edu	37	17	8273246	8273246	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	61	259	0	0.271111	0	.	.	none	.	KRBA2	34	.	NM_213597	exon2	c.G685A	p.V229I	ATAAGACAATAAC	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253819	39253819	+	Missense_Mutation	SNP	G	G	C	rs201814486		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	46	240	0	0.275449	0	.	.	weak	.	KRTAP4-8	57	.	NM_031960	exon1	c.C518G	p.T173S	GGGCAGGTGGAGA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721899	101721899	+	Nonsense_Mutation	SNP	C	C	A	rs142985461	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	59	167	0	0.239837	0	C|0.842;A|0.159	0.159	strong	PABPC1,colon,carcinoma,+2,1	PABPC1	76	1	NM_002568	exon8	c.G1033T	p.E345X	TGGCTTCTTCTGG	.	scavenged	Atlas-SNP
RBM11	54033	hgsc.bcm.edu	37	21	15591968	15591968	+	Missense_Mutation	SNP	G	G	A	rs141942958	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	88	143	0	0.60274	0	G|0.995;A|0.005	0.005	strong	RBM11,NS,neuroblastoma,-1,1	RBM11	41	1	NM_144770	exon2	c.G181A	p.E61K	CACCCAGAATCGG	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113403684	113403684	+	Silent	SNP	C	C	T	rs2240188	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	64	90	0	0.481203	0	C|0.728;T|0.272	0.272	strong	.	OAS3	63	.	NM_006187	exon12	c.C2539T	p.L847L	GCCCAGCTGGAGG	.	PASS	Atlas-SNP
RPS26	6231	hgsc.bcm.edu	37	12	56437917	56437917	+	Silent	SNP	T	T	A	rs56696262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	59	107	0	0.460938	0	T|0.925;A|0.075	0.075	strong	.	RPS26	9	.	NM_001029	exon4	c.T327A	p.R109R	CCCACGTCCCCCA	.	PASS	Atlas-SNP
SMG8	55181	hgsc.bcm.edu	37	17	57288251	57288251	+	Missense_Mutation	SNP	C	C	T	rs8068240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	44	88	0	0.423077	0	C|0.967;T|0.033	0.033	strong	.	SMG8	79	.	NM_018149	exon1	c.C839T	p.P280L	AACCTCCTCGGAA	.	PASS	Atlas-SNP
SRL	6345	hgsc.bcm.edu	37	16	4245656	4245656	+	Silent	SNP	G	G	A	rs76988584	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	118	220	0	0.475806	0	G|0.992;A|0.008	0.008	strong	.	SRL	56	.	NM_001098814	exon5	c.C508T	p.L170L	TCTCTAGGAAATT	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112309331	112309331	+	Missense_Mutation	SNP	T	T	C	rs85276	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	151	200	1	0.993421	0.005	A|0.004;C|0.196	0.196	strong	.	DDX20	50	.	NM_007204	exon11	c.T2285C	p.I762T	GGGAAATACGTCT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253797	39253797	+	Silent	SNP	G	G	A	rs142150852	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	81	274	0	0.356828	0	G|0.982;A|0.018	0.018	strong	KRTAP4-8,colon,carcinoma,-2,1	KRTAP4-8	57	1	NM_031960	exon1	c.C540T	p.C180C	GGAGGCGCAGCAC	.	PASS	Atlas-SNP
C5AR2	27202	hgsc.bcm.edu	37	19	47844653	47844653	+	Silent	SNP	G	G	A	rs36046934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	72	128	0	0.45	0	G|0.979;A|0.021	0.021	strong	GPR77,NS,carcinoma,+1,1	.	.	1	NM_001271750	exon2	c.G597A	p.A199A	GAATGCGGTGACT	.	PASS	Atlas-SNP
TEAD3	7005	hgsc.bcm.edu	37	6	35452346	35452346	+	Silent	SNP	C	C	T	rs11756089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	112	204	1	0.509091	0.00490196	C|0.863;T|0.137	0.137	strong	.	TEAD3	52	.	NM_003214	exon3	c.G258A	p.T86T	TTTTCTCGTCCGA	.	PASS	Atlas-SNP
DEFB110	245913	hgsc.bcm.edu	37	6	49989622	49989622	+	Silent	SNP	A	A	G	rs9473719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	46	86	0	0.516854	0	A|0.986;G|0.014	0.014	strong	.	DEFB110	5	.	NM_001037728	exon1	c.T27C	p.I9I	GTGCAGAATAAAG	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	34	91	0	0.43038	0	A|0.943;T|0.057	0.057	strong	.	ATP9B	96	.	NM_198531	exon19	c.A2194T	p.M732L	AGGGAGATGGAAC	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	70	79	0	0.57377	0	C|0.896;N|0.000	.	strong	CDON,NS,carcinoma,0,1	CDON	137	1	NM_016952	exon4	c.G484A	p.E162K	AATGTTCCAGCCA	.	PASS	Atlas-SNP
RFPL4A	342931	hgsc.bcm.edu	37	19	56273285	56273285	+	Missense_Mutation	SNP	A	A	G	rs2019945	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	914	113	809	4	0.123632	0.00494438	.	.	weak	ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	NM_001145014	exon2	c.A119G	p.K40R	TCCAGAAGGAGCC	.	scavenged	Atlas-SNP
JAG2	3714	hgsc.bcm.edu	37	14	105609161	105609161	+	Silent	SNP	G	G	A	rs61750260	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	28	58	0	0.482759	0	G|0.961;A|0.039	0.039	strong	.	JAG2	69	.	NM_002226	exon26	c.C3588T	p.F1196F	TGAGAGGAACTTC	.	PASS	Atlas-SNP
SAMD11	148398	hgsc.bcm.edu	37	1	871215	871215	+	Silent	SNP	C	C	G	rs28419423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	108	189	0	0.571429	0	C|0.975;G|0.025	0.025	strong	.	SAMD11	34	.	NM_152486	exon5	c.C369G	p.P123P	TATGCCCGAGCAT	.	PASS	Atlas-SNP
C1orf174	339448	hgsc.bcm.edu	37	1	3807388	3807388	+	Silent	SNP	G	G	A	rs4131373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	69	96	0	0.560976	0	G|0.835;A|0.165	0.165	strong	.	C1orf174	20	.	NM_207356	exon3	c.C363T	p.L121L	GCCACCGAGAGGA	.	PASS	Atlas-SNP
TOP2B	7155	hgsc.bcm.edu	37	3	25639849	25639849	+	Silent	SNP	A	A	G	rs11548723	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	60	137	0	0.444444	0	A|0.977;G|0.023	0.023	strong	.	TOP2B	98	.	NM_001068	exon36	c.T4815C	p.F1605F	CTCTGCAAAATAT	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79603423	79603423	+	Silent	SNP	C	C	T	rs12257229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	94	195	0	0.467662	0	C|0.888;T|0.112	0.112	strong	.	DLG5	154	.	NM_004747	exon6	c.G906A	p.L302L	GTCATACAGTTTG	.	PASS	Atlas-SNP
PLA1A	51365	hgsc.bcm.edu	37	3	119336962	119336962	+	Missense_Mutation	SNP	G	G	A	rs2692622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	132	177	0	0.552301	0	G|0.946;A|0.054	0.054	strong	.	PLA1A	65	.	NM_015900	exon7	c.G851A	p.S284N	GTGCCAGCTACAA	.	PASS	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166868775	166868775	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	119	179	0	0.626316	0	.	.	none	.	SCN1A	641	.	NM_001165963	exon19	c.T3723C	p.Y1241Y	ATCAATATATATA	.	PASS	Atlas-SNP
ATP13A1	57130	hgsc.bcm.edu	37	19	19766365	19766365	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	79	134	0	0.537415	0	.	.	none	.	ATP13A1	82	.	NM_020410	exon10	c.C1368T	p.I456I	TGCAGCGATGGCA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149477544	149477544	+	Missense_Mutation	SNP	G	G	A	rs855677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	53	111	0	0.438017	0	G|0.955;T|0.023	.	strong	.	.	.	.	NM_198455	exon12	c.G1615A	p.V539M	GACACCGTGCGCC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487169	32487169	+	Silent	SNP	C	C	T	rs34555743	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	11	50	6	0.146667	0.12	C|0.100;T|0.900	0.900	weak	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G630A	p.T210T	AGGGCTCGTCACG	.	scavenged	Atlas-SNP
H2AFY	9555	hgsc.bcm.edu	37	5	134670765	134670765	+	Silent	SNP	A	A	G	rs3210047	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	126	255	0	0.504	0	A|0.875;G|0.125	0.125	strong	.	H2AFY	61	.	NM_138610	exon9	c.T1020C	p.S340S	CATTGTAGACACG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608883	+	Silent	SNP	A	A	G	rs1134580	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	14	57	0	0.325581	0	A|0.773;G|0.227	0.227	strong	UBXN11,NS,carcinoma,-2,2	UBXN11	54	2	NM_183008	exon16	c.T1470C	p.G490G	GCCGGGACCGGGA	.	PASS	Atlas-SNP
ATAT1	79969	hgsc.bcm.edu	37	6	30596135	30596135	+	Silent	SNP	A	A	G	rs6904236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	72	157	0	0.464516	0	A|0.957;G|0.043	0.043	strong	.	ATAT1	30	.	NM_001254952	exon6	c.A465G	p.A155A	ACTGGCAATTGAC	.	PASS	Atlas-SNP
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	66	121	0	0.492537	0	A|0.911;G|0.089	0.089	strong	.	HPSE	55	.	NM_001098540	exon11	c.T1377C	p.N459N	GGTGACATTATGG	.	PASS	Atlas-SNP
OR5R1	219479	hgsc.bcm.edu	37	11	56185327	56185327	+	Missense_Mutation	SNP	T	T	C	rs7933772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	28	33	0	0.651163	0	C|0.324;N|0.000	0.324	strong	.	OR5R1	83	.	NM_001004744	exon1	c.A382G	p.S128G	GGGGACTACAGAT	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909627	123909627	+	Missense_Mutation	SNP	T	T	C	rs11219420	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	110	419	0	0.491071	0	T|0.681;C|0.319	0.319	strong	OR10G7,NS,carcinoma,0,1	OR10G7	103	1	NM_001004463	exon1	c.A82G	p.I28V	GGAAGATTCCAAA	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12381687	12381687	+	Missense_Mutation	SNP	G	G	A	rs116125922	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	44	76	0	0.494382	0	G|0.990;A|0.010	0.010	strong	.	VWDE	123	.	NM_001135924	exon23	c.C4268T	p.T1423I	TTACCTGTACTAC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78262161	78262161	+	Missense_Mutation	SNP	T	T	C	rs17857135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	31	78	0	0.397436	0	T|0.785;C|0.215	0.215	strong	RNF213_ENST00000456466,NS,carcinoma,0,6	RNF213	766	6	NM_001256071	exon4	c.T809C	p.M270T	CCTCTATGGTGAG	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848121	123848121	+	Missense_Mutation	SNP	T	T	C	rs17686210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	29	92	0	0.329545	0	T|0.785;C|0.215	0.215	strong	.	OR10S1	78	.	NM_001004474	exon1	c.A278G	p.K93R	ATGACCTTGGGCA	.	PASS	Atlas-SNP
RRM2B	50484	hgsc.bcm.edu	37	8	103251034	103251034	+	Missense_Mutation	SNP	A	A	C	rs72554092	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	15	28	0	0.576923	0	A|0.975;C|0.025	0.025	strong	.	RRM2B	31	.	NM_001172477	exon1	c.T17G	p.L6R	GGGGGAAGACGCA	.	PASS	Atlas-SNP
ENG	2022	hgsc.bcm.edu	37	9	130616621	130616621	+	Missense_Mutation	SNP	G	G	A	rs35400405	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	86	133	0	0.666667	0	G|0.950;A|0.050	0.050	strong	.	ENG	44	.	NM_001114753	exon1	c.C14T	p.T5M	GGGAGCGTGCCGC	.	PASS	Atlas-SNP
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	117	212	0	0.52	0	G|0.693;A|0.307	0.307	strong	.	MED14	108	.	NM_004229	exon5	c.C525T	p.D175D	AATTTTGTCCTGC	.	PASS	Atlas-SNP
CNKSR1	10256	hgsc.bcm.edu	37	1	26508997	26508997	+	Silent	SNP	C	C	T	rs2802347	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	93	156	0	0.510989	0	C|0.940;T|0.060	0.060	strong	.	CNKSR1	66	.	NM_006314	exon6	c.C546T	p.H182H	CTGCCACAACATC	.	PASS	Atlas-SNP
SPINT1	6692	hgsc.bcm.edu	37	15	41146880	41146880	+	Silent	SNP	T	T	C	rs8028552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	29	72	0	0.432836	0	C|0.286;N|0.000	0.286	strong	.	SPINT1	28	.	NM_181642	exon8	c.T1158C	p.S386S	CCCCAGTGACAAA	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23080634	23080634	+	Missense_Mutation	SNP	C	C	A	rs10083789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	29	60	0	0.408451	0	C|0.785;A|0.215	0.215	strong	.	USP31	122	.	NM_020718	exon16	c.G2792T	p.R931L	TCACGGCGACTAT	.	PASS	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107450589	107450589	+	Silent	SNP	C	C	T	rs3796111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	157	145	1	1	0.00689655	C|0.716;T|0.284	0.284	strong	.	ST6GAL2	159	.	NM_032528	exon3	c.G957A	p.A319A	CAAAACCGCATCA	.	PASS	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32476390	32476390	+	Silent	SNP	T	T	G	rs408813	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	195	233	0	0.994898	0	T|0.422;G|0.578	0.578	strong	NLRC4_ENST00000404025,NS,carcinoma,-1,4	NLRC4	165	4	NM_001199138	exon4	c.A543C	p.R181R	GGCAATTCGCTGC	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156347834	156347834	+	Missense_Mutation	SNP	T	T	A	rs11586833	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	94	191	1	0.494737	0.0052356	T|0.733;A|0.267	0.267	strong	RHBG,NS,carcinoma,0,1	RHBG	133	1	NM_020407	exon3	c.T428A	p.V143D	GTGCCGTCCTGGG	.	scavenged	Atlas-SNP
GPR35	2859	hgsc.bcm.edu	37	2	241569535	241569535	+	Missense_Mutation	SNP	C	C	T	rs115880579	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	94	0	0.45	0	C|0.993;T|0.007	0.007	strong	GPR35,NS,malignant_melanoma,-1,1	GPR35	43	1	NM_001195382	exon6	c.C259T	p.R87C	GAGACCCGCATCT	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54120820	54120820	+	Silent	SNP	G	G	A	rs805412	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	60	143	0	0.582524	0	G|0.521;A|0.479	0.479	strong	.	PSME4	247	.	NM_014614	exon35	c.C4029T	p.C1343C	AAAGAGGCAAAAA	.	PASS	Atlas-SNP
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743130	22743130	+	Silent	SNP	C	C	T	rs376169003		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	45	169	0	0.175781	0	.	.	weak	.	GOLGA6L1	20	.	NM_001001413	exon8	c.C1515T	p.H505H	GATGCACGACCAG	.	PASS	Atlas-SNP
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739779	140739779	+	Missense_Mutation	SNP	C	C	G	rs17097231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	75	164	0	0.39267	0	C|0.880;G|0.120	0.120	strong	.	PCDHGB2	196	.	NM_018923	exon1	c.C77G	p.P26R	TGTTCCCCGGGGC	.	PASS	Atlas-SNP
CLSTN2	64084	hgsc.bcm.edu	37	3	140281768	140281768	+	Silent	SNP	G	G	A	rs35951028	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	127	114	0	0.992188	0	G|0.973;A|0.027	0.027	strong	.	CLSTN2	190	.	NM_022131	exon14	c.G2328A	p.G776G	CAATGGGCGCTAC	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39853163	39853163	+	Silent	SNP	T	T	C	rs79901102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	74	0	0.545455	0	T|0.975;C|0.025	0.025	strong	.	MACF1	909	.	NM_012090	exon54	c.T8463C	p.H2821H	AAACCATTGGGAA	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84861723	84861723	+	Silent	SNP	C	C	T	rs7570005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	53	115	0	0.46087	0	C|0.843;T|0.157	0.157	strong	.	DNAH6	194	.	NM_001370	exon30	c.C4611T	p.I1537I	CGTCATCGCGCAG	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121154974	121154974	+	Missense_Mutation	SNP	T	T	C	rs1381057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	115	174	0	0.511111	0	T|0.298;C|0.702	0.702	strong	.	POLQ	273	.	NM_199420	exon28	c.A7538G	p.Q2513R	CCTGTTTGGTCAC	.	PASS	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	30	98	0	0.294118	0	T|0.809;C|0.191	0.191	strong	.	GABBR2	126	.	NM_005458	exon2	c.A360G	p.A120A	TTTTATTGCATCG	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124732426	124732426	+	Missense_Mutation	SNP	G	G	A	rs113838848	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	72	123	0	0.553846	0	G|0.986;A|0.014	0.014	strong	.	HEG1	109	.	NM_020733	exon6	c.C1997T	p.S666F	GAGGAGGAGGAGG	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238449007	238449007	+	Missense_Mutation	SNP	T	T	C	rs3817362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	118	0	1	0	T|0.643;C|0.357	0.357	strong	.	MLPH	41	.	NM_024101	exon10	c.T1121C	p.V374A	CTGGAGTGCGCAC	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206013	98206013	+	Missense_Mutation	SNP	C	C	T	rs188661236	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	127	295	1	0.484733	0.00338983	C|0.989;T|0.011	0.011	strong	.	.	.	.	NM_025190	exon1	c.G136A	p.A46T	TATTGGCGTCATA	.	PASS	Atlas-SNP
CAPN11	11131	hgsc.bcm.edu	37	6	44151490	44151490	+	Missense_Mutation	SNP	G	G	A	rs7761137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	203	184	0	0.980676	0	G|0.721;A|0.279	0.279	strong	.	CAPN11	66	.	NM_007058	exon22	c.G2183A	p.S728N	GCTTGAGCCTGGA	.	PASS	Atlas-SNP
LRRC16A	55604	hgsc.bcm.edu	37	6	25606442	25606442	+	Missense_Mutation	SNP	A	A	G	rs201300946	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	53	99	0	0.456897	0	.	.	weak	.	LRRC16A	168	.	NM_017640	exon35	c.A3788G	p.K1263R	CCCCCAAACCCAG	.	PASS	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	37	3	41266971	41266971	+	Silent	SNP	C	C	G	rs3856747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	110	165	0	0.547264	0	C|0.994;T|0.006	.	strong	CTNNB1,colon,carcinoma,+2,2	CTNNB1	4904	2	NM_001098209	exon5	c.C642G	p.T214T	TTGTACCGCTGGG	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62172269	62172269	+	Missense_Mutation	SNP	C	C	A	rs310654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	83	60	0	0.988095	0	C|0.822;A|0.178	0.178	strong	.	SRMS	48	.	NM_080823	exon8	c.G1369T	p.V457L	TGAGCACGTAGAC	.	PASS	Atlas-SNP
NFU1	27247	hgsc.bcm.edu	37	2	69659126	69659126	+	Missense_Mutation	SNP	A	A	T	rs4453725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	56	1	1	0.0178571	A|0.636;T|0.364	0.364	strong	NFU1,NS,carcinoma,0,1	NFU1	19	1	NM_001002755	exon2	c.T74A	p.M25K	TTCAACATATGAC	.	scavenged	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107040985	107040985	+	Silent	SNP	T	T	C	rs140856347	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	14	42	0	0.933333	0	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	NM_001144013	exon20	c.A3438G	p.R1146R	TGCCAATCGCTCT	.	scavenged	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76753063	76753063	+	Silent	SNP	C	C	T	rs2472643	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	15	24	0	0.652174	0	C|0.915;T|0.085	0.085	strong	SALL3,NS,carcinoma,0,1	SALL3	162	1	NM_171999	exon2	c.C1072T	p.L358L	CCCGGCCTGCCAA	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	35	73	0	0.625	0	C|0.739;T|0.261	0.261	strong	B3GNTL1,NS,malignant_melanoma,0,2	B3GNTL1	40	2	NM_001009905	exon7	c.G591A	p.E197E	ACCTCCCTCGTTA	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47535816	47535816	+	Missense_Mutation	SNP	G	G	A	rs61735835	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	32	42	0	0.551724	0	G|0.991;A|0.009	0.009	strong	.	COL6A2	351	.	NM_058175	exon6	c.G832A	p.E278K	CCGGGAGAGCCTG	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721622	49721622	+	Missense_Mutation	SNP	C	C	T	rs200268600		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	556	34	501	22	0.0611511	0.0439122	C|0.999;T|0.001	0.001	weak	MST1,NS,carcinoma,0,2	MST1	84	2	NM_020998	exon18	c.G2017A	p.G673S	AGTCACCCTGGCA	.	scavenged	Atlas-SNP
MYBL2	4605	hgsc.bcm.edu	37	20	42310426	42310426	+	Silent	SNP	C	C	T	rs2227937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	131	141	0	1	0	C|0.967;T|0.033	0.033	strong	.	MYBL2	82	.	NM_002466	exon3	c.C117T	p.D39D	GCAGGACGAGCAG	.	PASS	Atlas-SNP
DTNBP1	84062	hgsc.bcm.edu	37	6	15523388	15523388	+	Missense_Mutation	SNP	T	T	C	rs73369534	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	55	136	0	0.413534	0	T|0.967;C|0.033	0.033	strong	.	DTNBP1	56	.	NM_032122	exon10	c.A874G	p.R292G	TGGCTCTTAATTC	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113379720	113379720	+	Missense_Mutation	SNP	G	G	A	rs114838141	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	78	173	0	0.39	0	G|0.996;A|0.004	0.004	strong	.	KIAA2018	180	.	NM_001009899	exon7	c.C809T	p.S270F	TGCAAAGAATGAT	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549082	158549082	+	Missense_Mutation	SNP	A	A	T	rs61755876	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	100	185	0	0.483092	0	A|0.972;T|0.028	0.028	strong	.	OR10X1	96	.	NM_001004477	exon1	c.T608A	p.L203Q	CAAGACAGCCTAA	.	PASS	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546686	11546686	+	Missense_Mutation	SNP	C	C	T	rs76832300	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	603	165	672	2	0.273632	0.00297619	.	.	weak	PRB2_ENST00000389362,bladder,carcinoma,0,2	PRB2	168	2	NM_006248	exon3	c.G326A	p.R109Q	GGACTTCGGGACT	.	scavenged	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879517	39879517	+	Missense_Mutation	SNP	G	G	A	rs587523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	96	179	0	0.502618	0	G|0.932;A|0.068	0.068	strong	.	KIAA0754	93	.	NM_015038	exon1	c.G3580A	p.E1194K	CTGGAGGAACCCA	.	PASS	Atlas-SNP
GIMAP6	474344	hgsc.bcm.edu	37	7	150325177	150325177	+	Missense_Mutation	SNP	C	C	T	rs11974345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	23	47	0	0.442308	0	C|0.960;T|0.040	0.040	strong	GIMAP6,NS,carcinoma,+1,1	GIMAP6	60	1	NM_001244072	exon3	c.G719A	p.G240D	GAGCCGCCAGCCA	.	PASS	Atlas-SNP
OR9Q2	219957	hgsc.bcm.edu	37	11	57958497	57958497	+	Missense_Mutation	SNP	T	T	C	rs34337292	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	384	194	358	2	0.505208	0.00558659	T|0.754;C|0.246	0.246	strong	OR9Q2,NS,carcinoma,-1,1	OR9Q2	78	1	NM_001005283	exon1	c.T535C	p.C179R	ATTTTCTGTGACC	.	scavenged	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114386723	114386723	+	Silent	SNP	G	G	A	rs7979406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	121	216	0	0.489879	0	G|0.971;A|0.029	0.029	strong	.	RBM19	117	.	NM_001146699	exon10	c.C1191T	p.D397D	GGCCAGGTCCTCC	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16327909	16327909	+	Missense_Mutation	SNP	C	C	T	rs6777976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	105	189	0	0.475113	0	C|0.824;T|0.176	0.176	strong	OXNAD1,NS,carcinoma,-1,1	OXNAD1	31	1	NM_138381	exon5	c.C244T	p.R82C	AGCCTCCGCTTGC	.	PASS	Atlas-SNP
WDSUB1	151525	hgsc.bcm.edu	37	2	160132089	160132089	+	Missense_Mutation	SNP	T	T	G	rs16843852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	55	148	0	0.366667	0	G|0.185;N|0.000	0.185	strong	.	WDSUB1	39	.	NM_152528	exon4	c.A644C	p.K215T	CAAATTTTGACTT	.	PASS	Atlas-SNP
CLPB	81570	hgsc.bcm.edu	37	11	72040784	72040784	+	Silent	SNP	T	T	C	rs36049191	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	60	132	0	0.491803	0	C|0.101;T|0.899	0.101	strong	.	CLPB	45	.	NM_030813	exon7	c.A930G	p.E310E	CATCACTTCCCCT	.	PASS	Atlas-SNP
OR5H1	26341	hgsc.bcm.edu	37	3	97851689	97851689	+	Missense_Mutation	SNP	T	T	C	rs201501927	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1086	26	913	5	0.0239411	0.00547645	T|0.796;C|0.204	0.204	strong	OR5H1,NS,carcinoma,0,4	OR5H1	71	4	NM_001005338	exon1	c.T148C	p.W50R	GTCATCTGGAAAG	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408811	105408811	+	Missense_Mutation	SNP	A	A	G	rs2819421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	108	247	1	0.453782	0.00404858	A|0.505;G|0.495	0.495	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T12977C	p.L4326P	ACCTTCAGCGCAG	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	28	88	0	0.444444	0	A|0.694;G|0.306	0.306	strong	.	DHRS4	22	.	NM_021004	exon1	c.A93G	p.A31A	GCTCGCAAATAAG	.	PASS	Atlas-SNP
POLR3A	11128	hgsc.bcm.edu	37	10	79781326	79781326	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	29	77	0	0.42029	0	.	.	none	.	POLR3A	104	.	NM_007055	exon8	c.A1163G	p.K388R	AGAATTTTGGCCA	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179069413	179069413	+	Missense_Mutation	SNP	A	A	G	rs374415765		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	35	134	0	0.315315	0	.	.	weak	.	C5orf60	24	.	NM_001142306	exon5	c.T761C	p.I254T	TGTCTTATGCGTC	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848121	54848121	+	Missense_Mutation	SNP	C	C	T	rs141881690	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	37	220	0	0.143969	0	C|0.999;T|0.001	0.001	weak	.	LILRA4	91	.	NM_012276	exon6	c.G1246A	p.V416M	AGACCACGAGCTC	.	PASS	Atlas-SNP
TRPV4	59341	hgsc.bcm.edu	37	12	110238481	110238481	+	Silent	SNP	G	G	A	rs1344554	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	110	0	1	0	G|0.922;A|0.078	0.078	strong	.	TRPV4	88	.	NM_147204	exon4	c.C795T	p.H265H	CTGGGCGTGGACA	.	PASS	Atlas-SNP
C6orf118	168090	hgsc.bcm.edu	37	6	165715460	165715460	+	Silent	SNP	G	G	C	rs9459355	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	49	0	0.483871	0	G|0.804;C|0.196	0.196	strong	.	C6orf118	116	.	NM_144980	exon2	c.C351G	p.A117A	GACCAGGGCCGTG	.	PASS	Atlas-SNP
SORCS2	57537	hgsc.bcm.edu	37	4	7741941	7741941	+	Missense_Mutation	SNP	G	G	A	rs189272447	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	8	20	0	0.421053	0	G|0.999;A|0.001	0.001	strong	.	SORCS2	98	.	NM_020777	exon27	c.G3430A	p.V1144M	TCAGGCGTGGTCC	.	PASS	Atlas-SNP
CCS	9973	hgsc.bcm.edu	37	11	66366682	66366682	+	Missense_Mutation	SNP	G	G	A	rs61731812	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	57	80	0	0.626374	0	G|0.996;A|0.004	0.004	strong	.	CCS	22	.	NM_005125	exon3	c.G208A	p.G70R	GGCACGGGGCGGC	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2116037	2116037	+	Silent	SNP	G	G	A	rs6601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	32	85	0	0.426667	0	A|0.255;G|0.745;T|0.000	0.255	strong	.	SMARCA2	313	.	NM_139045	exon25	c.G3672A	p.E1224E	GCATGAGGAGGAA	.	PASS	Atlas-SNP
SNX4	8723	hgsc.bcm.edu	37	3	125179676	125179676	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	94	203	0	0.479592	0	.	.	none	.	SNX4	29	.	NM_003794	exon10	c.G883A	p.E295K	CATCTTCCAAAAT	.	PASS	Atlas-SNP
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628965	1628965	+	Silent	SNP	G	G	A	rs57186801	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	200	138	0	0.995025	0	G|0.525;A|0.475	0.475	strong	.	KRTAP5-3	33	.	NM_001012708	exon1	c.C651T	p.S217S	GCAGCAGCTGGAC	.	PASS	Atlas-SNP
C11orf21	29125	hgsc.bcm.edu	37	11	2320884	2320884	+	Silent	SNP	A	A	G	rs1501466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	90	200	1	0.428571	0.005	A|0.799;G|0.201	0.201	strong	C11orf21,NS,carcinoma,-2,1	C11orf21	11	1	NM_001142946	exon4	c.T339C	p.G113G	AAGGGCACCATGG	.	scavenged	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20295972	20295972	+	Missense_Mutation	SNP	G	G	A	rs76952476	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	383	171	486	0	0.446475	0	G|0.977;A|0.023	0.023	strong	OR4N2,NS,carcinoma,+1,5	OR4N2	125	5	NM_001004723	exon1	c.G365A	p.R122H	TTGACCGCTACAT	.	PASS	Atlas-SNP
ROBO2	6092	hgsc.bcm.edu	37	3	77614215	77614215	+	Missense_Mutation	SNP	T	T	C	rs185792666	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	44	61	0	0.536585	0	T|0.996;C|0.004	0.004	strong	.	ROBO2	527	.	NM_002942	exon12	c.T1793C	p.I598T	GAGCGATCAACCC	.	PASS	Atlas-SNP
RPP40	10799	hgsc.bcm.edu	37	6	4996611	4996611	+	Missense_Mutation	SNP	T	T	G	rs61730291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	47	132	0	0.479592	0	T|0.971;G|0.029	0.029	strong	.	RPP40	36	.	NM_006638	exon6	c.A603C	p.Q201H	CTGAATTTGGTAC	.	PASS	Atlas-SNP
THEM5	284486	hgsc.bcm.edu	37	1	151820324	151820324	+	Missense_Mutation	SNP	T	T	C	rs6587625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	120	0	1	0	T|0.206;C|0.794	0.794	strong	.	THEM5	41	.	NM_182578	exon5	c.A590G	p.D197G	AGAGAGTCCACGG	.	PASS	Atlas-SNP
ACER1	125981	hgsc.bcm.edu	37	19	6333476	6333476	+	Silent	SNP	G	G	A	rs16993553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	43	93	0	0.443299	0	G|0.938;A|0.062	0.062	strong	ACER1,NS,carcinoma,-2,1	ACER1	38	1	NM_133492	exon1	c.C87T	p.Y29Y	CGTGTTGTAGAAC	.	PASS	Atlas-SNP
ADIPOR2	79602	hgsc.bcm.edu	37	12	1890199	1890199	+	Silent	SNP	G	G	A	rs16928751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	84	195	0	0.430769	0	G|0.876;A|0.124	0.124	strong	.	ADIPOR2	30	.	NM_024551	exon6	c.G795A	p.Q265Q	CTCCCAGTGGGAC	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197638	39197638	+	Silent	SNP	A	A	G	rs112542604	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	114	291	1	0.401408	0.00343643	A|0.889;G|0.111	0.111	strong	.	KRTAP1-1	23	.	NM_030967	exon1	c.T12C	p.C4C	GGTCTGACAGCAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239114	31239114	+	Missense_Mutation	SNP	G	G	T	rs1071649	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	40	68	3	0.353982	0.0441176	T|0.197;G|0.798;A|0.005	0.197	strong	HLA-C_ENST00000383329,colon,carcinoma,0,4	HLA-C	92	4	NM_002117	exon3	c.C355A	p.L119I	TCTGGAGGGTGTG	.	scavenged	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95058477	95058477	+	Silent	SNP	G	G	A	rs6117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	77	126	0	0.620968	0	G|0.956;A|0.044	0.044	strong	.	SERPINA5	69	.	NM_000624	exon6	c.G1122A	p.S374S	CAGGTCGGCCCGC	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115004935	115004935	+	Silent	SNP	T	T	C	rs2296970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	35	74	0	0.384615	0	T|0.563;C|0.437	0.437	strong	.	CDC16	50	.	NM_003903	exon5	c.T351C	p.P117P	AGATCCTTCCAGC	.	PASS	Atlas-SNP
CS	1431	hgsc.bcm.edu	37	12	56676279	56676279	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	35	341	1	0.119048	0.00293255	.	.	none	CS,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CS	44	1	NM_004077	exon6	c.T513C	p.A171A	TGTAACAGCTGCA	.	scavenged	Atlas-SNP
DCXR	51181	hgsc.bcm.edu	37	17	79994600	79994600	+	Silent	SNP	C	C	T	rs61739740	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	68	0	0.478873	0	C|0.760;T|0.240	0.240	strong	.	DCXR	10	.	NM_016286	exon4	c.G345A	p.S115S	CACCTGCGACACC	.	PASS	Atlas-SNP
CLPTM1	1209	hgsc.bcm.edu	37	19	45490570	45490570	+	Silent	SNP	A	A	G	rs3786505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	55	87	0	0.539216	0	A|0.596;G|0.404	0.404	strong	.	CLPTM1	109	.	NM_001294	exon8	c.A927G	p.P309P	CTGCCCACTCTCG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218674697	218674697	+	Missense_Mutation	SNP	C	C	T	rs918949	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	116	120	0	0.991453	0	C|0.354;T|0.646	0.646	strong	.	TNS1	251	.	NM_022648	exon30	c.G4810A	p.V1604I	AGTTGACGAAGAG	.	PASS	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	64	145	0	0.52459	0	C|0.893;T|0.107	0.107	strong	ST6GAL2,NS,carcinoma,+1,1	ST6GAL2	159	1	NM_032528	exon2	c.G460A	p.G154R	GCTCCCCGGGGGA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228559225	228559225	+	Missense_Mutation	SNP	G	G	A	rs200269110	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	8	12	0	0.4	0	.	.	weak	.	OBSCN	2142	.	NM_001271223	exon105	c.G23617A	p.E7873K	CTGCGCGAGCCAC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	35	0	0.530612	0	G|0.722;C|0.278	0.278	strong	RP1L1,NS,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.C4484G	p.P1495R	TGGGTGGGTTGGG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	522	517	470	2	0.990421	0.00425532	A|0.687;G|0.313	0.313	strong	FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.T2508C	p.D836D	CTGACCATCTTGG	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19471388	19471388	+	Silent	SNP	A	A	G	rs2274000	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	108	203	1	0.514286	0.00492611	A|0.904;G|0.096	0.096	strong	UBR4,NS,carcinoma,0,1	UBR4	415	1	NM_020765	exon54	c.T7959C	p.I2653I	AGCTTCAATATGA	.	PASS	Atlas-SNP
ZFP62	643836	hgsc.bcm.edu	37	5	180278393	180278393	+	Missense_Mutation	SNP	C	C	G	rs705441	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	133	256	1	0.455479	0.00390625	C|0.260;G|0.740	0.740	strong	.	ZFP62	33	.	NM_001172638	exon2	c.G102C	p.M34I	TTCAGGCATAGGA	.	PASS	Atlas-SNP
TRIM67	440730	hgsc.bcm.edu	37	1	231339713	231339713	+	Silent	SNP	C	C	T	rs11806609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	37	80	0	0.425287	0	C|0.892;T|0.108	0.108	strong	.	TRIM67	160	.	NM_001004342	exon6	c.C1635T	p.D545D	CGTGGACGGCTAC	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38776107	38776107	+	Missense_Mutation	SNP	T	T	G	rs11096955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	104	106	0	0.990476	0	T|0.553;G|0.447	0.447	strong	TLR10,colon,carcinoma,0,1	TLR10	87	1	NM_001017388	exon2	c.A1105C	p.I369L	GTTGGATAGTTCT	.	PASS	Atlas-SNP
LYPD4	147719	hgsc.bcm.edu	37	19	42343355	42343355	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	49	112	0	0.480392	0	.	.	none	.	LYPD4	30	.	NM_173506	exon2	c.G5C	p.G2A	TGGGGTCCCATGG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7023371	7023371	+	Silent	SNP	A	A	G	rs684634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	102	0	1	0	A|0.524;G|0.476	0.476	strong	LAMA1,NS,adenoma,0,1	LAMA1	458	1	NM_005559	exon19	c.T2493C	p.C831C	ATCTGCACATCTG	.	PASS	Atlas-SNP
MICAL1	64780	hgsc.bcm.edu	37	6	109767931	109767931	+	Missense_Mutation	SNP	C	C	T	rs59056467	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	133	263	1	0.505703	0.00380228	C|0.695;G|0.000;T|0.305	0.305	strong	.	MICAL1	79	.	NM_022765	exon18	c.G2272A	p.A758T	CTTCCGCTTTGTG	.	PASS	Atlas-SNP
GPN2	54707	hgsc.bcm.edu	37	1	27210721	27210721	+	Missense_Mutation	SNP	T	T	C	rs3170660	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	105	1	1	0.00952381	T|0.213;C|0.787	0.787	strong	.	GPN2	18	.	NM_018066	exon4	c.A790G	p.R264G	GGGCTCTGAAACA	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136509370	136509370	+	Missense_Mutation	SNP	G	G	T	rs4531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	49	57	0	0.653333	0	G|0.913;T|0.087	0.087	strong	.	DBH	86	.	NM_000787	exon5	c.G952T	p.A318S	GGCCTTGCCTTCG	.	PASS	Atlas-SNP
ANK2	287	hgsc.bcm.edu	37	4	114279770	114279770	+	Silent	SNP	T	T	C	rs145557320	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	45	74	0	0.483871	0	T|0.992;C|0.008	0.008	strong	.	ANK2	576	.	NM_001148	exon38	c.T9996C	p.S3332S	ATCCAGTGTAGAT	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42562027	42562027	+	Missense_Mutation	SNP	A	A	T	rs6905054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	22	64	0	0.333333	0	A|0.966;T|0.034	0.034	strong	.	UBR2	134	.	NM_001184801	exon4	c.A516T	p.E172D	CTCTGAAATTGAG	.	PASS	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	37	9	119249690	119249690	+	Missense_Mutation	SNP	C	C	T	rs16933591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	50	70	0	0.632911	0	C|0.979;T|0.021	0.021	strong	ASTN2_ENST00000361477,NS,carcinoma,0,1	ASTN2	307	1	NM_014010	exon19	c.G3292A	p.V1098I	TACTGACTTCAGG	.	PASS	Atlas-SNP
PLA1A	51365	hgsc.bcm.edu	37	3	119347623	119347623	+	Missense_Mutation	SNP	C	C	A	rs115172544	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	65	156	0	0.460993	0	C|0.984;A|0.016	0.016	strong	.	PLA1A	65	.	NM_015900	exon10	c.C1197A	p.F399L	GAAATTCAAGTTT	.	PASS	Atlas-SNP
FXR1	8087	hgsc.bcm.edu	37	3	180630500	180630500	+	Silent	SNP	C	C	T	rs1805578	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	304	168	312	1	0.552632	0.00320513	C|0.961;T|0.039	0.039	strong	.	FXR1	75	.	NM_001013438	exon1	c.C27T	p.R9R	GGTTCGCGGCTCT	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8150353	8150353	+	Silent	SNP	C	C	T	rs61729617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	21	36	0	0.446809	0	C|0.967;T|0.033	0.033	strong	.	FBN3	300	.	NM_032447	exon55	c.G6981A	p.G2327G	GCCACCCCCACAG	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370629	240370629	+	Silent	SNP	C	C	G	rs10926166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	69	101	0	0.556452	0	C|0.679;G|0.321	0.321	strong	.	FMN2	451	.	NM_020066	exon5	c.C2517G	p.T839T	TCAAACCAGCCAC	.	PASS	Atlas-SNP
IFNA16	3449	hgsc.bcm.edu	37	9	21217022	21217022	+	Missense_Mutation	SNP	C	C	G	rs28368160	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	175	303	1	0.50578	0.00330033	C|0.957;G|0.043	0.043	strong	.	IFNA16	27	.	NM_002173	exon1	c.G283C	p.D95H	ATGAATCCTTTGT	.	PASS	Atlas-SNP
TRIP10	9322	hgsc.bcm.edu	37	19	6751103	6751103	+	Missense_Mutation	SNP	G	G	A	rs139253875	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	65	118	0	0.445205	0	G|0.999;A|0.001	0.001	strong	TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	2	NM_004240	exon14	c.G1519A	p.E507K	ATGGCCGAGGGTG	.	PASS	Atlas-SNP
TSPAN8	7103	hgsc.bcm.edu	37	12	71533534	71533534	+	Missense_Mutation	SNP	C	C	G	rs3763978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	58	94	0	0.471545	0	C|0.707;G|0.293	0.293	strong	TSPAN8,colon,carcinoma,0,1	TSPAN8	30	1	NM_004616	exon4	c.G218C	p.G73A	CAGCATCCCAGGA	.	PASS	Atlas-SNP
HDHD2	84064	hgsc.bcm.edu	37	18	44660923	44660923	+	Missense_Mutation	SNP	C	C	T	rs7230131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	128	0	0.494624	0	C|0.966;T|0.034	0.034	strong	.	HDHD2	12	.	NM_032124	exon3	c.G254A	p.R85Q	TGTTTCCGCTCTA	.	PASS	Atlas-SNP
LEPROTL1	23484	hgsc.bcm.edu	37	8	29994923	29994923	+	Missense_Mutation	SNP	G	G	A	rs77053651	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	56	118	0	0.414815	0	G|0.984;A|0.016	0.016	strong	.	LEPROTL1	16	.	NM_001128208	exon4	c.G415A	p.V139M	CAACCCGTGCTGA	.	PASS	Atlas-SNP
WFIKKN2	124857	hgsc.bcm.edu	37	17	48917609	48917609	+	Silent	SNP	C	C	T	rs36031777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	44	74	0	0.564103	0	C|0.933;T|0.067	0.067	strong	WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	NM_175575	exon2	c.C960T	p.G320G	CAATGGCACGGCT	.	PASS	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2752026	2752026	+	Silent	SNP	G	G	A	rs61743920	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	22	55	0	0.55	0	G|0.988;A|0.012	0.012	strong	.	AMZ1	41	.	NM_133463	exon7	c.G1011A	p.P337P	GGAGCCGTCAGTG	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	37	19	20044810	20044810	+	Missense_Mutation	SNP	C	C	T	rs75974774	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	47	70	0	0.51087	0	C|0.998;T|0.002	0.002	strong	.	ZNF93	81	.	NM_031218	exon4	c.C1046T	p.A349V	GCAAAGCCTTTAT	.	PASS	Atlas-SNP
IGSF9	57549	hgsc.bcm.edu	37	1	159898437	159898437	+	Missense_Mutation	SNP	G	G	A	rs35574000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	56	96	0	0.538462	0	G|0.987;A|0.013	0.013	strong	.	IGSF9	123	.	NM_001135050	exon19	c.C2741T	p.P914L	GGACTGGGTGGGG	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	37	6	97533193	97533193	+	Silent	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	4	52	0	0.0481928	0	.	.	none	KLHL32,mouth,carcinoma,+1,1	KLHL32	85	1	NM_052904	exon6	c.C603A	p.S201S	GACCTCCCTGAGT	.	PASS	Atlas-SNP
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	83	165	0	0.5	0	A|0.770;G|0.230	0.230	strong	.	.	.	.	NM_014283	exon14	c.A1368G	p.E456E	GGAAGAATATGAA	.	PASS	Atlas-SNP
ANKMY2	57037	hgsc.bcm.edu	37	7	16640491	16640491	+	Silent	SNP	G	G	A	rs541797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	35	105	0	0.368421	0	G|0.835;A|0.165	0.165	strong	.	ANKMY2	46	.	NM_020319	exon10	c.C1221T	p.S407S	AGGATTGGAATCC	.	PASS	Atlas-SNP
TMCO4	255104	hgsc.bcm.edu	37	1	20009837	20009837	+	Missense_Mutation	SNP	G	G	C	rs116650784	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	95	175	0	0.472637	0	G|0.975;C|0.025	0.025	strong	.	TMCO4	46	.	NM_181719	exon16	c.C1601G	p.A534G	CCTGGGGCCAGCA	.	PASS	Atlas-SNP
SIGLEC11	114132	hgsc.bcm.edu	37	19	50463670	50463670	+	Missense_Mutation	SNP	T	T	G	rs79085301	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	71	184	1	0.972603	0.00543478	T|0.840;G|0.160	0.160	strong	.	SIGLEC11	70	.	NM_052884	exon3	c.A469C	p.K157Q	GCTTCTTAGTCAG	.	PASS	Atlas-SNP
CNTROB	116840	hgsc.bcm.edu	37	17	7843053	7843053	+	Silent	SNP	C	C	T	rs11078719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	26	58	0	0.52	0	C|0.506;T|0.494	0.494	strong	.	CNTROB	61	.	NM_001037144	exon8	c.C1150T	p.L384L	GCTCAGCTGGAAA	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8825192	8825192	+	Silent	SNP	A	A	G	rs581894	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	106	0	1	0	A|0.389;G|0.611	0.611	strong	CCDC165,NS,carcinoma,0,1	.	.	1	NM_015210	exon15	c.A3684G	p.G1228G	CAAGGGAGGCCCT	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160469542	160469542	+	Silent	SNP	A	A	G	rs8191809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	65	0	0.485294	0	A|0.988;G|0.012	0.012	strong	.	IGF2R	251	.	NM_000876	exon18	c.A2481G	p.A827A	ATATGCATCGGCT	.	PASS	Atlas-SNP
OR13C4	138804	hgsc.bcm.edu	37	9	107289352	107289352	+	Missense_Mutation	SNP	T	T	C	rs61738891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	32	86	0	0.390244	0	T|0.992;C|0.008	0.008	strong	.	OR13C4	55	.	NM_001001919	exon1	c.A139G	p.I47V	TTGCTATGATCAG	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7267502	7267502	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	3	225	1	0.0125523	0.00444444	.	.	none	INSR_ENST00000302850,NS,carcinoma,+1,2	INSR	265	2	NM_000208	exon2	c.A506G	p.D169G	TAATTATCCTCCA	.	scavenged	Atlas-SNP
CCDC125	202243	hgsc.bcm.edu	37	5	68588029	68588029	+	Missense_Mutation	SNP	T	T	C	rs112794294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	79	240	0	0.438889	0	T|0.986;C|0.014	0.014	strong	.	CCDC125	41	.	NM_176816	exon9	c.A1085G	p.H362R	TTAAGGTGCTTCC	.	PASS	Atlas-SNP
AEBP1	165	hgsc.bcm.edu	37	7	44147485	44147485	+	Missense_Mutation	SNP	C	C	A	rs2537188	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	76	171	0	0.447059	0	C|0.678;A|0.322	0.322	strong	AEBP1,NS,carcinoma,0,1	AEBP1	102	1	NM_001129	exon5	c.C817A	p.P273T	CCAGAGCCCCCTG	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	76	165	0	0.439306	0	C|0.971;G|0.029	0.029	strong	.	BDP1	204	.	NM_018429	exon23	c.C5026G	p.Q1676E	TCAGCACAAATGA	.	PASS	Atlas-SNP
SLC36A2	153201	hgsc.bcm.edu	37	5	150696447	150696447	+	Silent	SNP	C	C	T	rs369907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	136	0	1	0	C|0.415;T|0.585	0.585	strong	.	SLC36A2	71	.	NM_181776	exon10	c.G1383A	p.Q461Q	CAGGGCCTGGTAG	.	PASS	Atlas-SNP
VPS54	51542	hgsc.bcm.edu	37	2	64160864	64160864	+	Missense_Mutation	SNP	G	G	C	rs34015596	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	50	88	0	0.568182	0	G|0.970;C|0.030	0.030	strong	.	VPS54	57	.	NM_016516	exon12	c.C1682G	p.S561C	GATGAAGAATCAG	.	PASS	Atlas-SNP
LMNB1	4001	hgsc.bcm.edu	37	5	126140540	126140540	+	Silent	SNP	G	G	A	rs34224885	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	49	92	0	0.429825	0	G|0.972;A|0.028	0.028	strong	LMNB1,colon,carcinoma,+1,1	LMNB1	49	1	NM_005573	exon2	c.G432A	p.S144S	GAATTCGAAAGAT	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3747890	3747890	+	Silent	SNP	C	C	T	rs10409928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	76	91	0	0.575758	0	C|0.946;T|0.054	0.054	strong	.	TJP3	79	.	NM_001267561	exon19	c.C2448T	p.Y816Y	CGACTACGAGACG	.	PASS	Atlas-SNP
USP17L2	377630	hgsc.bcm.edu	37	8	11996074	11996074	+	Missense_Mutation	SNP	T	T	C	rs142023572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	50	120	0	0.403226	0	T|0.955;C|0.045	0.045	strong	USP17L2,bladder,carcinoma,+2,1	USP17L2	47	1	NM_201402	exon1	c.A196G	p.K66E	GCTTCTTCCTGGG	.	scavenged	Atlas-SNP
CLCC1	23155	hgsc.bcm.edu	37	1	109479953	109479953	+	Missense_Mutation	SNP	G	G	A	rs150665002	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	54	97	0	0.509434	0	G|1.000;A|0.000	0.000	strong	.	CLCC1	55	.	NM_001048210	exon10	c.C1129T	p.R377W	TATCCCGTGGCCG	.	PASS	Atlas-SNP
OR2AE1	81392	hgsc.bcm.edu	37	7	99474007	99474007	+	Missense_Mutation	SNP	T	T	C	rs60737583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	42	91	0	0.461538	0	T|0.932;C|0.068	0.068	strong	.	OR2AE1	32	.	NM_001005276	exon1	c.A650G	p.Y217C	AAGACATAGGATG	.	PASS	Atlas-SNP
FSCN2	25794	hgsc.bcm.edu	37	17	79495890	79495890	+	Silent	SNP	C	C	T	rs117946784	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	5	9	0	0.5	0	C|0.990;T|0.010	0.010	strong	.	FSCN2	35	.	NM_001077182	exon1	c.C333T	p.F111F	CTTCTTCGGAGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515435	195515435	+	Missense_Mutation	SNP	C	C	T	rs199540819	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	580	21	218	5	0.0362069	0.0229358	C|0.970;T|0.030	0.030	strong	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.G3016A	p.A1006T	GGGTGGCGTGACC	.	scavenged	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42233529	42233529	+	Silent	SNP	G	G	A	rs79466811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	42	87	0	0.4375	0	G|0.981;A|0.019	0.019	strong	.	TRERF1	124	.	NM_033502	exon6	c.C1444T	p.L482L	CAGGTAGGTGCAT	.	PASS	Atlas-SNP
SLC16A5	9121	hgsc.bcm.edu	37	17	73096199	73096199	+	Silent	SNP	C	C	T	rs142993518	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	52	130	0	0.422764	0	C|0.998;T|0.002	0.002	strong	.	SLC16A5	80	.	NM_001271765	exon5	c.C441T	p.G147G	GATGGGCGTCTCC	.	PASS	Atlas-SNP
HLA-DOA	3111	hgsc.bcm.edu	37	6	32976013	32976013	+	Silent	SNP	G	G	A	rs78635760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	60	66	0	0.674157	0	G|0.984;A|0.016	0.016	strong	HLA-DOA,colon,carcinoma,0,1	HLA-DOA	22	1	NM_002119	exon2	c.C108T	p.P36P	GAAGGCGGGTCCG	.	PASS	Atlas-SNP
MOGS	7841	hgsc.bcm.edu	37	2	74690039	74690039	+	Missense_Mutation	SNP	G	G	A	rs2268416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	33	0	1	0	G|0.582;A|0.418	0.418	strong	.	MOGS	58	.	NM_006302	exon4	c.C877T	p.P293S	CAGGGGGGGCCCC	.	PASS	Atlas-SNP
PCDHGA10	56106	hgsc.bcm.edu	37	5	140793007	140793007	+	Missense_Mutation	SNP	A	A	G	rs4912751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	170	137	1	0.994152	0.00729927	A|0.483;G|0.517	0.517	strong	.	PCDHGA10	114	.	NM_032090	exon1	c.A265G	p.I89V	AGCTTGATCACCG	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	99027184	99027184	+	Missense_Mutation	SNP	T	T	C	rs2903150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	94	0	0.421687	0	T|0.617;C|0.383	0.383	strong	.	.	.	.	NM_174952	exon5	c.A532G	p.I178V	TCTTGATGTTAAC	.	PASS	Atlas-SNP
ZAR1L	646799	hgsc.bcm.edu	37	13	32885654	32885654	+	Missense_Mutation	SNP	T	T	C	rs445909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	10	0	1	0	T|0.596;C|0.404	0.404	strong	ZAR1L,NS,meningioma,0,1	ZAR1L	17	1	NM_001136571	exon1	c.A409G	p.T137A	GGCCGGTGGCGGG	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909441	123909441	+	Missense_Mutation	SNP	T	T	C	rs470208	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	630	107	843	18	0.169841	0.0213523	T|0.874;C|0.126	0.126	strong	OR10G7,right_upper_lobe,carcinoma,+1,1	OR10G7	103	1	NM_001004463	exon1	c.A268G	p.T90A	AGATAGTCCTGCC	.	scavenged	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151859495	151859495	+	Missense_Mutation	SNP	C	C	G	rs115580901	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	93	158	0	0.528409	0	C|0.998;G|0.002	0.002	strong	.	MLL3	1564	.	NM_170606	exon43	c.G11167C	p.A3723P	TCTCAGCCTTTTC	.	PASS	Atlas-SNP
LPL	4023	hgsc.bcm.edu	37	8	19819724	19819724	+	Nonsense_Mutation	SNP	C	C	G	rs328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	45	100	0	0.6	0	C|0.914;G|0.086	0.086	strong	.	LPL	78	.	NM_000237	exon9	c.C1421G	p.S474X	AGAAGTCAGGCTG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6585838	6585838	+	Silent	SNP	G	G	A	rs11825255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	42	64	0	0.512195	0	G|0.816;A|0.184	0.184	strong	.	DNHD1	198	.	NM_144666	exon32	c.G10560A	p.Q3520Q	GGAGCAGTACCAG	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34112303	34112303	+	Silent	SNP	G	G	A	rs10798976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	52	116	0	0.390977	0	G|0.905;A|0.095	0.095	strong	.	CSMD2	946	.	NM_052896	exon29	c.C4599T	p.L1533L	GAAGGCGAGGAAG	.	PASS	Atlas-SNP
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	40	103	0	0.444444	0	A|0.624;G|0.376	0.376	strong	NSA2,NS,carcinoma,+1,1	NSA2	18	1	NM_014886	exon5	c.A693G	p.T231T	TGTGACACAAGGA	.	PASS	Atlas-SNP
TMEM200B	399474	hgsc.bcm.edu	37	1	29447765	29447765	+	Silent	SNP	G	G	T	rs115927590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	23	72	0	0.410714	0	G|0.990;T|0.010	0.010	strong	.	TMEM200B	9	.	NM_001171868	exon2	c.C576A	p.S192S	ACGCGGGGACGGG	.	PASS	Atlas-SNP
ZNF253	56242	hgsc.bcm.edu	37	19	20003109	20003109	+	Silent	SNP	A	A	G	rs8106559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	35	39	0	1	0	A|0.602;G|0.398	0.398	strong	.	ZNF253	99	.	NM_021047	exon4	c.A1053G	p.L351L	TCACCTATCCTCA	.	PASS	Atlas-SNP
PSMA4	5685	hgsc.bcm.edu	37	15	78841220	78841220	+	Silent	SNP	T	T	C	rs8053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	128	156	0	0.992248	0	T|0.307;C|0.693	0.693	strong	.	PSMA4	17	.	NM_001102667	exon9	c.T720C	p.H240H	AAAACATGAGGAA	.	PASS	Atlas-SNP
CKAP2L	150468	hgsc.bcm.edu	37	2	113514159	113514159	+	Missense_Mutation	SNP	T	T	A	rs17042341	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	161	0	0.482517	0	T|0.919;A|0.081	0.081	strong	.	CKAP2L	54	.	NM_152515	exon4	c.A789T	p.R263S	TGCTCCTCTAGAG	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113479820	113479820	+	Missense_Mutation	SNP	A	A	G	rs368865	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	212	203	0	0.995305	0	A|0.187;G|0.813	0.813	strong	ATP11A,NS,carcinoma,0,1	ATP11A	225	1	NM_032189	exon11	c.A949G	p.M317V	AAATACATGTGGC	.	PASS	Atlas-SNP
NOS3	4846	hgsc.bcm.edu	37	7	150710392	150710392	+	Silent	SNP	G	G	A	rs3730011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	41	68	0	0.546667	0	G|0.995;A|0.005	0.005	strong	NOS3,NS,carcinoma,+2,1	NOS3	131	1	NM_000603	exon25	c.G3180A	p.E1060E	CGACGAGGTGCAG	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201046164	201046164	+	Missense_Mutation	SNP	C	C	T	rs114191482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	187	311	0	0.508152	0	C|0.997;T|0.003	0.003	strong	.	CACNA1S	249	.	NM_000069	exon12	c.G1711A	p.V571I	AGATGACGATGAA	.	PASS	Atlas-SNP
OR11H1	81061	hgsc.bcm.edu	37	22	16449539	16449539	+	Missense_Mutation	SNP	A	A	G	rs61969156		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	700	74	729	3	0.105714	0.00411523	.	.	weak	OR11H1,NS,carcinoma,0,5	OR11H1	44	5	NM_001005239	exon1	c.T266C	p.V89A	GAAGAGACATACC	.	scavenged	Atlas-SNP
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736814	140736814	+	Missense_Mutation	SNP	G	G	C	rs11575951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	80	137	0	0.5	0	G|0.957;C|0.043	0.043	strong	.	PCDHGA4	150	.	NM_018917	exon1	c.G2047C	p.D683H	TCAGCAGACCCAG	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3606947	3606947	+	Missense_Mutation	SNP	G	G	T	rs116349864	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	46	108	0	0.511111	0	G|0.985;T|0.015	0.015	strong	.	NLRC3	103	.	NM_178844	exon8	c.C2148A	p.D716E	CAAAGCGTCTGCC	.	PASS	Atlas-SNP
FAM83B	222584	hgsc.bcm.edu	37	6	54805688	54805688	+	Missense_Mutation	SNP	A	A	C	rs239798	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	61	0	1	0	A|0.690;C|0.310	0.310	strong	FAM83B,NS,carcinoma,0,1	FAM83B	186	1	NM_001010872	exon5	c.A1919C	p.K640T	TATATAAAACCTT	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183951135	183951135	+	Silent	SNP	C	C	T	rs729377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	5	4	0	0.625	0	C|0.708;T|0.292	0.292	strong	.	VWA5B2	47	.	NM_138345	exon3	c.C480T	p.A160A	GCTGGCCCCGCCA	.	PASS	Atlas-SNP
CHST12	55501	hgsc.bcm.edu	37	7	2472599	2472599	+	Missense_Mutation	SNP	C	C	A	rs17132395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	8	10	0	0.8	0	C|0.976;A|0.024	0.024	strong	.	CHST12	39	.	NM_018641	exon2	c.C325A	p.R109S	TCCCCGCGCGACG	.	PASS	Atlas-SNP
PTGFRN	5738	hgsc.bcm.edu	37	1	117452869	117452869	+	Missense_Mutation	SNP	C	C	G	rs77292583	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	4	16	0	0.5	0	C|0.978;G|0.022	0.022	strong	PTGFRN,NS,carcinoma,0,1	PTGFRN	91	1	NM_020440	exon1	c.C44G	p.S15W	TCCTGTCGTTGGG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511755	169511755	+	Missense_Mutation	SNP	T	T	C	rs4524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	147	231	1	0.506897	0.004329	T|0.760;C|0.240	0.240	strong	.	F5	301	.	NM_000130	exon13	c.A2573G	p.K858R	TGACTTTTGAATT	.	PASS	Atlas-SNP
TMEM156	80008	hgsc.bcm.edu	37	4	39033851	39033851	+	Missense_Mutation	SNP	G	G	A	rs61732938	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	79	0	0.493333	0	G|0.998;A|0.002	0.002	strong	.	TMEM156	31	.	NM_024943	exon1	c.C83T	p.P28L	CCTTTCGGTGTCT	.	PASS	Atlas-SNP
OR4S2	219431	hgsc.bcm.edu	37	11	55419147	55419147	+	Silent	SNP	C	C	T	rs74538149	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	72	111	1	0.986301	0.00900901	C|0.988;T|0.012	0.012	strong	.	OR4S2	89	.	NM_001004059	exon1	c.C768T	p.Y256Y	TATGTACATGCGC	.	PASS	Atlas-SNP
ST3GAL4	6484	hgsc.bcm.edu	37	11	126277216	126277216	+	Silent	SNP	C	C	T	rs2230278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	68	128	0	0.581197	0	C|0.657;T|0.343	0.343	strong	.	ST3GAL4	25	.	NM_001254757	exon5	c.C252T	p.Y84Y	TGCTTACGAGCTG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16682062	16682062	+	Silent	SNP	C	C	T	rs16868979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	64	111	0	0.503937	0	C|0.960;T|0.040	0.040	strong	MYO10,NS,carcinoma,0,1	MYO10	198	1	NM_012334	exon31	c.G4107A	p.P1369P	CTCCTCCGGCGTG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149503843	149503843	+	Missense_Mutation	SNP	T	T	G	rs10260959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	200	209	0	1	0	T|0.674;G|0.326	0.326	strong	.	.	.	.	NM_198455	exon59	c.T8671G	p.L2891V	AACATGTTGTTCC	.	PASS	Atlas-SNP
CIZ1	25792	hgsc.bcm.edu	37	9	130948018	130948018	+	Silent	SNP	G	G	A	rs45545033	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	43	49	0	0.68254	0	G|0.962;A|0.038	0.038	strong	.	CIZ1	75	.	NM_001257975	exon5	c.C486T	p.L162L	GGCTGCGAGGCCT	.	PASS	Atlas-SNP
ZNF841	284371	hgsc.bcm.edu	37	19	52570714	52570714	+	Missense_Mutation	SNP	C	C	G	rs16983412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	95	195	0	0.482233	0	C|0.844;G|0.156	0.156	strong	.	ZNF841	183	.	NM_001136499	exon7	c.G421C	p.V141L	AGTCAACTTCCTG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109577465	109577465	+	Silent	SNP	C	C	T	rs11065655	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	57	91	0	0.6	0	C|0.936;T|0.064	0.064	strong	.	ACACB	330	.	NM_001093	exon1	c.C255T	p.A85A	AGATGCCGGTCGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149518148	149518148	+	Missense_Mutation	SNP	A	A	G	rs10233245	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	26	44	0	0.604651	0	A|0.578;G|0.422	0.422	strong	.	.	.	.	NM_198455	exon87	c.A12491G	p.H4164R	GGAGCCACTGGTC	.	PASS	Atlas-SNP
ALDH8A1	64577	hgsc.bcm.edu	37	6	135271178	135271178	+	Missense_Mutation	SNP	T	T	C	rs56954234	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	43	87	0	0.390909	0	T|0.985;C|0.015	0.015	strong	.	ALDH8A1	68	.	NM_022568	exon1	c.A14G	p.N5S	AGTGCGTTTGTTC	.	PASS	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49446040	49446040	+	Missense_Mutation	SNP	C	C	T	rs1064210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	65	114	0	0.488722	0	C|0.937;T|0.063	0.063	strong	.	MLL2	1173	.	NM_003482	exon10	c.G1426A	p.A476T	GGGATGCGGGCAA	.	PASS	Atlas-SNP
LIPE	3991	hgsc.bcm.edu	37	19	42906914	42906914	+	Missense_Mutation	SNP	G	G	T	rs7246232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	115	0	0.467213	0	G|0.970;T|0.030	0.030	strong	.	LIPE	83	.	NM_005357	exon9	c.C2812A	p.R938S	CGGCACGGACGCC	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127220392	127220392	+	Missense_Mutation	SNP	G	G	C	rs58155983	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	51	132	0	0.375	0	G|0.898;C|0.102	0.102	strong	.	GPR144	33	.	NM_001161808	exon9	c.G1562C	p.G521A	AGCCAGGCCTCTC	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38933869	38933869	+	Missense_Mutation	SNP	C	C	T	rs36058104	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	106	257	0	0.40613	0	C|0.979;T|0.021	0.021	strong	.	FAM114A1	42	.	NM_138389	exon12	c.C1337T	p.S446L	ACATGTCGTCCAT	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124857708	124857708	+	Missense_Mutation	SNP	G	G	A	rs4936966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	35	125	0	0.346535	0	G|0.721;A|0.279	0.279	strong	CCDC15_ENST00000344762,colon,carcinoma,0,7	CCDC15	134	7	NM_025004	exon8	c.G1586A	p.G529D	ATCAAGGCCAGGA	.	PASS	Atlas-SNP
OR5V1	81696	hgsc.bcm.edu	37	6	29323276	29323276	+	Missense_Mutation	SNP	C	C	T	rs61742983	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	21	46	0	0.477273	0	C|0.940;T|0.060	0.060	strong	.	OR5V1	63	.	NM_030876	exon1	c.G697A	p.G233R	GTCTTCCCTCTGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179614059	179614059	+	Silent	SNP	T	T	C	rs16866490	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	74	0	0.5	0	T|0.991;C|0.009	0.009	strong	.	TTN	18412	.	NM_133379	exon46	c.A13068G	p.Q4356Q	CTGACATTGTATG	.	PASS	Atlas-SNP
SAP130	79595	hgsc.bcm.edu	37	2	128767929	128767929	+	Silent	SNP	A	A	G	rs35775122	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	116	1	1	0.00862069	A|0.972;G|0.028	0.028	strong	.	SAP130	169	.	NM_001145928	exon7	c.T861C	p.P287P	CACAGCAGGAGGG	.	PASS	Atlas-SNP
WARS2	10352	hgsc.bcm.edu	37	1	119575818	119575818	+	Missense_Mutation	SNP	C	C	G	rs3790549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	50	119	0	0.409836	0	C|0.914;G|0.086	0.086	strong	.	WARS2	69	.	NM_015836	exon6	c.G799C	p.A267P	GGCCAGCCGGGTC	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11532787	11532787	+	Silent	SNP	C	C	T	rs73290804	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	78	132	0	0.490566	0	C|0.978;T|0.022	0.022	strong	.	DNAH9	695	.	NM_001372	exon7	c.C1404T	p.S468S	GTTCAGCGGCGTC	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188392	140188392	+	Silent	SNP	C	C	G	rs7707144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	29	83	0	0.315217	0	C|0.937;G|0.063	0.063	strong	PCDHA4_ENST00000530339,NS,carcinoma,0,2	PCDHA4	419	2	NM_031500	exon1	c.C1620G	p.A540A	CGATGCCGGCGTG	.	PASS	Atlas-SNP
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	31	33	0	0.516667	0	G|0.619;A|0.381	0.381	strong	PTK7,NS,carcinoma,+2,1	PTK7	101	1	NM_001270398	exon12	c.G1875A	p.G625G	CCAGGGGGACCCC	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108443511	108443511	+	Silent	SNP	C	C	G	rs7576738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	340	337	313	0	0.991176	0	C|0.408;G|0.592	0.592	strong	.	RGPD4	112	.	NM_182588	exon1	c.C42G	p.S14S	CGCCTCCGTGCAG	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6302519	6302519	+	Missense_Mutation	SNP	G	G	A	rs1801212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	480	476	458	0	0.991667	0	G|0.170;A|0.830	0.830	strong	.	WFS1	71	.	NM_001145853	exon8	c.G997A	p.V333I	TTCATCGTCAGCA	.	PASS	Atlas-SNP
ZNF276	92822	hgsc.bcm.edu	37	16	89790020	89790020	+	Silent	SNP	C	C	T	rs34629175	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	66	107	0	0.536585	0	C|0.976;T|0.024	0.024	strong	.	ZNF276	70	.	NM_001113525	exon4	c.C909T	p.P303P	CCTGCCCAGCACG	.	PASS	Atlas-SNP
PES1	23481	hgsc.bcm.edu	37	22	30977353	30977353	+	Missense_Mutation	SNP	T	T	A	rs42942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	32	43	0	0.426667	0	T|0.948;A|0.052	0.052	strong	.	PES1	55	.	NM_014303	exon8	c.A790T	p.T264S	CGTAGGTGCCCTC	.	PASS	Atlas-SNP
ST7L	54879	hgsc.bcm.edu	37	1	113153536	113153536	+	Silent	SNP	T	T	C	rs35364712	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	134	254	0	0.5	0	T|0.984;C|0.016	0.016	strong	.	ST7L	31	.	NM_138729	exon3	c.A378G	p.T126T	GCTCTCTGTTCCT	.	PASS	Atlas-SNP
ALS2	57679	hgsc.bcm.edu	37	2	202593280	202593280	+	Silent	SNP	G	G	A	rs3219161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	430	208	386	0	0.483721	0	G|0.900;A|0.100	0.100	strong	.	ALS2	172	.	NM_020919	exon15	c.C2796T	p.S932S	ATTCACGGAAAAC	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179347832	179347832	+	Silent	SNP	T	T	C	rs10798674	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	94	0	0.5	0	T|0.546;C|0.454	0.454	strong	.	AXDND1	142	.	NM_144696	exon5	c.T435C	p.V145V	GGCAGTTTGTCCC	.	PASS	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137150665	137150665	+	Silent	SNP	T	T	C	rs35245703	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	28	92	0	0.368421	0	T|0.910;C|0.090	0.090	strong	.	DGKI	335	.	NM_004717	exon27	c.A2625G	p.E875E	GGCTTGTTCCACC	.	PASS	Atlas-SNP
HAO1	54363	hgsc.bcm.edu	37	20	7920986	7920986	+	Silent	SNP	C	C	T	rs33931524	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	53	100	0	0.540816	0	C|0.966;T|0.034	0.034	strong	.	HAO1	71	.	NM_017545	exon1	c.G84A	p.R28R	CCCAGACCTGTAA	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765405	27765405	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	7	45	0	0.125	0	.	.	none	.	DCAF8L2	79	.	NM_001136533	exon1	c.G393A	p.E131E	AGAGGAGGAGGAG	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	88	153	0	0.556962	0	G|0.861;A|0.139	0.139	strong	MDS1,NS,carcinoma,0,1	MECOM	216	1	NM_004991	exon2	c.C358T	p.P120S	AACTGGGGTCTTT	.	PASS	Atlas-SNP
GPI	2821	hgsc.bcm.edu	37	19	34872382	34872382	+	Silent	SNP	G	G	A	rs1864139	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	80	114	1	0.592593	0.00877193	G|0.897;A|0.103	0.103	strong	GPI,NS,carcinoma,+1,1	GPI	63	1	NM_001184722	exon9	c.G795A	p.K265K	AGTGAAGGAGTTT	.	scavenged	Atlas-SNP
DCAF16	54876	hgsc.bcm.edu	37	4	17805379	17805379	+	Missense_Mutation	SNP	G	G	A	rs7690457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	110	211	0	0.470085	0	G|0.893;A|0.107	0.107	strong	.	DCAF16	19	.	NM_017741	exon3	c.C386T	p.T129I	GGACTTGTAAGAG	.	PASS	Atlas-SNP
EFCAB3	146779	hgsc.bcm.edu	37	17	60451185	60451185	+	Missense_Mutation	SNP	G	G	C	rs6504103	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	71	145	0	0.489655	0	G|0.983;C|0.017	0.017	strong	.	EFCAB3	71	.	NM_001144933	exon2	c.G45C	p.K15N	TGGAAAGATTAAT	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169621536	169621536	+	Silent	SNP	A	A	G	rs1132742	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	106	0	0.463636	0	G|0.242;N|0.001	0.242	strong	THBS2,NS,carcinoma,0,1	THBS2	230	1	NM_003247	exon21	c.T3360C	p.T1120T	GTAGCCAGTCTTG	.	PASS	Atlas-SNP
CYP51A1	1595	hgsc.bcm.edu	37	7	91743072	91743072	+	Silent	SNP	A	A	G	rs149576331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	74	134	0	0.48366	0	A|0.999;G|0.001	0.001	strong	.	CYP51A1	30	.	NM_000786	exon10	c.T1437C	p.D479D	AATGAGATCAAAT	.	PASS	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	33	68	0	0.589286	0	A|0.728;G|0.272	0.272	strong	.	FOXK1	64	.	NM_001037165	exon9	c.A2142G	p.V714V	TGCTGTAACCACA	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128381861	128381861	+	Missense_Mutation	SNP	G	G	A	rs61743523	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	40	69	0	0.540541	0	G|0.993;A|0.007	0.007	strong	.	MYO7B	359	.	NM_001080527	exon29	c.G3935A	p.R1312Q	TCCTCCGAGGAGT	.	PASS	Atlas-SNP
NMS	129521	hgsc.bcm.edu	37	2	101096960	101096960	+	Silent	SNP	C	C	T	rs1519654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	98	242	0	0.478049	0	C|0.321;T|0.679	0.679	strong	NMS,colon,carcinoma,0,3	NMS	26	3	NM_001011717	exon7	c.C339T	p.G113G	GCAGGGCTCGGGG	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38156677	38156677	+	Missense_Mutation	SNP	C	C	T	rs1801687	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	92	174	0	0.474227	0	C|0.904;T|0.096	0.096	strong	.	RPGR	175	.	NM_001034853	exon11	c.G1274A	p.R425K	GTTCTCCTCATTG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548554	32548554	+	Silent	SNP	G	G	C	rs3830126	bycluster;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	483	36	233	0	0.0745342	0	.	.	alt	.	HLA-DRB1	41	.	NM_002124	exon4	c.C732G	p.A244A	CAGCCCGGCCCCA	.	PASS	Atlas-SNP
STK40	83931	hgsc.bcm.edu	37	1	36820015	36820015	+	Silent	SNP	T	T	C	rs115120808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	81	184	0	0.468208	0	T|0.990;C|0.010	0.010	strong	.	STK40	53	.	NM_032017	exon7	c.A573G	p.K191K	GATATTTTTCTGT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612518	17612518	+	Missense_Mutation	SNP	A	A	G	rs61733696	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	46	71	0	0.547619	0	A|0.971;G|0.029	0.029	strong	.	MTUS1	144	.	NM_001001924	exon2	c.T799C	p.S267P	CTGAAGAACATGC	.	PASS	Atlas-SNP
SSBP4	170463	hgsc.bcm.edu	37	19	18542201	18542201	+	Silent	SNP	C	C	T	rs113198578	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	425	236	367	0	0.555294	0	C|0.976;T|0.024	0.024	strong	SSBP4,NS,neuroblastoma,0,1	SSBP4	19	1	NM_032627	exon6	c.C408T	p.N136N	CCCCAACGCCCCC	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862780	5862780	+	Silent	SNP	T	T	C	rs4362172	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	79	173	0	0.441341	0	T|0.607;C|0.393	0.393	strong	.	OR52E6	70	.	NM_001005167	exon1	c.A348G	p.V116V	CACCAATACGATG	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29161202	29161202	+	Missense_Mutation	SNP	A	A	T	rs9910051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	36	111	0	0.391304	0	A|0.786;N|0.000	.	strong	.	ATAD5	150	.	NM_024857	exon2	c.A103T	p.T35S	ACATCTACCTGCA	.	PASS	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	37	X	102979184	102979184	+	Missense_Mutation	SNP	G	G	A	rs16984014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	98	144	0	0.653333	0	0|0.009;A|0.067	0.067	strong	.	GLRA4	86	.	NM_001024452	exon4	c.C316T	p.R106C	ACAGGCGTGGGTC	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150046	11150046	+	Missense_Mutation	SNP	G	G	T	rs12226920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	48	113	0	0.432432	0	G|0.671;T|0.329	0.329	strong	.	TAS2R20	17	.	NM_176889	exon1	c.C429A	p.H143Q	CACAAGGTGACAA	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	157	349	0	0.484568	0	T|0.917;G|0.083	0.083	strong	.	SALL4	168	.	NM_020436	exon2	c.A2392C	p.I798L	ACTTGATGCTTTC	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721532	49721532	+	Missense_Mutation	SNP	G	G	A	rs3197999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	474	204	466	0	0.43038	0	G|0.749;A|0.251	0.251	strong	MST1,NS,carcinoma,0,1	MST1	84	1	NM_020998	exon18	c.C2107T	p.R703C	GCCAGCGGGACCT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73716810	73716810	+	Missense_Mutation	SNP	G	G	A	rs3820700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	32	74	0	0.450704	0	G|0.855;A|0.145	0.145	strong	.	ALMS1	384	.	NM_015120	exon10	c.G7721A	p.S2574N	TATGTAGTCACAT	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2930339	2930339	+	Silent	SNP	G	G	A	rs4790115	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	153	275	0	0.5	0	G|0.567;A|0.433	0.433	strong	RAP1GAP2_ENST00000254695,colon,carcinoma,0,2	RAP1GAP2	90	2	NM_015085	exon22	c.G2082A	p.P694P	CACCCCGATCATC	.	PASS	Atlas-SNP
LAMB1	3912	hgsc.bcm.edu	37	7	107591720	107591720	+	Silent	SNP	G	G	A	rs25660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	150	152	0	1	0	G|0.957;A|0.043	0.043	strong	.	LAMB1	185	.	NM_002291	exon24	c.C3342T	p.C1114C	CTCGCTGCAGGTG	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	55	76	0	0.491071	0	G|0.893;C|0.107	0.107	strong	.	MYO18A	217	.	NM_078471	exon12	c.C2199G	p.P733P	CTCCTCGGGGCCC	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	27	73	0	0.402985	0	T|0.652;C|0.348	0.348	strong	.	.	.	.	NM_019600	exon6	c.A1827G	p.S609S	GGAAGTTGATAAA	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126133252	126133252	+	Silent	SNP	C	C	T	rs55965026	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	33	59	0	0.647059	0	C|0.962;T|0.038	0.038	strong	.	CRB2	86	.	NM_173689	exon7	c.C1920T	p.C640C	CACGTGCGCTGAT	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905661	15905661	+	Missense_Mutation	SNP	C	C	A	rs67455341	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	124	179	1	0.571429	0.00558659	C|0.733;A|0.267	0.267	strong	.	OR10H5	49	.	NM_001004466	exon1	c.C803A	p.S268Y	CCCAGTCTCCGGA	.	PASS	Atlas-SNP
PSG4	5672	hgsc.bcm.edu	37	19	43709647	43709647	+	Silent	SNP	G	G	A	rs12985206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	21	23	0	0.724138	0	G|0.536;A|0.464	0.464	strong	.	PSG4	129	.	NM_002780	exon1	c.C42T	p.P14P	CTTCCAGGTGATG	.	PASS	Atlas-SNP
SYNE4	163183	hgsc.bcm.edu	37	19	36497747	36497747	+	Missense_Mutation	SNP	C	C	G	rs77925409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	36	81	0	0.423529	0	C|0.979;G|0.021	0.021	strong	.	.	.	.	NM_001039876	exon4	c.G523C	p.A175P	CCAGGGCTGCCCA	.	PASS	Atlas-SNP
PCYOX1	51449	hgsc.bcm.edu	37	2	70503954	70503954	+	Silent	SNP	G	G	T	rs36012096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	89	197	0	0.447236	0	G|0.926;T|0.074	0.074	strong	.	PCYOX1	34	.	NM_016297	exon6	c.G948T	p.P316P	CACTCCGTTGAAT	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4308360	4308360	+	Missense_Mutation	SNP	C	C	T	rs11981816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	72	153	0	0.486486	0	C|0.967;T|0.033	0.033	strong	.	SDK1	361	.	NM_001079653	exon20	c.C2018T	p.P673L	TGGCTCCCCGTGG	.	PASS	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124663987	124663987	+	Missense_Mutation	SNP	C	C	G	rs16898691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	41	60	0	0.554054	0	C|0.903;G|0.097	0.097	strong	.	KLHL38	81	.	NM_001081675	exon1	c.G1180C	p.G394R	CCTGCCCTTCTCC	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110408347	110408347	+	Silent	SNP	C	C	T	rs6469258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	25	61	0	0.510204	0	C|0.975;T|0.025	0.025	strong	PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	NM_177531	exon11	c.C903T	p.P301P	TTTCCCCGTCAGA	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81219187	81219187	+	Missense_Mutation	SNP	C	C	T	rs13339342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	30	71	0	0.434783	0	C|0.865;T|0.135	0.135	strong	PKD1L2_ENST00000525539,NS,carcinoma,-1,2	PKD1L2	361	2	NM_001076780	exon11	c.G1907A	p.R636H	GCCAGGCGCAGGG	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62226423	62226423	+	Missense_Mutation	SNP	T	T	G	rs112236709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	59	154	0	0.430657	0	T|0.980;G|0.020	0.020	strong	.	VPS13C	506	.	NM_020821	exon49	c.A5863C	p.N1955H	CCTGGTTGATATC	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130287096	130287096	+	Silent	SNP	C	C	T	rs61730501	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	126	243	0	0.510121	0	C|0.993;T|0.007	0.007	strong	.	COL6A6	497	.	NM_001102608	exon5	c.C2049T	p.S683S	CCAAAGCGACATT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179401015	179401015	+	Missense_Mutation	SNP	G	G	A	rs72629779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	85	178	0	0.47486	0	G|0.990;A|0.010	0.010	strong	.	TTN	18412	.	NM_001267550	exon357	c.C100459T	p.P33487S	ATTTGGGAGTGAT	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536047	1536047	+	Missense_Mutation	SNP	T	T	C	rs59554810	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	23	56	0	0.5	0	T|0.942;C|0.058	0.058	strong	.	PTX4	46	.	NM_001013658	exon3	c.A1315G	p.I439V	TCCCGATGGCAAG	.	PASS	Atlas-SNP
SLC27A3	11000	hgsc.bcm.edu	37	1	153750650	153750650	+	Missense_Mutation	SNP	G	G	A	rs35102232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	16	37	0	0.444444	0	G|0.979;A|0.021	0.021	strong	.	SLC27A3	42	.	NM_024330	exon5	c.G1316A	p.R439H	CAGAACGTGGCCA	.	PASS	Atlas-SNP
SMTNL2	342527	hgsc.bcm.edu	37	17	4497160	4497160	+	Silent	SNP	T	T	C	rs8080130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	150	151	0	0.993378	0	T|0.350;C|0.650	0.650	strong	.	SMTNL2	57	.	NM_001114974	exon4	c.T774C	p.Y258Y	TGGCTATGGGGCA	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235972435	235972435	+	Silent	SNP	T	T	C	rs3820553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	110	0	0.5	0	T|0.616;C|0.384	0.384	strong	.	LYST	370	.	NM_000081	exon5	c.A1683G	p.L561L	CTGCTGTAGTAAG	.	PASS	Atlas-SNP
LYSMD4	145748	hgsc.bcm.edu	37	15	100269613	100269613	+	Silent	SNP	C	C	T	rs11852387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	60	0	0.493333	0	C|0.903;T|0.097	0.097	strong	.	LYSMD4	21	.	NM_152449	exon6	c.G609A	p.P203P	AGGTGCCGGGAGC	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209788703	209788703	+	Silent	SNP	T	T	C	rs1049607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	24	79	0	0.436364	0	T|0.560;C|0.440	0.440	strong	.	LAMB3	136	.	NM_000228	exon23	c.A3432G	p.S1144S	GTCCGCTGAGCGC	.	PASS	Atlas-SNP
TMEM247	388946	hgsc.bcm.edu	37	2	46707886	46707886	+	Missense_Mutation	SNP	G	G	A	rs12612916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	56	153	0	0.444444	0	G|0.798;A|0.202	0.202	strong	.	.	.	.	NM_001145051	exon2	c.G460A	p.E154K	CAGCAAGAGGCGG	.	PASS	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	37	2	210557380	210557380	+	Silent	SNP	C	C	T	rs6720659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	50	86	0	0.581395	0	C|0.852;T|0.148	0.148	strong	.	MAP2	372	.	NM_002374	exon7	c.C486T	p.H162H	GTTCCACGATCAA	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	15	35	0	0.348837	0	C|0.859;T|0.141	0.141	strong	GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	NM_001145118	exon1	c.G60A	p.R20R	ACCTAGCCGGAAG	.	PASS	Atlas-SNP
ADPRH	141	hgsc.bcm.edu	37	3	119305169	119305169	+	Silent	SNP	G	G	A	rs20569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	69	141	0	0.514925	0	G|0.802;A|0.198	0.198	strong	.	ADPRH	33	.	NM_001125	exon4	c.G336A	p.P112P	GAAGCCGGGCAAG	.	PASS	Atlas-SNP
POU6F2	11281	hgsc.bcm.edu	37	7	39379325	39379325	+	Missense_Mutation	SNP	C	C	T	rs2074936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	8	17	0	0.444444	0	C|0.764;T|0.236	0.236	strong	POU6F2,NS,NS,0,1	POU6F2	117	1	NM_007252	exon6	c.C596T	p.P199L	CTCCCCCGTCAAC	.	PASS	Atlas-SNP
ITGB5	3693	hgsc.bcm.edu	37	3	124492734	124492734	+	Silent	SNP	T	T	C	rs16835978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	120	0	0.5	0	T|0.943;C|0.057	0.057	strong	ITGB5,mouth,carcinoma,-2,1	ITGB5	66	1	NM_002213	exon11	c.A1719G	p.E573E	CTTGCATTCCCCG	.	PASS	Atlas-SNP
VN1R2	317701	hgsc.bcm.edu	37	19	53761740	53761740	+	Missense_Mutation	SNP	T	T	C	rs2965249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	33	108	0	0.347368	0	T|0.678;C|0.322	0.322	strong	.	VN1R2	71	.	NM_173856	exon1	c.T112C	p.C38R	TATCAGTGCAGCC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	108	0	1	0	A|0.428;G|0.572	0.572	strong	CPAMD8,colon,carcinoma,-2,1	CPAMD8	192	1	NM_015692	exon13	c.T1437C	p.P479P	CCCCACAGGCTTC	.	PASS	Atlas-SNP
NUBP2	10101	hgsc.bcm.edu	37	16	1838050	1838050	+	Missense_Mutation	SNP	A	A	G	rs57822546	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	78	0	0.45	0	A|0.895;G|0.105	0.105	strong	.	NUBP2	25	.	NM_012225	exon5	c.A598G	p.T200A	CACTGCACGGTGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677502	100677502	+	Silent	SNP	G	G	A	rs10267904	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	55	135	0	0.227273	0	G|0.969;A|0.031	0.031	strong	MUC17,right_upper_lobe,carcinoma,+2,1	MUC17	804	1	NM_001040105	exon3	c.G2805A	p.P935P	CACGCCGGTAGTC	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	621242	621242	+	Silent	SNP	C	C	T	rs112269777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	88	173	0	0.431373	0	C|0.953;T|0.047	0.047	strong	.	CDHR5	77	.	NM_031264	exon7	c.G627A	p.P209P	CTCCCCCGGAGTG	.	PASS	Atlas-SNP
NXPH4	11247	hgsc.bcm.edu	37	12	57619362	57619362	+	Silent	SNP	G	G	A	rs10783816	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	44	84	0	0.505747	0	G|0.659;A|0.341	0.341	strong	NXPH4,NS,carcinoma,0,3	NXPH4	40	3	NM_007224	exon2	c.G759A	p.P253P	CGACCCGTCGCAG	.	PASS	Atlas-SNP
LCMT2	9836	hgsc.bcm.edu	37	15	43621947	43621947	+	Silent	SNP	A	A	G	rs3742969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	13	41	0	0.393939	0	A|0.668;G|0.332	0.332	strong	.	LCMT2	48	.	NM_014793	exon1	c.T741C	p.R247R	AGGAAAACGCTCC	.	PASS	Atlas-SNP
ADRA2A	150	hgsc.bcm.edu	37	10	112838135	112838135	+	Silent	SNP	C	C	G	rs142434876	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	97	145	0	0.563953	0	C|0.998;G|0.002	0.002	strong	.	ADRA2A	38	.	NM_000681	exon1	c.C381G	p.L127L	GGCGCTCGACGTG	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239040218	239040218	+	Missense_Mutation	SNP	G	G	A	rs73102309	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	7	6	0	0.5	0	G|0.865;A|0.135	0.135	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2863A	p.A955T	CACGCCGCCGTCC	.	PASS	Atlas-SNP
MAPKAP1	79109	hgsc.bcm.edu	37	9	128206855	128206855	+	Silent	SNP	C	C	T	rs35549826	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	67	112	1	0.403614	0.00892857	C|0.994;T|0.006	0.006	strong	MAPKAP1_ENST00000265960,NS,carcinoma,-1,4	MAPKAP1	68	4	NM_001006617	exon11	c.G1368A	p.T456T	TAGATACGTGAGT	.	scavenged	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41384702	41384702	+	Missense_Mutation	SNP	T	T	C	rs117539170	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	118	347	0	0.398649	0	T|0.870;C|0.130	0.130	strong	.	CYP2A7	71	.	NM_000764	exon5	c.A794G	p.Q265R	AAGTCCTGTGGGG	.	PASS	Atlas-SNP
HKR1	284459	hgsc.bcm.edu	37	19	37854580	37854580	+	Missense_Mutation	SNP	C	C	T	rs3745764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	82	114	0	0.463277	0	C|0.794;T|0.206	0.206	strong	.	HKR1	74	.	NM_181786	exon6	c.C1883T	p.T628I	AGAGGACACATTC	.	PASS	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106967778	106967778	+	Missense_Mutation	SNP	T	T	C	rs3747787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	94	155	0	0.482051	0	T|0.805;C|0.195	0.195	strong	.	AIM1	161	.	NM_001624	exon2	c.T1471C	p.C491R	TTCCCATGCACTG	.	PASS	Atlas-SNP
IFNGR2	3460	hgsc.bcm.edu	37	21	34787312	34787312	+	Missense_Mutation	SNP	A	A	G	rs9808753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	122	0	1	0	A|0.793;G|0.207	0.207	strong	.	IFNGR2	30	.	NM_005534	exon2	c.A191G	p.Q64R	TCTACCAAGTGCA	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30492550	30492550	+	Silent	SNP	G	G	A	rs72551114	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	54	80	0	0.5625	0	G|0.895;A|0.105	0.105	strong	.	NOD1	79	.	NM_006092	exon6	c.C483T	p.D161D	GATGGTGTCCATG	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136577770	136577770	+	Silent	SNP	C	C	T	rs147188337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	42	59	0	0.724138	0	C|0.996;T|0.004	0.004	strong	.	SARDH	112	.	NM_007101	exon10	c.G1299A	p.P433P	CTTCTCCGGGCGC	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18881225	18881225	+	Missense_Mutation	SNP	T	T	A	rs200348726	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	35	54	0	0.59322	0	T|1.000;A|0.000	0.000	strong	.	FAM83G	51	.	NM_001039999	exon5	c.A1754T	p.D585V	TAGTCGTCATCAT	.	PASS	Atlas-SNP
PDHX	8050	hgsc.bcm.edu	37	11	34988343	34988343	+	Silent	SNP	T	T	C	rs61760973	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	90	0	1	0	T|0.897;C|0.103	0.103	strong	.	PDHX	40	.	NM_003477	exon6	c.T798C	p.P266P	AACTCCTGGACAA	.	PASS	Atlas-SNP
SLC18B1	116843	hgsc.bcm.edu	37	6	133105120	133105120	+	Missense_Mutation	SNP	C	C	T	rs6926101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	43	110	0	0.394495	0	C|0.812;T|0.188	0.188	strong	.	.	.	.	NM_052831	exon6	c.G610A	p.V204I	AAACGACGCATCC	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55523860	55523860	+	Missense_Mutation	SNP	A	A	C	rs7305779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	44	67	0	0.53012	0	A|0.677;C|0.323	0.323	strong	.	OR9K2	63	.	NM_001005243	exon1	c.A308C	p.E103A	TTATTGAACCCAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417738	105417738	+	Silent	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	107	371	0	0.403774	0	.	.	none	.	AHNAK2	719	.	NM_138420	exon7	c.C4050G	p.S1350S	GTCCACGGAGGCC	.	PASS	Atlas-SNP
C2orf83	56918	hgsc.bcm.edu	37	2	228476140	228476140	+	Nonsense_Mutation	SNP	C	C	T	rs2176186	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	337	172	298	0	0.510386	0	C|0.703;T|0.297	0.297	strong	.	C2orf83	15	.	NM_020161	exon3	c.G423A	p.W141X	ATGGCTCCAGAGC	.	PASS	Atlas-SNP
HIST1H2BH	8345	hgsc.bcm.edu	37	6	26252148	26252148	+	Silent	SNP	C	C	T	rs61746493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	91	136	0	0.532164	0	C|0.968;T|0.032	0.032	strong	.	HIST1H2BH	36	.	NM_003524	exon1	c.C270T	p.I90I	GACCATCACCTCC	.	PASS	Atlas-SNP
COX6B1	1340	hgsc.bcm.edu	37	19	36142187	36142187	+	Silent	SNP	C	C	T	rs7991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	55	0	0.460526	0	C|0.859;T|0.141	0.141	strong	COX6B1_ENST00000392201,NS,carcinoma,0,2	COX6B1	20	2	NM_001863	exon2	c.C42T	p.T14T	CAAGACCGCCCCT	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24828449	24828449	+	Missense_Mutation	SNP	C	C	T	rs61741706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	12	51	0	0.24	0	C|0.984;T|0.016	0.016	strong	.	FAM65B	134	.	NM_014722	exon19	c.G2644A	p.V882I	CAGTGACGACTTC	.	PASS	Atlas-SNP
LRRC8A	56262	hgsc.bcm.edu	37	9	131670457	131670457	+	Silent	SNP	T	T	C	rs3750320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	39	106	0	0.375	0	T|0.745;C|0.255	0.255	strong	.	LRRC8A	69	.	NM_001127244	exon3	c.T1014C	p.Y338Y	CATGTATACACTG	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153418516	153418516	+	Silent	SNP	G	G	T	rs5986964	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1088	321	464	1	0.295037	0.00215517	.	.	weak	.	OPN1LW	87	.	NM_020061	exon3	c.G513T	p.V171V	CATCGTGGGCATT	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39915677	39915677	+	Missense_Mutation	SNP	G	G	A	rs34603507	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	17	27	0	0.653846	0	G|0.970;A|0.030	0.030	strong	.	PLEKHG2	329	.	NM_022835	exon19	c.G3904A	p.A1302T	GCCCCCGCAGCCT	.	PASS	Atlas-SNP
TATDN3	128387	hgsc.bcm.edu	37	1	212969889	212969889	+	Missense_Mutation	SNP	G	G	A	rs55709122	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	52	78	0	0.525253	0	G|0.997;A|0.003	0.003	strong	.	TATDN3	23	.	NM_001146170	exon3	c.G130A	p.E44K	GTTGCCGAACATT	.	PASS	Atlas-SNP
ULK1	8408	hgsc.bcm.edu	37	12	132404101	132404101	+	Silent	SNP	C	C	T	rs143340589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	28	102	0	0.363636	0	C|0.998;T|0.002	0.002	strong	.	ULK1	92	.	NM_003565	exon25	c.C2769T	p.A923A	CCGGGCCGGCAAG	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200959305	200959305	+	Silent	SNP	G	G	A	rs2297910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	147	399	0	0.515789	0	G|0.957;A|0.043	0.043	strong	.	KIF21B	208	.	NM_017596	exon20	c.C2991T	p.T997T	GCAGTCGGTGATG	.	PASS	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45473265	45473265	+	Silent	SNP	G	G	A	rs17092470	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	16	27	0	0.432432	0	G|0.948;A|0.052	0.052	strong	.	FAM179B	115	.	NM_015091	exon4	c.G2340A	p.V780V	TACAGTGTATGCT	.	PASS	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	37	3	73453325	73453325	+	Silent	SNP	C	C	T	rs2291463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	68	134	0	0.489209	0	C|0.427;T|0.573	0.573	strong	.	PDZRN3	196	.	NM_015009	exon4	c.G1140A	p.V380V	ATCCAGCACGGGT	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50720949	50720949	+	Missense_Mutation	SNP	G	G	A	rs34773557	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	47	115	0	0.419643	0	G|0.987;A|0.013	0.013	strong	.	MYH14	261	.	NM_001077186	exon3	c.G483A	p.M161I	GGAGATGTACCGG	.	PASS	Atlas-SNP
CDS2	8760	hgsc.bcm.edu	37	20	5166418	5166418	+	Silent	SNP	G	G	A	rs3818196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	95	213	0	0.456731	0	G|0.966;A|0.034	0.034	strong	.	CDS2	27	.	NM_003818	exon9	c.G774A	p.K258K	GAAGAAGACCTGG	.	PASS	Atlas-SNP
GPR17	2840	hgsc.bcm.edu	37	2	128408747	128408747	+	Silent	SNP	C	C	A	rs34722685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	84	0	0.5	0	C|0.985;A|0.015	0.015	strong	.	GPR17	56	.	NM_005291	exon3	c.C522A	p.L174L	GCCCCTCTACGCA	.	PASS	Atlas-SNP
APLNR	187	hgsc.bcm.edu	37	11	57004344	57004344	+	Silent	SNP	G	G	T	rs948847	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	60	121	0	0.495868	0	G|0.455;T|0.545	0.545	strong	APLNR,colon,carcinoma,0,1	APLNR	62	1	NM_005161	exon1	c.C135A	p.G45G	ACCGTTGCCCGTG	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95604547	95604547	+	Silent	SNP	C	C	T	rs4762288	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	59	131	0	0.495798	0	C|0.948;T|0.052	0.052	strong	.	FGD6	127	.	NM_018351	exon2	c.G513A	p.G171G	AACAACCCCACCC	.	PASS	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122396424	122396424	+	Silent	SNP	C	C	A	rs73415652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	68	119	0	0.552846	0	C|0.963;A|0.037	0.037	strong	.	WDR66	143	.	NM_001178003	exon12	c.C1977A	p.P659P	CAACCCCGAAGGT	.	PASS	Atlas-SNP
GSTP1	2950	hgsc.bcm.edu	37	11	67353970	67353970	+	Silent	SNP	T	T	C	rs4891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	47	87	0	0.505376	0	T|0.688;C|0.312	0.312	strong	.	GSTP1	21	.	NM_000852	exon7	c.T555C	p.S185S	CCTCAGTGCCCGG	.	PASS	Atlas-SNP
CXorf30	645090	hgsc.bcm.edu	37	X	36403036	36403036	+	Missense_Mutation	SNP	A	A	G	rs6527569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	378	378	402	0	1	0	A|0.585;0|0.030	.	strong	.	CXorf30	76	.	NM_001098843	exon19	c.A1817G	p.H606R	GTCCACATAATTT	.	PASS	Atlas-SNP
ZFP36	7538	hgsc.bcm.edu	37	19	39898521	39898521	+	Missense_Mutation	SNP	C	C	T	rs2229272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	18	25	0	0.5625	0	C|0.998;T|0.002	0.002	strong	.	ZFP36	19	.	NM_003407	exon2	c.C181T	p.P61S	CGCCTGCCTGGCC	.	PASS	Atlas-SNP
ZBTB8OS	339487	hgsc.bcm.edu	37	1	33099637	33099637	+	Silent	SNP	A	A	G	rs704878	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	119	257	0	0.459459	0	A|0.831;G|0.169	0.169	strong	.	ZBTB8OS	9	.	NM_178547	exon3	c.T195C	p.F65F	TTGCTCAAATGCT	.	PASS	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190632	209190632	+	Missense_Mutation	SNP	T	T	G	rs999890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	101	0	1	0	T|0.884;G|0.116	0.116	strong	.	PIKFYVE	223	.	NM_015040	exon20	c.T3097G	p.S1033A	GTCACCTCCTCTG	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170878793	170878793	+	Silent	SNP	T	T	C	rs1042327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	143	106	0	0.986207	0	T|0.400;C|0.600	0.600	strong	.	TBP	58	.	NM_003194	exon6	c.T771C	p.N257N	TCAGAATATGGTG	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33498978	33498978	+	Silent	SNP	A	A	G	rs2163807	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	152	117	1	0.993464	0.00854701	A|0.580;G|0.420	0.420	strong	.	RHPN2	107	.	NM_033103	exon7	c.T702C	p.C234C	CCGATCACACCGG	.	PASS	Atlas-SNP
CSNK1G1	53944	hgsc.bcm.edu	37	15	64508763	64508763	+	Silent	SNP	G	G	A	rs6494466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	65	0	1	0	G|0.548;A|0.451	0.451	strong	.	CSNK1G1	56	.	NM_022048	exon5	c.C442T	p.L148L	TTACCAGCTGGAT	.	PASS	Atlas-SNP
GAN	8139	hgsc.bcm.edu	37	16	81398635	81398635	+	Silent	SNP	C	C	T	rs2608555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	35	101	0	0.402299	0	C|0.800;T|0.200	0.200	strong	.	GAN	59	.	NM_022041	exon8	c.C1293T	p.Y431Y	CTCCTACGGAAAG	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127816695	127816695	+	Silent	SNP	C	C	T	rs2228955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	57	99	0	0.537736	0	T|0.033;G|0.270;C|0.678;A|0.019	0.033	strong	BIN1_ENST00000259238,colon,carcinoma,0,2	BIN1	85	2	NM_139345	exon11	c.G894A	p.S298S	TGGAGGCGAAGGG	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170732300	170732300	+	Missense_Mutation	SNP	G	G	A	rs5400	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	75	147	0	0.503356	0	G|0.776;A|0.224	0.224	strong	.	SLC2A2	71	.	NM_000340	exon3	c.C329T	p.T110I	GATGCAGTCATTC	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	37	3	14745857	14745857	+	Missense_Mutation	SNP	G	G	A	rs17040196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	36	103	0	0.387097	0	G|0.588;A|0.412	0.412	strong	.	C3orf20	109	.	NM_032137	exon7	c.G892A	p.A298T	GAAAGGGCCACAT	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14951889	14951889	+	Silent	SNP	A	A	G	rs3752194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	35	95	0	0.384615	0	A|0.922;G|0.078	0.078	strong	.	OR7A10	33	.	NM_001005190	exon1	c.T801C	p.N267N	GTGTGAATTGTGG	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243328226	243328226	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	616	236	527	0	0.383117	0	.	.	none	.	CEP170	153	.	NM_014812	exon13	c.T3036C	p.S1012S	TCTCCCACTGGAC	.	PASS	Atlas-SNP
LRRC55	219527	hgsc.bcm.edu	37	11	56949529	56949529	+	Silent	SNP	C	C	T	rs80306837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	66	185	0	0.464789	0	C|0.952;T|0.048	0.048	strong	.	LRRC55	52	.	NM_001005210	exon1	c.C162T	p.P54P	CTGGCCCGGGCCA	.	PASS	Atlas-SNP
NCF4	4689	hgsc.bcm.edu	37	22	37273742	37273742	+	Silent	SNP	G	G	A	rs11552115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	38	109	0	0.387755	0	G|0.883;A|0.117	0.117	strong	.	NCF4	66	.	NM_000631	exon10	c.G897A	p.S299S	GCTGTCGGATGAG	.	PASS	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76867899	76867899	+	Missense_Mutation	SNP	T	T	C	rs7912300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	57	131	0	0.413043	0	T|0.574;C|0.426	0.426	strong	.	DUSP13	82	.	NM_001007271	exon2	c.A218G	p.K73R	AGGCCCTTGTGGG	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1637458	1637458	+	Silent	SNP	G	G	A	rs8065251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	14	25	0	0.4	0	G|0.782;A|0.218	0.218	strong	WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	NM_001163809	exon7	c.G5127A	p.P1709P	GGCCCCGCAGCAC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680939	100680939	+	Missense_Mutation	SNP	C	C	A	rs36120435	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	58	119	0	0.527273	0	C|0.880;A|0.120	0.120	strong	.	MUC17	804	.	NM_001040105	exon3	c.C6242A	p.A2081D	CTGAAGCCAGTTC	.	PASS	Atlas-SNP
S1PR1	1901	hgsc.bcm.edu	37	1	101704772	101704772	+	Silent	SNP	C	C	A	rs150493209	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	62	164	0	0.446043	0	C|1.000;A|0.000	0.000	strong	.	S1PR1	87	.	NM_001400	exon2	c.C232A	p.R78R	TTCCACCGACCCA	.	PASS	Atlas-SNP
NPR2	4882	hgsc.bcm.edu	37	9	35802583	35802583	+	Silent	SNP	C	C	T	rs5812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	195	238	0	0.994898	0	C|0.695;T|0.305	0.305	strong	.	NPR2	162	.	NM_003995	exon11	c.C1794T	p.Y598Y	TGAATACTGTCCT	.	PASS	Atlas-SNP
CYFIP1	23191	hgsc.bcm.edu	37	15	22939192	22939192	+	Silent	SNP	G	G	A	rs11633474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	80	169	0	0.454545	0	G|0.574;A|0.426	0.426	strong	CYFIP1,NS,carcinoma,0,1	CYFIP1	159	1	NM_014608	exon10	c.G918A	p.P306P	GGTTCCGCTATTT	.	PASS	Atlas-SNP
ZBED2	79413	hgsc.bcm.edu	37	3	111312965	111312965	+	Silent	SNP	A	A	T	rs34083626	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	304	136	265	1	0.447368	0.00377358	A|0.950;T|0.050	0.050	strong	.	ZBED2	22	.	NM_024508	exon2	c.T84A	p.I28I	CTCACTAATCTCT	.	PASS	Atlas-SNP
PPAP2B	8613	hgsc.bcm.edu	37	1	57002627	57002627	+	Silent	SNP	C	C	T	rs1136164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	113	265	1	0.434615	0.00377358	C|0.922;T|0.078	0.078	strong	.	PPAP2B	30	.	NM_003713	exon2	c.G297A	p.A99A	ACTTACCGCGAGG	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25266547	25266547	+	Missense_Mutation	SNP	C	C	A	rs113273135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	58	92	0	0.574257	0	C|0.991;A|0.009	0.009	strong	ZKSCAN2,NS,carcinoma,-1,1	ZKSCAN2	90	1	NM_001012981	exon2	c.G566T	p.R189L	GGCCGACGTTCTC	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169111345	169111345	+	Missense_Mutation	SNP	C	C	T	rs78243868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	48	100	0	0.40678	0	C|0.987;T|0.013	0.013	strong	.	DOCK2	389	.	NM_004946	exon8	c.C752T	p.T251M	AGCAAACGGTCAT	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120057002	120057002	+	Missense_Mutation	SNP	T	T	C	rs6205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	111	219	0	0.440476	0	T|0.859;C|0.141	0.141	strong	.	HSD3B1	53	.	NM_000862	exon4	c.T856C	p.F286L	TGGAGCTTTCCTT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	39068641	39068641	+	Silent	SNP	A	A	C	rs1468571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	48	82	0	0.6	0	A|0.871;C|0.128	0.128	strong	.	RYR1	708	.	NM_000540	exon98	c.A14256C	p.T4752T	GATCACAGCCCAC	.	PASS	Atlas-SNP
PSMB10	5699	hgsc.bcm.edu	37	16	67969531	67969531	+	Silent	SNP	A	A	G	rs14178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	54	143	1	0.428571	0.00699301	A|0.831;G|0.169	0.169	strong	PSMB10,colon,carcinoma,0,1	PSMB10	19	1	NM_002801	exon5	c.T453C	p.G151G	ATGCACACCGTAG	.	scavenged	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115393948	115393948	+	Missense_Mutation	SNP	C	C	T	rs11196400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	67	117	0	0.577586	0	C|0.811;T|0.189	0.189	strong	.	NRAP	208	.	NM_001261463	exon15	c.G1450A	p.D484N	ACTTGTCGATGCT	.	PASS	Atlas-SNP
ITGA4	3676	hgsc.bcm.edu	37	2	182376480	182376480	+	Missense_Mutation	SNP	T	T	A	rs35322532	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	149	192	0	1	0	T|0.987;A|0.013	0.013	strong	.	ITGA4	142	.	NM_000885	exon17	c.T1900A	p.S634T	CAGGTTTCTGCAA	.	PASS	Atlas-SNP
DIABLO	56616	hgsc.bcm.edu	37	12	122692958	122692958	+	Silent	SNP	C	C	T	rs35426428	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	168	130	1	1	0.00769231	C|0.906;T|0.094	0.094	strong	DIABLO,NS,carcinoma,-2,1	DIABLO	16	1	NM_019887	exon7	c.G690A	p.S230S	CTGCTCCGACTCA	.	PASS	Atlas-SNP
SMCO2	0	hgsc.bcm.edu	37	12	27628521	27628521	+	Silent	SNP	G	G	C	rs77197438	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	65	0	0.483871	0	G|0.993;C|0.007	0.007	strong	.	.	.	.	NM_001145010	exon5	c.G369C	p.L123L	GTGTCTGAAGGGC	.	PASS	Atlas-SNP
ZNF737	100129842	hgsc.bcm.edu	37	19	20727463	20727463	+	Missense_Mutation	SNP	T	T	C	rs10411329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	16	23	0	0.615385	0	T|0.588;C|0.412	0.412	strong	.	ZNF737	50	.	NM_001159293	exon4	c.A1546G	p.K516E	AGCCTTTGCCACA	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43243238	43243238	+	Missense_Mutation	SNP	A	A	G	rs78870781		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	176	245	0	0.99435	0	.	.	weak	.	PSG3	82	.	NM_021016	exon2	c.T68C	p.L23S	AAAAGTAATGCTA	.	PASS	Atlas-SNP
SLURP1	57152	hgsc.bcm.edu	37	8	143822612	143822612	+	Silent	SNP	G	G	A	rs62636564	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	41	74	0	0.518987	0	G|0.979;A|0.021	0.021	strong	.	SLURP1	16	.	NM_020427	exon3	c.C261T	p.A87A	GTGGGCGGCCCCG	.	PASS	Atlas-SNP
STAP2	55620	hgsc.bcm.edu	37	19	4325433	4325433	+	Silent	SNP	G	G	A	rs1138253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	58	150	0	0.479339	0	G|0.493;N|0.001	.	strong	.	STAP2	38	.	NM_001013841	exon10	c.C939T	p.P313P	TCCAATGGGGGTC	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27205021	27205021	+	Silent	SNP	G	G	A	rs542913	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	103	199	0	0.453745	0	G|0.808;A|0.192	0.192	strong	.	TEK	250	.	NM_000459	exon14	c.G2322A	p.R774R	GAAGAGGGCAAAT	.	PASS	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129830796	129830796	+	Missense_Mutation	SNP	C	C	T	rs11221912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	49	93	0	0.401639	0	C|0.776;T|0.224	0.224	strong	PRDM10,NS,carcinoma,0,1	PRDM10	120	1	NM_020228	exon2	c.G64A	p.A22T	CCTGTGCGGCATT	.	PASS	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60767303	60767303	+	Missense_Mutation	SNP	G	G	A	rs77299955	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	75	0	0.452381	0	G|0.991;A|0.009	0.009	strong	.	MRC2	126	.	NM_006039	exon25	c.G3622A	p.G1208S	TACGTGGGCTGGC	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125891269	125891269	+	Missense_Mutation	SNP	C	C	T	rs3740912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	66	128	0	0.468085	0	C|0.401;T|0.599	0.599	strong	CDON,NS,carcinoma,0,1	CDON	137	1	NM_016952	exon3	c.G223A	p.V75I	TCTTAACATGTTC	.	PASS	Atlas-SNP
KLRF1	51348	hgsc.bcm.edu	37	12	9985915	9985915	+	Missense_Mutation	SNP	G	G	T	rs2232548	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	23	62	0	0.547619	0	G|0.914;T|0.086	0.086	strong	.	KLRF1	27	.	NM_016523	exon3	c.G201T	p.L67F	AGTATTGCTAAAA	.	PASS	Atlas-SNP
CRIM1	51232	hgsc.bcm.edu	37	2	36691680	36691680	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	4	360	0	0.0123839	0	.	.	none	CRIM1,caecum,carcinoma,0,1	CRIM1	88	1	NM_016441	exon5	c.C873T	p.C291C	CAGATGCGAGTGT	.	scavenged	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587103	15587103	+	Silent	SNP	C	C	T	rs35973013	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	76	125	0	0.558824	0	C|0.981;T|0.019	0.019	strong	.	PGLYRP2	116	.	NM_052890	exon2	c.G378A	p.A126A	CAGCCCCGCCAGC	.	PASS	Atlas-SNP
ZNF678	339500	hgsc.bcm.edu	37	1	227842561	227842561	+	Missense_Mutation	SNP	A	A	G	rs116552491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	23	49	0	0.5	0	A|0.996;G|0.004	0.004	strong	.	ZNF678	137	.	NM_178549	exon4	c.A775G	p.S259G	ATTCATAGTGGAG	.	PASS	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37323569	37323569	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	3	163	0	0.0170455	0	.	.	none	GOLGA4,NS,carcinoma,-1,2	GOLGA4	173	2	NM_001172713	exon4	c.C349T	p.R117X	TTGGTACGAACAT	.	scavenged	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69988472	69988472	+	Missense_Mutation	SNP	C	C	T	rs75776403	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	391	187	374	0	0.478261	0	C|0.743;T|0.257	0.257	strong	.	CLEC18A	9	.	NM_001271197	exon4	c.C452T	p.T151M	ACTACACGCAGGT	.	PASS	Atlas-SNP
C7orf71	285941	hgsc.bcm.edu	37	7	26678910	26678910	+	Silent	SNP	C	C	T	rs111516571	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	20	38	0	0.952381	0	C|0.925;T|0.075	0.075	strong	.	C7orf71	6	.	NM_001145531	exon2	c.C147T	p.L49L	GGGCCTCGGGGAA	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117848368	117848368	+	Missense_Mutation	SNP	C	C	T	rs61729478	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	108	181	0	0.654545	0	C|0.990;T|0.010	0.010	strong	.	TNC	282	.	NM_002160	exon3	c.G1642A	p.V548M	GGCACACGCACTG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	237	230	1	1	0.00434783	A|0.549;G|0.451	0.451	strong	ARID4B_ENST00000264183,NS,carcinoma,0,1	ARID4B	142	1	NM_016374	exon16	c.T1503C	p.D501D	TTTGTCATCCAGA	.	PASS	Atlas-SNP
KRT38	8687	hgsc.bcm.edu	37	17	39595536	39595536	+	Silent	SNP	C	C	T	rs17494404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	68	110	0	0.576271	0	C|0.928;T|0.072	0.072	strong	.	KRT38	63	.	NM_006771	exon3	c.G651A	p.A217A	CAGGGTCGCATCA	.	PASS	Atlas-SNP
SLC12A2	6558	hgsc.bcm.edu	37	5	127469859	127469859	+	Silent	SNP	A	A	G	rs2228112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	76	148	0	0.575758	0	A|0.627;C|0.000;G|0.373;T|0.000	0.373	strong	.	SLC12A2	119	.	NM_001046	exon6	c.A1191G	p.E397E	CTAGGAACATTCC	.	PASS	Atlas-SNP
CES5A	221223	hgsc.bcm.edu	37	16	55907811	55907811	+	Missense_Mutation	SNP	C	C	T	rs2397965	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	60	119	0	0.545455	0	C|0.743;T|0.257	0.257	strong	.	CES5A	206	.	NM_001190158	exon3	c.G299A	p.R100Q	GTAAATCGCAGGG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82834630	82834630	+	Silent	SNP	T	T	C	rs309557	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	32	67	0	0.507937	0	T|0.507;C|0.493	0.493	strong	.	VCAN	498	.	NM_004385	exon8	c.T5808C	p.G1936G	CAGTGGTGACTTT	.	PASS	Atlas-SNP
GALNT5	11227	hgsc.bcm.edu	37	2	158140806	158140806	+	Missense_Mutation	SNP	G	G	C	rs6759356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	136	0	1	0	G|0.851;C|0.149	0.149	strong	.	GALNT5	112	.	NM_014568	exon2	c.G1467C	p.Q489H	AGAGCAGCTAGTT	.	PASS	Atlas-SNP
C17orf50	146853	hgsc.bcm.edu	37	17	34091130	34091130	+	Missense_Mutation	SNP	C	C	A	rs140052043	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	34	71	0	0.447368	0	C|0.993;A|0.007	0.007	strong	.	C17orf50	4	.	NM_145272	exon2	c.C118A	p.Q40K	GACAACCAGAGGC	.	PASS	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	166	187	0	0.988095	0	A|0.789;G|0.211	0.211	strong	PIGN,NS,carcinoma,0,1	PIGN	62	1	NM_176787	exon11	c.T939C	p.N313N	CTTCCAATTCTCC	.	PASS	Atlas-SNP
TRIM6-TRIM34	445372	hgsc.bcm.edu	37	11	5625784	5625784	+	Silent	SNP	A	A	G	rs3751005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	26	55	0	0.509804	0	A|0.949;G|0.051	0.051	strong	.	TRIM6-TRIM34	68	.	NM_001003819	exon3	c.A528G	p.L176L	GTCTCTAAAGAAG	.	PASS	Atlas-SNP
TNS3	64759	hgsc.bcm.edu	37	7	47343079	47343079	+	Missense_Mutation	SNP	A	A	G	rs61731305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	55	73	0	0.585106	0	A|0.989;G|0.011	0.011	strong	.	TNS3	140	.	NM_022748	exon22	c.T2926C	p.S976P	TACCGGAGAACTC	.	PASS	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	37	19	50097784	50097784	+	Silent	SNP	T	T	C	rs10414643	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	82	74	0	1	0	T|0.712;C|0.288	0.288	strong	PRR12_ENST00000418929,NS,carcinoma,0,1	PRR12	157	1	NM_020719	exon3	c.T273C	p.L91L	GAACCTTATCTCG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573759	140573759	+	Missense_Mutation	SNP	C	C	T	rs17844584	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	68	147	1	0.468966	0.00680272	C|0.993;T|0.007	0.007	strong	PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	NM_018930	exon1	c.C1634T	p.A545V	GAGAGGCGCTGGT	.	scavenged	Atlas-SNP
TIGD7	91151	hgsc.bcm.edu	37	16	3349300	3349300	+	Missense_Mutation	SNP	C	C	G	rs151295470	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	142	264	0	0.473333	0	C|1.000;G|0.000	0.000	weak	.	TIGD7	41	.	NM_033208	exon2	c.G1315C	p.V439L	ACCACACCCTATC	.	PASS	Atlas-SNP
WDR26	80232	hgsc.bcm.edu	37	1	224607296	224607296	+	Silent	SNP	T	T	C	rs142827296	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	77	0	0.46	0	T|0.999;C|0.001	0.001	strong	WDR26_ENST00000414423,NS,carcinoma,0,2	WDR26	104	2	NM_025160	exon5	c.A786G	p.A262A	GTCTTCTGCATGG	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	37	19	50157980	50157980	+	Silent	SNP	G	G	A	rs61741228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	53	0	0.439394	0	G|0.993;A|0.007	0.007	strong	.	SCAF1	78	.	NM_021228	exon9	c.G3471A	p.L1157L	GGGTCTGCCCCCT	.	PASS	Atlas-SNP
PINK1	65018	hgsc.bcm.edu	37	1	20975047	20975047	+	Silent	SNP	T	T	C	rs45499398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	52	81	0	0.514852	0	T|0.989;C|0.011	0.011	strong	.	PINK1	37	.	NM_032409	exon6	c.T1173C	p.D391D	GGCTGATGAGAGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678616	100678616	+	Missense_Mutation	SNP	G	G	A	rs113959201	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	19	111	0	0.141791	0	G|0.941;A|0.059	0.059	strong	.	MUC17	804	.	NM_001040105	exon3	c.G3919A	p.G1307S	ACTAAAGGTCCTG	.	PASS	Atlas-SNP
FAM101A	144347	hgsc.bcm.edu	37	12	124798797	124798797	+	Missense_Mutation	SNP	C	C	T	rs116090335	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	80	114	0	0.555556	0	C|0.998;T|0.002	0.002	strong	.	FAM101A	10	.	NM_181709	exon3	c.C134T	p.A45V	TCTATGCGCCCGT	.	PASS	Atlas-SNP
SLC12A9	56996	hgsc.bcm.edu	37	7	100458795	100458795	+	Silent	SNP	T	T	C	rs314378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	152	0	1	0	T|0.465;C|0.535	0.535	strong	.	SLC12A9	81	.	NM_001267812	exon10	c.T1254C	p.A418A	ACTGGCTGCTGTG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238243369	238243369	+	Silent	SNP	G	G	A	rs10201909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	72	128	1	0.483221	0.0078125	G|0.933;A|0.067	0.067	strong	COL6A3,colon,carcinoma,-1,2	COL6A3	608	2	NM_004369	exon41	c.C9129T	p.R3043R	AATGACGCGGTCC	.	scavenged	Atlas-SNP
CYLC1	1538	hgsc.bcm.edu	37	X	83128911	83128911	+	Missense_Mutation	SNP	G	G	C	rs12008888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	106	0	0.483516	0	0|0.017;C|0.055	0.055	strong	.	CYLC1	272	.	NM_021118	exon4	c.G1195C	p.D399H	AAAAAGGATGCAA	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23728528	23728528	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	10	190	0	0.047619	0	.	.	none	CST1,NS,carcinoma,0,2	CST1	37	2	NM_001898	exon3	c.G351A	p.L117L	AGAGCACAACTGT	.	scavenged	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85436352	85436352	+	Missense_Mutation	SNP	G	G	A	rs641393	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	107	105	0	0.990741	0	G|0.451;A|0.549	0.549	strong	SYTL2,NS,carcinoma,+1,1	SYTL2	231	1	NM_206927	exon1	c.C1148T	p.T383M	ATTTCCGTTTGAG	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95054012	95054012	+	Missense_Mutation	SNP	A	A	G	rs6119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	29	49	0	0.483333	0	A|0.750;G|0.250	0.250	strong	.	SERPINA5	69	.	NM_000624	exon3	c.A313G	p.K105E	TCAGAGAAGGAGC	.	PASS	Atlas-SNP
TMPRSS4	56649	hgsc.bcm.edu	37	11	117982464	117982464	+	Missense_Mutation	SNP	A	A	G	rs12270001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	31	62	0	0.596154	0	A|0.911;G|0.089	0.089	strong	.	TMPRSS4	46	.	NM_019894	exon8	c.A592G	p.K198E	TGTGGGAAGAGCC	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108029133	108029133	+	Silent	SNP	C	C	T	rs61742583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	78	138	0	0.45614	0	C|0.991;T|0.009	0.009	strong	.	SCML4	65	.	NM_198081	exon7	c.G1056A	p.V352V	AAACCACACCACG	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96106322	96106322	+	Missense_Mutation	SNP	A	A	G	rs2289043	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	79	154	0	0.593985	0	G|0.520;N|0.000	0.520	strong	.	UNC5C	141	.	NM_003728	exon13	c.T2162C	p.M721T	CCTCCCATCTGTC	.	PASS	Atlas-SNP
GMPPB	29925	hgsc.bcm.edu	37	3	49760073	49760073	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	4	138	0	0.0239521	0	.	.	none	GMPPB,NS,carcinoma,0,1	GMPPB	14	1	NM_021971	exon5	c.G517A	p.A173T	TGCCTGCGTTGAT	.	scavenged	Atlas-SNP
KLHL31	401265	hgsc.bcm.edu	37	6	53517035	53517035	+	Silent	SNP	G	G	A	rs3823111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	62	78	0	0.659574	0	G|0.903;A|0.097	0.097	strong	KLHL31,NS,carcinoma,-2,1	KLHL31	48	1	NM_001003760	exon3	c.C1266T	p.Y422Y	CGCGGCGTACACG	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235950002	235950002	+	Missense_Mutation	SNP	G	G	A	rs3731646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	60	100	0	0.454545	0	G|0.786;A|0.214	0.214	strong	.	SH3BP4	109	.	NM_014521	exon4	c.G589A	p.A197T	TTTGACGCAGGTA	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305760	39305760	+	Missense_Mutation	SNP	C	C	T	rs427961		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	44	150	0	0.488889	0	T|1.000;|0.000	1.000	weak	.	KRTAP4-5	34	.	NM_033188	exon1	c.G260A	p.R87K	GTGGTCCTGCAGC	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47608983	47608983	+	Missense_Mutation	SNP	G	G	T	rs4926581	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	818	318	759	4	0.388753	0.00527009	G|0.849;T|0.151	0.151	strong	CYP4A22,colon,carcinoma,-2,1	CYP4A22	60	1	NM_001010969	exon5	c.G553T	p.V185F	CTGGAGGTCTTTC	.	scavenged	Atlas-SNP
FAM71E2	284418	hgsc.bcm.edu	37	19	55870319	55870319	+	Silent	SNP	C	C	T	rs143731075	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	30	83	0	0.454545	0	C|0.983;T|0.017	0.017	strong	.	FAM71E2	41	.	NM_001145402	exon9	c.G1917A	p.Q639Q	CTTCCCCTGGCCC	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	37	17	1538561	1538561	+	Missense_Mutation	SNP	G	G	A	rs8072430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	25	53	0	0.367647	0	G|0.979;A|0.021	0.021	strong	.	SCARF1	46	.	NM_003693	exon11	c.C1984T	p.R662W	GGGGCCGCCGGTG	.	PASS	Atlas-SNP
PRKG1	5592	hgsc.bcm.edu	37	10	53822344	53822344	+	Silent	SNP	T	T	C	rs113994747	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	68	121	0	0.571429	0	T|0.976;C|0.024	0.024	strong	.	PRKG1	167	.	NM_006258	exon7	c.T888C	p.L296L	CTTTCTTAGAACT	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125315557	125315557	+	Missense_Mutation	SNP	T	T	C	rs1831370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	71	214	0	0.348039	0	T|0.471;C|0.529	0.529	strong	OR1N2,colon,carcinoma,-1,2	OR1N2	51	2	NM_001004457	exon1	c.T109C	p.W37R	TCTGAGTGGCCAG	.	PASS	Atlas-SNP
TMX4	56255	hgsc.bcm.edu	37	20	7963041	7963041	+	Missense_Mutation	SNP	C	C	T	rs2076015	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	175	170	0	0.988701	0	C|0.693;T|0.307	0.307	strong	.	TMX4	39	.	NM_021156	exon8	c.G907A	p.G303R	CCTCTCCTGGGGG	.	PASS	Atlas-SNP
ESYT3	83850	hgsc.bcm.edu	37	3	138176436	138176436	+	Silent	SNP	A	A	G	rs35605373	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	75	130	0	0.487013	0	A|0.975;G|0.025	0.025	strong	.	ESYT3	64	.	NM_031913	exon4	c.A531G	p.A177A	CAAGGCACACACT	.	PASS	Atlas-SNP
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23021346	23021346	+	Missense_Mutation	SNP	G	G	A	rs11135703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	35	80	0	0.507246	0	G|0.820;A|0.180	0.180	strong	.	TNFRSF10D	21	.	NM_003840	exon1	c.C103T	p.P35S	TCTTGGGGTCCAG	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	37	19	12807187	12807187	+	Missense_Mutation	SNP	C	C	T	rs6511833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	33	44	0	0.478261	0	C|0.880;T|0.120	0.120	strong	.	FBXW9	30	.	NM_032301	exon1	c.G209A	p.R70K	GAAACCCTGGACG	.	PASS	Atlas-SNP
HMMR	3161	hgsc.bcm.edu	37	5	162910136	162910136	+	Missense_Mutation	SNP	A	A	G	rs112257004	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	53	121	0	0.414062	0	A|0.990;G|0.010	0.010	strong	.	HMMR	64	.	NM_001142556	exon14	c.A1643G	p.Q548R	AGCAACAGGAGGA	.	PASS	Atlas-SNP
MMP15	4324	hgsc.bcm.edu	37	16	58079268	58079268	+	Missense_Mutation	SNP	C	C	T	rs141377329	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	51	77	0	0.566667	0	C|0.997;T|0.003	0.003	strong	.	MMP15	58	.	NM_002428	exon10	c.C1928T	p.T643I	GCCTCACCTACGC	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56650012	56650012	+	Missense_Mutation	SNP	G	G	C	rs4681904	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	33	60	0	0.428571	0	A|0.009;C|0.230;G|0.761	0.230	strong	.	CCDC66	145	.	NM_001141947	exon13	c.G1774C	p.E592Q	TCTGATGAAATCA	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6272078	6272078	+	Missense_Mutation	SNP	G	G	A	rs12073329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	74	152	0	0.486842	0	G|0.882;A|0.118	0.118	strong	.	RNF207	45	.	NM_207396	exon13	c.G1261A	p.A421T	CCCTTCGCAGAGC	.	PASS	Atlas-SNP
PDLIM7	9260	hgsc.bcm.edu	37	5	176915143	176915143	+	Missense_Mutation	SNP	C	C	T	rs2306764	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	26	56	0	0.42623	0	C|0.916;T|0.084	0.084	strong	.	PDLIM7	32	.	NM_005451	exon10	c.G976A	p.A326T	AGATGGCGCCCTT	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808711	18808711	+	Silent	SNP	G	G	C	rs2992751	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	15	35	0	0.357143	0	G|0.795;C|0.205	0.205	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.G1236C	p.G412G	GGCCGGGACCAAT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016442	25016442	+	Missense_Mutation	SNP	C	C	T	rs3895576	bycluster;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	663	44	531	14	0.066365	0.0263653	.	.	weak	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon8	c.C530T	p.A177V	CGGCAGCCCTGGA	.	scavenged	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535831	88535831	+	Missense_Mutation	SNP	G	G	A	rs200378069	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	58	351	0	0.160665	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.G2017A	p.D673N	AGCAGTGATAGCA	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38411444	38411444	+	Missense_Mutation	SNP	C	C	T	rs56993041	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	118	191	1	0.548837	0.0052356	C|0.978;T|0.022	0.022	strong	.	INPP5B	76	.	NM_005540	exon3	c.G136A	p.G46S	GGCCGCCGTGCTC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32023903	32023903	+	Missense_Mutation	SNP	G	G	C	rs440160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	63	101	0	0.5	0	G|0.931;C|0.069	0.069	strong	.	TNXB	553	.	NM_019105	exon24	c.C8192G	p.P2731R	GGCTCCGGGGCCT	.	PASS	Atlas-SNP
IKZF1	10320	hgsc.bcm.edu	37	7	50467767	50467767	+	Silent	SNP	C	C	A	rs61731355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	30	36	0	0.545455	0	C|0.852;A|0.148	0.148	strong	IKZF1_ENST00000331340,NS,carcinoma,0,1	IKZF1	613	1	NM_006060	exon8	c.C1002A	p.P334P	GACGCCCCCGGGC	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31075364	31075364	+	Silent	SNP	G	G	A	rs34889904	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	29	38	0	0.483333	0	G|0.990;A|0.010	0.010	strong	.	ZNF668	121	.	NM_001172669	exon3	c.C486T	p.P162P	GCGGAAGGGCAGT	.	PASS	Atlas-SNP
ZNF439	90594	hgsc.bcm.edu	37	19	11977147	11977147	+	Splice_Site	SNP	G	G	A	rs10420385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	121	248	0	0.495902	0	G|0.968;A|0.032	0.032	strong	.	ZNF439	67	.	NM_152262	exon1	c.175+1G>A	.	CTATAGGTAAGGA	.	PASS	Atlas-SNP
CEP135	9662	hgsc.bcm.edu	37	4	56837458	56837458	+	Missense_Mutation	SNP	A	A	G	rs141602415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	141	0	0.467213	0	A|0.998;G|0.002	0.002	strong	CEP135,NS,carcinoma,+1,1	CEP135	115	1	NM_025009	exon10	c.A1133G	p.E378G	AGAAAGAAAAGGA	.	PASS	Atlas-SNP
LCLAT1	253558	hgsc.bcm.edu	37	2	30863108	30863108	+	Missense_Mutation	SNP	A	A	G	rs12471868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	157	0	0.482517	0	A|0.870;G|0.130	0.130	strong	.	LCLAT1	51	.	NM_182551	exon7	c.A868G	p.I290V	TATCCAATAGACA	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6713291	6713291	+	Silent	SNP	C	C	T	rs2230201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	80	0	1	0	T|0.156;G|0.000;C|0.844	0.156	strong	.	C3	192	.	NM_000064	exon9	c.G912A	p.R304R	TACCTTCCGGCTC	.	PASS	Atlas-SNP
SOX9	6662	hgsc.bcm.edu	37	17	70118935	70118935	+	Silent	SNP	C	C	T	rs2229989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	118	266	0	0.430657	0	C|0.848;T|0.152	0.152	strong	SOX9,NS,carcinoma,0,1	SOX9	91	1	NM_000346	exon2	c.C507T	p.H169H	GGACCACCCGGAT	.	PASS	Atlas-SNP
POF1B	79983	hgsc.bcm.edu	37	X	84600948	84600948	+	Missense_Mutation	SNP	T	T	C	rs60768249	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	106	228	0	0.524752	0	T|0.958;C|0.042	0.042	strong	.	POF1B	77	.	NM_024921	exon6	c.A641G	p.Q214R	ATGGCTTGGATTT	.	PASS	Atlas-SNP
PSG9	5678	hgsc.bcm.edu	37	19	43773574	43773574	+	Missense_Mutation	SNP	G	G	A	rs73037706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	40	62	0	0.597015	0	G|0.929;A|0.071	0.071	strong	PSG9,NS,carcinoma,0,1	PSG9	77	1	NM_002784	exon1	c.C10T	p.L4F	CTGGGAGGGGCCC	.	PASS	Atlas-SNP
CD1E	913	hgsc.bcm.edu	37	1	158324425	158324425	+	Missense_Mutation	SNP	A	A	G	rs1065457	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	134	0	1	0	A|0.437;G|0.563	0.563	strong	.	CD1E	129	.	NM_001185107	exon2	c.A317G	p.Q106R	TTATCCAGATAGT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361312	107361312	+	Missense_Mutation	SNP	T	T	C	rs75876188	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	455	281	444	2	0.617582	0.0045045	.	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.A383G	p.N128S	AGAGGGTTGCAGA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512027	169512027	+	Silent	SNP	T	T	C	rs6021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	59	145	0	0.479675	0	T|0.763;C|0.237	0.237	strong	.	F5	301	.	NM_000130	exon13	c.A2301G	p.S767S	TGTGTTTGAAGAA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79051801	79051801	+	Missense_Mutation	SNP	C	C	A	rs201472223		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	6	11	0	0.315789	0	.	.	weak	ADAMTS7,NS,carcinoma,0,1	ADAMTS7	142	1	NM_014272	exon24	c.G5023T	p.A1675S	AGGGGGCGCCGTG	.	PASS	Atlas-SNP
KRT31	3881	hgsc.bcm.edu	37	17	39553547	39553547	+	Missense_Mutation	SNP	G	G	A	rs6503627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	98	156	0	0.569767	0	G|0.938;A|0.062	0.062	strong	.	KRT31	158	.	NM_002277	exon1	c.C245T	p.A82V	AGCTCCGCGTTGT	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144991428	144991428	+	Silent	SNP	G	G	A	rs11998271	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	22	40	0	0.52381	0	G|0.957;A|0.043	0.043	strong	.	PLEC	1144	.	NM_201380	exon32	c.C12972T	p.D4324D	CACGCCGTCCGAG	.	PASS	Atlas-SNP
NRSN2	80023	hgsc.bcm.edu	37	20	330408	330408	+	Missense_Mutation	SNP	C	C	G	rs11556643	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	33	67	0	0.375	0	C|0.879;G|0.121	0.121	strong	.	NRSN2	20	.	NM_024958	exon3	c.C121G	p.L41V	ACTGCTCTCAGCG	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408270	29408270	+	Missense_Mutation	SNP	C	C	T	rs2074468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	53	119	0	0.464912	0	C|0.901;T|0.099	0.099	strong	.	OR10C1	58	.	NM_013941	exon1	c.C478T	p.P160S	CACACCCCTTTCA	.	PASS	Atlas-SNP
SEC14L6	730005	hgsc.bcm.edu	37	22	30934887	30934887	+	Silent	SNP	G	G	A	rs5753191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	55	88	0	0.486726	0	G|0.494;A|0.506	0.506	strong	.	SEC14L6	6	.	NM_001193336	exon2	c.C57T	p.F19F	CTCCCGGAACTGA	.	PASS	Atlas-SNP
C11orf95	65998	hgsc.bcm.edu	37	11	63531175	63531175	+	Silent	SNP	C	C	G	rs2959886	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	5	7	0	0.357143	0	C|0.857;G|0.143	0.143	strong	.	.	.	.	NM_001144936	exon5	c.G1752C	p.R584R	CCGCCACCGCGGC	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122634665	122634665	+	Missense_Mutation	SNP	G	G	C	rs34037493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	144	255	0	0.514286	0	G|0.970;C|0.030	0.030	strong	.	SEMA5B	303	.	NM_001256347	exon13	c.C1923G	p.D641E	GGAGCTGTCCTCG	.	PASS	Atlas-SNP
RGL3	57139	hgsc.bcm.edu	37	19	11516007	11516007	+	Silent	SNP	T	T	G	rs10416704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	45	65	0	0.529412	0	T|0.794;G|0.206	0.206	strong	.	RGL3	100	.	NM_001035223	exon8	c.A1092C	p.A364A	GCTCACTGCCCCC	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	54	103	0	0.524272	0	T|0.663;A|0.337	0.337	strong	.	.	.	.	NM_001080479	exon35	c.T4920A	p.H1640Q	TTTCCATGAAAGC	.	PASS	Atlas-SNP
CRB3	92359	hgsc.bcm.edu	37	19	6466482	6466482	+	Silent	SNP	A	A	G	rs348362	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	59	113	0	0.531532	0	A|0.494;G|0.506	0.506	strong	.	CRB3	8	.	NM_174881	exon4	c.A162G	p.P54P	GCGTCCAGAAGCC	.	PASS	Atlas-SNP
RPL39	6170	hgsc.bcm.edu	37	X	118920652	118920652	+	Missense_Mutation	SNP	G	G	A	rs79192437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	334	296	0	0.994048	0	G|0.953;A|0.047	0.047	strong	.	RPL39	9	.	NM_001000	exon3	c.A151T	p.M51L	CTTATAGACCCAG	.	PASS	Atlas-SNP
GNA13	10672	hgsc.bcm.edu	37	17	63049709	63049709	+	Missense_Mutation	SNP	C	C	T	rs116700192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	102	104	0	0.971429	0	C|0.988;T|0.012	0.012	strong	.	GNA13	69	.	NM_006572	exon2	c.G421A	p.V141I	AGAAAACCCTTGT	.	PASS	Atlas-SNP
MYOZ3	91977	hgsc.bcm.edu	37	5	150056307	150056307	+	Missense_Mutation	SNP	C	C	A	rs7737542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	32	50	0	0.438356	0	C|0.887;A|0.113	0.113	strong	MYOZ3,colon,carcinoma,0,1	MYOZ3	21	1	NM_001122853	exon7	c.C626A	p.T209N	GGGGCACTTTTCC	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444845	61444845	+	Silent	SNP	G	G	A	rs112106909	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	15	25	1	0.714286	0.04	G|0.500;A|0.500	0.500	weak	OGFR,NS,carcinoma,0,3	OGFR	63	3	NM_007346	exon7	c.G1878A	p.P626P	CCGCCCGGCAGGA	.	scavenged	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19403331	19403331	+	Silent	SNP	G	G	A	rs142064832	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	88	195	0	0.455959	0	G|0.999;A|0.001	0.001	strong	.	UBR4	415	.	NM_020765	exon105	c.C15390T	p.N5130N	CATGTCGTTGTGG	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305731	48305731	+	Silent	SNP	G	G	T	rs79291962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	60	111	0	0.465116	0	G|0.993;T|0.007	0.007	strong	.	TPRX1	46	.	NM_198479	exon2	c.C537A	p.I179I	GCCTGGGATCGGG	.	PASS	Atlas-SNP
NPHS1	4868	hgsc.bcm.edu	37	19	36334419	36334419	+	Silent	SNP	G	G	A	rs437168	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	67	115	0	0.471831	0	G|0.821;A|0.179	0.179	strong	.	NPHS1	165	.	NM_004646	exon17	c.C2289T	p.V763V	GGCATCGACAGTG	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229772285	229772285	+	Missense_Mutation	SNP	C	C	T	rs115230066	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	130	215	0	0.513834	0	C|0.999;T|0.001	0.001	strong	.	URB2	152	.	NM_014777	exon4	c.C1925T	p.S642L	AGATCTCGAACCT	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34824636	34824636	+	Missense_Mutation	SNP	A	A	G	rs11755393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	35	81	0	0.472973	0	A|0.531;G|0.469	0.469	strong	.	UHRF1BP1	102	.	NM_017754	exon11	c.A1361G	p.Q454R	CCTTTCAGCCTCC	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	129	390	0	0.399381	0	T|0.621;C|0.379	0.379	strong	ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	NM_001137674	exon2	c.T1051C	p.F351L	AAGGCTTTCAGGC	.	PASS	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17413127	17413127	+	Silent	SNP	G	G	A	rs35184728	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	62	84	0	0.563636	0	G|0.976;A|0.024	0.024	strong	PADI2,NS,malignant_melanoma,-1,1	PADI2	72	1	NM_007365	exon7	c.C723T	p.Y241Y	ACCCGTGTACTTG	.	PASS	Atlas-SNP
PTH2R	5746	hgsc.bcm.edu	37	2	209353800	209353800	+	Silent	SNP	A	A	G	rs16841294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	196	176	0	1	0	A|0.858;G|0.142	0.142	strong	.	PTH2R	92	.	NM_005048	exon11	c.A1140G	p.V380V	GTTCGTATGCCTG	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458536	4458536	+	Silent	SNP	T	T	C	rs144321472	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	39	59	0	0.609375	0	T|0.995;C|0.005	0.005	strong	.	MYBBP1A	69	.	NM_014520	exon1	c.A84G	p.L28L	CTTCAATAGGCCA	.	PASS	Atlas-SNP
DERL3	91319	hgsc.bcm.edu	37	22	24179132	24179132	+	Missense_Mutation	SNP	G	G	A	rs1128127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	316	168	262	0	0.531646	0	G|0.750;A|0.250	0.250	strong	.	DERL3	14	.	NM_001002862	exon7	c.C632T	p.A211V	GCAGGGGCATCCA	.	PASS	Atlas-SNP
SYT7	9066	hgsc.bcm.edu	37	11	61291922	61291922	+	Silent	SNP	A	A	G	rs10897167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	133	0	1	0	A|0.836;G|0.164	0.164	strong	.	SYT7	39	.	NM_001252065	exon7	c.T930C	p.I310I	CTCCCCAATGGGG	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15276739	15276739	+	Silent	SNP	A	A	G	rs16980398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	62	88	0	0.590476	0	A|0.883;G|0.117	0.117	strong	.	NOTCH3	340	.	NM_000435	exon30	c.T5526C	p.A1842A	GTGCAAAGCAGTC	.	PASS	Atlas-SNP
TCEB3	6924	hgsc.bcm.edu	37	1	24078234	24078234	+	Missense_Mutation	SNP	T	T	C	rs34394004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	63	0	0.486486	0	T|0.935;C|0.065	0.065	strong	.	TCEB3	61	.	NM_003198	exon4	c.T1217C	p.L406S	CTAATTTGGATAG	.	PASS	Atlas-SNP
KLF4	9314	hgsc.bcm.edu	37	9	110249415	110249415	+	Silent	SNP	T	T	C	rs45596731	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	171	270	1	0.635688	0.0037037	T|0.996;C|0.004	0.004	strong	.	KLF4	106	.	NM_004235	exon4	c.A1158G	p.R386R	CCACGATCGTCTT	.	PASS	Atlas-SNP
AAR2	25980	hgsc.bcm.edu	37	20	34828459	34828459	+	Silent	SNP	T	T	C	rs716431	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	72	89	0	0.541353	0	T|0.854;C|0.146	0.146	strong	C20orf4,colon,carcinoma,0,1	.	.	1	NM_001271874	exon2	c.T669C	p.A223A	GCCAGCTGAGATA	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	70841703	70841703	+	Missense_Mutation	SNP	A	A	G	rs116730273	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	142	273	0	0.458065	0	A|0.994;G|0.006	0.006	strong	.	HYDIN	788	.	NM_001270974	exon86	c.T15146C	p.M5049T	GTCACCATGTGAT	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19178854	19178854	+	Missense_Mutation	SNP	G	G	A	rs190366603	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	51	91	0	0.579545	0	G|0.999;A|0.001	0.001	strong	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	1	NM_001835	exon27	c.C4285T	p.R1429W	CCAGCCGGGGTGA	.	PASS	Atlas-SNP
ERLEC1	27248	hgsc.bcm.edu	37	2	54035447	54035447	+	Silent	SNP	A	A	G	rs1127362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	22	62	0	0.478261	0	A|0.835;G|0.165	0.165	strong	ERLEC1,NS,carcinoma,0,1	ERLEC1	32	1	NM_015701	exon9	c.A891G	p.Q297Q	TTTGCAATCAACT	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186460110	186460110	+	Missense_Mutation	SNP	G	G	C	rs5030087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	45	0	0.428571	0	G|0.963;C|0.037	0.037	strong	.	KNG1	129	.	NM_001102416	exon10	c.G1925C	p.G642A	CTGATGGCCTTTC	.	PASS	Atlas-SNP
DUSP21	63904	hgsc.bcm.edu	37	X	44703935	44703935	+	Missense_Mutation	SNP	T	T	C	rs1045031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	130	134	0	0.977444	0	0|0.015;C|0.254	0.254	strong	.	DUSP21	39	.	NM_022076	exon1	c.T557C	p.M186T	TACGTATGATGAT	.	PASS	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	37	7	95820500	95820500	+	Silent	SNP	C	C	T	rs78247004	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	34	77	0	0.507463	0	C|0.985;T|0.015	0.015	strong	SLC25A13,NS,carcinoma,-1,2	SLC25A13	131	2	NM_001160210	exon7	c.G675A	p.S225S	AAGGAGCGAATTA	.	PASS	Atlas-SNP
ARRDC2	27106	hgsc.bcm.edu	37	19	18121466	18121466	+	Silent	SNP	C	C	T	rs8100681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	34	51	0	0.566667	0	C|0.939;T|0.061	0.061	strong	.	ARRDC2	60	.	NM_015683	exon7	c.C1098T	p.D366D	CCCCGACATGAGC	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184293769	184293769	+	Silent	SNP	T	T	C	rs7652597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	169	148	1	1	0.00675676	T|0.621;C|0.379	0.379	strong	.	EPHB3	114	.	NM_004443	exon4	c.T1008C	p.C336C	TGCCTGTACCAGT	.	PASS	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77758597	77758597	+	Missense_Mutation	SNP	C	C	T	rs76915888	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	32	55	0	0.542373	0	C|0.942;T|0.058	0.058	strong	.	CBX2	50	.	NM_005189	exon5	c.C1355T	p.A452V	GCAAGGCGGCCAC	.	PASS	Atlas-SNP
NFRKB	4798	hgsc.bcm.edu	37	11	129752426	129752426	+	Silent	SNP	G	G	A	rs76967949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	51	89	0	0.6	0	G|0.985;A|0.015	0.015	strong	.	NFRKB	101	.	NM_006165	exon8	c.C1077T	p.A359A	CGGCTCGGCCAGG	.	PASS	Atlas-SNP
DLGAP5	9787	hgsc.bcm.edu	37	14	55619311	55619311	+	Silent	SNP	A	A	G	rs15870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	32	75	0	0.561404	0	A|0.621;G|0.379	0.379	strong	.	DLGAP5	84	.	NM_014750	exon16	c.T2118C	p.N706N	TACATGATTTTCT	.	PASS	Atlas-SNP
RAB25	57111	hgsc.bcm.edu	37	1	156039960	156039960	+	Missense_Mutation	SNP	C	C	T	rs115837676	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	317	157	331	1	0.495268	0.00302115	C|0.996;T|0.004	0.004	strong	RAB25,NS,carcinoma,-1,1	RAB25	18	1	NM_020387	exon5	c.C524T	p.A175V	TCTTTGCGAAGGT	.	PASS	Atlas-SNP
GRAMD3	65983	hgsc.bcm.edu	37	5	125696127	125696127	+	Missense_Mutation	SNP	A	A	G	rs78682130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	80	181	0	0.380952	0	A|0.975;G|0.025	0.025	strong	.	GRAMD3	30	.	NM_001146319	exon1	c.A104G	p.K35R	AAGTGAAGCCAGT	.	PASS	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38615698	38615698	+	Missense_Mutation	SNP	C	C	T	rs1832313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	83	176	0	0.506098	0	C|0.550;T|0.450	0.450	strong	.	ANKRD18A	49	.	NM_147195	exon3	c.G388A	p.E130K	TATCCTCAATGTT	.	PASS	Atlas-SNP
CRYBG3	131544	hgsc.bcm.edu	37	3	97660084	97660084	+	Silent	SNP	C	C	T	rs11544446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	107	0	0.508475	0	C|0.790;T|0.210	0.210	strong	.	CRYBG3	86	.	NM_153605	exon20	c.C8598T	p.C2866C	TGTGTGCATTTCT	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56443519	56443519	+	Silent	SNP	C	C	T	rs12610617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	43	100	0	0.472527	0	C|0.928;T|0.072	0.072	strong	NLRP13,colon,carcinoma,-1,1	NLRP13	220	1	NM_176810	exon1	c.G159A	p.P53P	GATACGCGGGAAG	.	PASS	Atlas-SNP
DPEP2	64174	hgsc.bcm.edu	37	16	68024850	68024850	+	Silent	SNP	A	A	G	rs10500542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	67	165	0	0.443709	0	A|0.942;G|0.058	0.058	strong	.	DPEP2	43	.	NM_022355	exon7	c.T783C	p.H261H	TGAGACATGGGAT	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160087410	160087410	+	Missense_Mutation	SNP	C	C	T	rs77049231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	94	193	0	0.569697	0	C|0.980;T|0.020	0.020	strong	.	TANC1	157	.	NM_033394	exon27	c.C5473T	p.H1825Y	GTTTCTCATCTGT	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5352659	5352659	+	Silent	SNP	G	G	T	rs138591330	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	10	5	0	0.625	0	G|0.653;T|0.347	0.347	strong	TNRC18_ENST00000430969,NS,carcinoma,0,3	TNRC18	311	3	NM_001080495	exon27	c.C7863A	p.S2621S	GGAGGAGGAGGAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476366	228476366	+	Missense_Mutation	SNP	G	G	T	rs3795789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	63	118	0	0.516393	0	G|0.927;T|0.073	0.073	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.G11403T	p.E3801D	CCAAGAGAGCATA	.	PASS	Atlas-SNP
CCDC142	84865	hgsc.bcm.edu	37	2	74708453	74708453	+	Silent	SNP	A	A	T	rs115125840	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	56	173	0	0.388889	0	A|0.997;T|0.003	0.003	strong	.	CCDC142	40	.	NM_032779	exon3	c.T1155A	p.L385L	TGTGGGAAGGCTG	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	17	225	0	0.0586207	0	.	.	weak	DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	NM_030653	exon18	c.C1774G	p.Q592E	CTCAGTCAGAGCA	.	scavenged	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153420176	153420176	+	Missense_Mutation	SNP	A	A	G	rs78093925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	929	485	618	1	0.522067	0.00161812	A|0.814;G|0.186	0.186	strong	.	OPN1LW	87	.	NM_020061	exon4	c.A706G	p.M236V	ATCATCATGCTCT	.	PASS	Atlas-SNP
IFNA14	3448	hgsc.bcm.edu	37	9	21239504	21239504	+	Missense_Mutation	SNP	T	T	C	rs140823004	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	401	47	357	0	0.117207	0	T|1.000;C|0.000	0.000	strong	IFNA14,NS,carcinoma,0,1	IFNA14	29	1	NM_002172	exon1	c.A431G	p.K144R	TATTTCTTCACAG	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	13	96	0	0.104	0	T|0.998;C|0.002	0.002	strong	SIGLEC12_ENST00000439889,rectum,carcinoma,0,2	SIGLEC10	112	2	NM_001171157	exon5	c.A874G	p.N292D	CTCTGTTCTGCAG	.	PASS	Atlas-SNP
ZNF432	9668	hgsc.bcm.edu	37	19	52538428	52538428	+	Silent	SNP	A	A	G	rs11881700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	75	118	0	0.619835	0	A|0.839;G|0.161	0.161	strong	ZNF432,NS,carcinoma,-1,1	ZNF432	172	1	NM_014650	exon5	c.T504C	p.G168G	ATAGTTACCATGA	.	PASS	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12980305	12980305	+	Missense_Mutation	SNP	G	G	A	rs373273540		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	73	118	0	0.62931	0	.	.	weak	DDX47,colon,carcinoma,+1,1	DDX47	37	1	NM_016355	exon11	c.G1232A	p.R411Q	TTGCCCGAATGGT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406646	50406646	+	Silent	SNP	A	A	G	rs143601538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	158	323	0	0.523179	0	A|0.999;G|0.001	0.001	strong	.	SALL4	168	.	NM_020436	exon2	c.T2376C	p.N792N	TTGACTATTGGCC	.	PASS	Atlas-SNP
NXPE1	120400	hgsc.bcm.edu	37	11	114393066	114393066	+	Missense_Mutation	SNP	A	A	G	rs34993124	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	74	172	0	0.459627	0	A|0.982;G|0.018	0.018	strong	.	NXPE1	8	.	NM_152315	exon6	c.T842C	p.I281T	CGGTCAATTTCCC	.	PASS	Atlas-SNP
SMC2	10592	hgsc.bcm.edu	37	9	106901506	106901506	+	Silent	SNP	A	A	G	rs16923746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	66	177	0	0.340206	0	A|0.935;G|0.065	0.065	strong	.	SMC2	127	.	NM_006444	exon25	c.A3504G	p.V1168V	TACAGTAGCCAGA	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	55	0	0.490196	0	A|0.654;G|0.346	0.346	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon37	c.A5091G	p.Q1697Q	TATCCAAGGCCTG	.	PASS	Atlas-SNP
FUT3	2525	hgsc.bcm.edu	37	19	5844792	5844792	+	Missense_Mutation	SNP	A	A	C	rs28362459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	111	239	0	0.497758	0	A|0.832;C|0.168	0.168	strong	FUT3,NS,carcinoma,0,1	FUT3	30	1	NM_001097640	exon3	c.T59G	p.L20R	AATAGCAGTGCGG	.	PASS	Atlas-SNP
PRDM14	63978	hgsc.bcm.edu	37	8	70964399	70964399	+	Silent	SNP	A	A	G	rs10089937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	152	0	0.992754	0	A|0.364;G|0.636	0.636	strong	.	PRDM14	102	.	NM_024504	exon8	c.T1629C	p.D543D	GCCATCATCCTCC	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49442933	49442933	+	Silent	SNP	T	T	C	rs2270939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	47	0	1	0	T|0.623;C|0.377	0.377	strong	.	DHDH	35	.	NM_014475	exon4	c.T594C	p.S198S	GATTTCTGTCGTG	.	PASS	Atlas-SNP
SRL	6345	hgsc.bcm.edu	37	16	4245693	4245693	+	Silent	SNP	A	A	G	rs10852643	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	200	182	1	0.995025	0.00549451	A|0.226;G|0.774	0.774	strong	.	SRL	56	.	NM_001098814	exon5	c.T471C	p.R157R	GAAGGAACGGGCG	.	PASS	Atlas-SNP
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604427	80604427	+	Silent	SNP	C	C	T	rs149561750	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	78	187	1	0.433333	0.00534759	C|0.998;T|0.002	0.002	strong	ZCCHC9,bladder,carcinoma,0,1	ZCCHC9	26	1	NM_001131036	exon3	c.C432T	p.P144P	TTGCCCCGCCGCC	.	scavenged	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76521121	76521121	+	Silent	SNP	T	T	C	rs17729253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	27	69	0	0.457627	0	T|0.830;C|0.170	0.170	strong	.	DNAH17	347	.	NM_173628	exon25	c.A3834G	p.L1278L	CTTCAGTAGGCGG	.	PASS	Atlas-SNP
PTPRE	5791	hgsc.bcm.edu	37	10	129871690	129871690	+	Silent	SNP	A	A	G	rs2275803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	112	0	1	0	G|0.223;N|0.000	0.223	strong	PTPRE,NS,carcinoma,0,1	PTPRE	132	1	NM_006504	exon17	c.A1554G	p.K518K	ATGGAAATCCCAC	.	PASS	Atlas-SNP
CDKN1A	1026	hgsc.bcm.edu	37	6	36652135	36652135	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	23	41	0	0.425926	0	.	.	none	CDKN1A,NS,carcinoma,+1,1	CDKN1A	27	1	NM_001220778	exon2	c.G257A	p.R86Q	GAGGCCGGGATGA	.	PASS	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	37	12	89916781	89916781	+	Missense_Mutation	SNP	G	G	T	rs139995124	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	46	82	0	0.547619	0	G|0.996;T|0.004	0.004	strong	.	GALNT4	38	.	NM_003774	exon1	c.C1546A	p.Q516K	AATTTTGCATTCC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918963	12918963	+	Missense_Mutation	SNP	G	G	T	rs9661554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	518	243	454	2	0.469112	0.00440529	G|0.891;T|0.109	0.109	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.G99T	p.R33S	GCCCAGGGTGCTC	.	PASS	Atlas-SNP
PTGIR	5739	hgsc.bcm.edu	37	19	47124579	47124579	+	Silent	SNP	C	C	T	rs2229130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	136	0	0.5	0	C|0.984;T|0.016	0.016	strong	.	PTGIR	31	.	NM_000960	exon3	c.G1119A	p.T373T	GGACGACGTTCCC	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107979475	107979475	+	Missense_Mutation	SNP	G	G	A	rs1801162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	103	151	0	0.651899	0	G|0.943;A|0.057	0.057	strong	.	IRS4	253	.	NM_003604	exon1	c.C100T	p.L34F	AAAGAAGCGGGGT	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128381717	128381717	+	Missense_Mutation	SNP	G	G	A	rs2245408	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	51	78	0	0.566667	0	G|0.990;A|0.010	0.010	strong	.	MYO7B	359	.	NM_001080527	exon29	c.G3791A	p.R1264Q	TCGCCCGGTGTGA	.	PASS	Atlas-SNP
SEBOX	645832	hgsc.bcm.edu	37	17	26691916	26691916	+	Silent	SNP	T	T	C	rs2277667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	66	98	0	0.519685	0	T|0.855;C|0.145	0.145	strong	.	SEBOX	20	.	NM_001080837	exon2	c.A171G	p.L57L	CTCCAGTAGCTGC	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42893328	42893328	+	Missense_Mutation	SNP	T	T	C	rs115331994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	50	62	0	0.588235	0	T|0.994;C|0.006	0.006	strong	.	PTCRA	24	.	NM_001243168	exon4	c.T799C	p.C267R	GCCTGGTGCTCAA	.	PASS	Atlas-SNP
SEMA3D	223117	hgsc.bcm.edu	37	7	84697540	84697540	+	Missense_Mutation	SNP	C	C	T	rs148351346	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	99	0	0.469388	0	C|0.999;T|0.001	0.001	strong	.	SEMA3D	177	.	NM_152754	exon5	c.G556A	p.D186N	GAGGATCGAAAGG	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581904	84581904	+	Silent	SNP	T	T	C	rs4842923	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	133	1	1	0.0075188	T|0.354;C|0.646	0.646	strong	ADAMTSL3,colon,carcinoma,+1,2	ADAMTSL3	290	2	NM_207517	exon16	c.T1761C	p.R587R	GGTCCGTGAGGTG	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50885775	50885775	+	Silent	SNP	A	A	G	rs1053744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	194	182	0	1	0	G|0.524;N|0.000	0.524	strong	.	SBF1	211	.	NM_002972	exon40	c.T5559C	p.T1853T	GTCCACAGTCTTA	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	110	0	0.46988	0	G|0.888;A|0.112	0.112	strong	.	UTP20	222	.	NM_014503	exon10	c.G1143A	p.P381P	CTTGCCGGAGACC	.	PASS	Atlas-SNP
SOWAHD	347454	hgsc.bcm.edu	37	X	118893390	118893390	+	Missense_Mutation	SNP	A	A	G	rs12841259	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	59	100	0	0.608247	0	A|0.958;G|0.042	0.042	strong	.	.	.	.	NM_001105576	exon1	c.A760G	p.T254A	GGGTGCACCAACC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551948	32551948	+	Missense_Mutation	SNP	G	G	A	rs17886882	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	11	31	4	0.478261	0.129032	.	.	weak	HLA-DRB1,brain,glioma,0,2	HLA-DRB1	41	2	NM_002124	exon2	c.C308T	p.A103V	TCCACCGCGGCCC	.	scavenged	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385131	16385131	+	Missense_Mutation	SNP	C	C	A	rs1832151	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	659	195	512	0	0.295903	0	C|0.837;A|0.163	0.163	strong	.	FAM131C	21	.	NM_182623	exon7	c.G644T	p.S215I	GAGGGGCTGGGCG	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74703022	74703022	+	Silent	SNP	G	G	A	rs2075592	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	118	0	0.456311	0	G|0.857;A|0.143	0.143	strong	.	SEMA7A	58	.	NM_003612	exon14	c.C1944T	p.A648A	GGAGGCGGCCAGG	.	PASS	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	37	1	38185169	38185169	+	Silent	SNP	G	G	A	rs35909785	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	88	185	0	0.458333	0	G|0.936;A|0.064	0.064	strong	.	EPHA10	120	.	NM_001099439	exon15	c.C2673T	p.P891P	GAACCTGGGCCGC	.	PASS	Atlas-SNP
GAPDH	2597	hgsc.bcm.edu	37	12	6647109	6647109	+	Silent	SNP	T	T	C	rs1803621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	19	47	0	0.345455	0	T|0.686;C|0.314	0.314	strong	.	GAPDH	20	.	NM_002046	exon8	c.T885C	p.F295F	CACCTTTGACGCT	.	PASS	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42793479	42793479	+	Silent	SNP	G	G	A	rs180870	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	112	116	0	0.982456	0	G|0.337;A|0.663	0.663	strong	.	DGKH	106	.	NM_001204504	exon28	c.G3327A	p.E1109E	AAATGAGGATGAG	.	PASS	Atlas-SNP
HECA	51696	hgsc.bcm.edu	37	6	139488364	139488364	+	Silent	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	59	95	0	0.614583	0	.	.	none	.	HECA	45	.	NM_016217	exon2	c.C1215G	p.L405L	GGCGCTCCCGGTG	.	PASS	Atlas-SNP
TBC1D16	125058	hgsc.bcm.edu	37	17	77984168	77984168	+	Silent	SNP	G	G	A	rs35393459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	64	141	0	0.571429	0	G|0.967;A|0.033	0.033	strong	.	TBC1D16	48	.	NM_019020	exon3	c.C570T	p.V190V	CGGACTGACCGTC	.	PASS	Atlas-SNP
FLII	2314	hgsc.bcm.edu	37	17	18148944	18148944	+	Silent	SNP	C	C	G	rs113208618	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	42	76	0	0.456522	0	C|0.964;G|0.036	0.036	strong	.	FLII	79	.	NM_002018	exon28	c.G3534C	p.V1178V	CTCAGTCACTGCA	.	PASS	Atlas-SNP
PABPN1L	390748	hgsc.bcm.edu	37	16	88931509	88931509	+	Silent	SNP	G	G	A	rs76746996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	34	93	0	0.395349	0	G|0.953;A|0.047	0.047	strong	.	PABPN1L	25	.	NM_001080487	exon4	c.C487T	p.L163L	CCTCCAGCTCCTC	.	PASS	Atlas-SNP
KAZN	23254	hgsc.bcm.edu	37	1	15438990	15438990	+	Missense_Mutation	SNP	G	G	A	rs10803354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	265	266	0	0.992509	0	G|0.601;A|0.399	0.399	strong	.	KAZN	57	.	NM_201628	exon14	c.G2116A	p.A706T	ACGCGGGCAGGAA	.	PASS	Atlas-SNP
KRT79	338785	hgsc.bcm.edu	37	12	53215684	53215684	+	Missense_Mutation	SNP	G	G	A	rs73303800	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	64	0	0.547945	0	G|0.990;A|0.010	0.010	strong	.	KRT79	78	.	NM_175834	exon9	c.C1580T	p.T527M	TTGACCGTAGTGG	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	37	2	135976740	135976740	+	Silent	SNP	T	T	C	rs16831460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	71	232	0	0.430303	0	T|0.947;C|0.053	0.053	strong	.	ZRANB3	109	.	NM_032143	exon16	c.A2259G	p.K753K	CATCTGTTTTCCA	.	PASS	Atlas-SNP
AQP12B	653437	hgsc.bcm.edu	37	2	241622008	241622008	+	Missense_Mutation	SNP	G	G	A	rs187845451	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	98	165	0	0.4	0	G|0.991;A|0.009	0.009	strong	AQP12B,colon,carcinoma,+2,1	AQP12B	33	1	NM_001102467	exon1	c.C247T	p.H83Y	CCCCGTGCGCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506483	195506483	+	Missense_Mutation	SNP	T	T	C	rs201375109	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	6	72	0	0.12766	0	C|0.002;G|0.002;T|0.996	0.002	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A11968G	p.T3990A	AGGAAGTGTCGGT	.	scavenged	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229622236	229622236	+	Missense_Mutation	SNP	G	G	A	rs35442997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	74	146	0	0.420455	0	G|0.990;A|0.010	0.010	strong	.	NUP133	111	.	NM_018230	exon11	c.C1382T	p.P461L	ATGATAGGAACAC	.	PASS	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150657130	150657130	+	Missense_Mutation	SNP	G	G	T	rs59596499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	46	98	0	0.414414	0	G|0.915;T|0.085	0.085	strong	.	SLC36A3	54	.	NM_001145017	exon11	c.C1360A	p.L454I	CCAGGAGGGCTGG	.	PASS	Atlas-SNP
AAED1	195827	hgsc.bcm.edu	37	9	99417000	99417000	+	Missense_Mutation	SNP	C	C	T	rs9886834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	41	90	0	0.594203	0	C|0.901;T|0.099	0.099	strong	.	.	.	.	NM_153698	exon2	c.G248A	p.R83K	AAACTCCTGGGGA	.	PASS	Atlas-SNP
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605983	1605983	+	Missense_Mutation	SNP	G	G	C	rs59007122	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	25	239	13	0.102041	0.0543933	G|0.500;C|0.500	0.500	weak	KRTAP5-1,caecum,carcinoma,0,3	KRTAP5-1	74	3	NM_001005922	exon1	c.C497G	p.A166G	CCACAGGCCCCCT	.	scavenged	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	722331	722331	+	Missense_Mutation	SNP	C	C	T	rs3177338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	48	0	0.478873	0	C|0.469;T|0.531	0.531	strong	.	RHOT2	35	.	NM_138769	exon15	c.C1273T	p.R425C	GGGGCCCGTGGAG	.	PASS	Atlas-SNP
CDK11A	728642	hgsc.bcm.edu	37	1	1635022	1635022	+	Silent	SNP	A	A	G	rs1136978	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	19	193	0	0.174312	0	A|0.852;G|0.148	0.148	strong	.	CDK11A	38	.	NM_024011	exon18	c.T1953C	p.S651S	GAGCTCACTGTAG	.	PASS	Atlas-SNP
AACS	65985	hgsc.bcm.edu	37	12	125587278	125587278	+	Silent	SNP	G	G	A	rs3763984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	60	116	0	0.472441	0	G|0.956;A|0.044	0.044	strong	.	AACS	59	.	NM_023928	exon6	c.G624A	p.E208E	TGTGGAGGCTGTT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057766	46057766	+	Missense_Mutation	SNP	G	G	C	rs142146787	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	53	155	0	0.30814	0	G|1.000;C|0.000	0.000	weak	.	KRTAP10-10	37	.	NM_181688	exon1	c.G432C	p.Q144H	CCAGCAGGCCTGC	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74466377	74466377	+	Silent	SNP	C	C	T	rs6453696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	214	259	0	1	0	C|0.387;T|0.613	0.613	strong	.	CD109	170	.	NM_133493	exon6	c.C645T	p.Y215Y	GACATACTATCAA	.	PASS	Atlas-SNP
GABRA4	2557	hgsc.bcm.edu	37	4	46995387	46995387	+	Missense_Mutation	SNP	C	C	T	rs16859837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	192	185	0	0.989691	0	C|0.984;T|0.016	0.016	strong	.	GABRA4	129	.	NM_000809	exon1	c.G55A	p.A19T	GGAGGGCGAAACT	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20067064	20067064	+	Silent	SNP	C	C	T	rs7125647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	33	65	0	0.55	0	C|0.384;T|0.616	0.616	strong	.	NAV2	255	.	NM_001244963	exon15	c.C3819T	p.D1273D	AACAGACAAGGAG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512637	4512637	+	Silent	SNP	A	A	G	rs57042059	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	189	194	0	1	0	A|0.864;G|0.136	0.136	strong	PLIN4_ENST00000301286,colon,carcinoma,-2,2	PLIN4	191	2	NM_001080400	exon3	c.T1293C	p.N431N	GGCCAAATTCATG	.	PASS	Atlas-SNP
ZNF618	114991	hgsc.bcm.edu	37	9	116811184	116811184	+	Silent	SNP	G	G	A	rs7852282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	38	55	0	0.633333	0	G|0.921;A|0.079	0.079	strong	.	ZNF618	184	.	NM_133374	exon14	c.G1323A	p.K441K	GGTGAAGGTGAAA	.	PASS	Atlas-SNP
ASPDH	554235	hgsc.bcm.edu	37	19	51017064	51017064	+	Missense_Mutation	SNP	G	G	C	rs7248272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	66	116	0	0.5	0	G|0.930;C|0.070	0.070	strong	.	ASPDH	22	.	NM_001114598	exon1	c.C17G	p.P6R	CTCCACGGGCCCC	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53993670	53993670	+	Missense_Mutation	SNP	G	G	A	rs2617667	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	91	219	0	0.541667	0	G|0.745;A|0.255	0.255	strong	.	ZNF813	81	.	NM_001004301	exon4	c.G184A	p.A62T	TCAACAGCACAAG	.	PASS	Atlas-SNP
SYK	6850	hgsc.bcm.edu	37	9	93606309	93606309	+	Silent	SNP	G	G	A	rs35758162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	32	60	0	0.363636	0	G|0.847;A|0.153	0.153	strong	.	SYK	132	.	NM_003177	exon2	c.G129A	p.Q43Q	GCGCCAGAGCCGC	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169469088	169469088	+	Silent	SNP	G	G	C	rs6555882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	242	225	0	1	0	G|0.867;C|0.133	0.133	strong	.	DOCK2	389	.	NM_004946	exon38	c.G3828C	p.L1276L	GCAGCTGAAGGAG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55105722	55105722	+	Missense_Mutation	SNP	G	G	C	rs28524012	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	107	221	0	1	0	G|0.797;C|0.203	0.203	strong	.	LILRA1	105	.	NM_006863	exon2	c.G13C	p.V5L	CCCATCGTCACAG	.	PASS	Atlas-SNP
DUOX1	53905	hgsc.bcm.edu	37	15	45427345	45427345	+	Silent	SNP	C	C	T	rs78022423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	95	170	0	0.461165	0	C|0.976;T|0.024	0.024	strong	.	DUOX1	125	.	NM_017434	exon6	c.C351T	p.G117G	TCCCGGCTGCCCC	.	PASS	Atlas-SNP
OR7G2	390882	hgsc.bcm.edu	37	19	9213396	9213396	+	Missense_Mutation	SNP	G	G	A	rs7247751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	102	207	0	0.472222	0	G|0.968;A|0.032	0.032	strong	OR7G2,NS,carcinoma,+1,1	OR7G2	48	1	NM_001005193	exon1	c.C587T	p.P196L	AAGAGCGGGATTT	.	PASS	Atlas-SNP
MERTK	10461	hgsc.bcm.edu	37	2	112722854	112722854	+	Missense_Mutation	SNP	G	G	A	rs7588635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	94	219	1	0.467662	0.00456621	G|0.947;A|0.053	0.053	strong	.	MERTK	112	.	NM_006343	exon5	c.G844A	p.A282T	ATCAAAGGTAAGC	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6602378	6602378	+	Silent	SNP	G	G	A	rs73796294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	40	80	0	0.506329	0	G|0.959;A|0.041	0.041	strong	.	MAN2B2	80	.	NM_015274	exon10	c.G1434A	p.S478S	TGCCTCGGTCTAC	.	PASS	Atlas-SNP
BRPF3	27154	hgsc.bcm.edu	37	6	36177597	36177597	+	Silent	SNP	C	C	T	rs73730485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	53	88	0	0.464912	0	C|0.987;T|0.013	0.013	strong	.	BRPF3	93	.	NM_015695	exon5	c.C1771T	p.L591L	CTGGAGCTGATGC	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	59	114	0	0.551402	0	C|0.898;T|0.102	0.102	strong	.	LRRC16B	120	.	NM_138360	exon16	c.C1269T	p.Y423Y	CGCCTACACACTG	.	PASS	Atlas-SNP
GFI1B	8328	hgsc.bcm.edu	37	9	135864547	135864547	+	Missense_Mutation	SNP	G	G	A	rs62638686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	41	112	0	0.338843	0	A|0.017;G|0.983;T|0.000	0.017	strong	.	GFI1B	37	.	NM_004188	exon5	c.G610A	p.A204T	GGCCACGCTGTGA	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32087374	32087374	+	Missense_Mutation	SNP	A	A	G	rs157496	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	57	134	0	0.425373	0	A|0.706;G|0.294	0.294	strong	.	PDZD2	306	.	NM_178140	exon19	c.A3820G	p.T1274A	AGGGTCACCAAGT	.	PASS	Atlas-SNP
NOL10	79954	hgsc.bcm.edu	37	2	10712278	10712278	+	Silent	SNP	C	C	T	rs3732114	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	175	260	1	0.513196	0.00384615	C|0.730;T|0.270	0.270	strong	.	NOL10	22	.	NM_024894	exon21	c.G1986A	p.L662L	TCGATGCAGTTTC	.	PASS	Atlas-SNP
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	35	37	0	1	0	C|0.639;T|0.361	0.361	strong	PDK2,NS,carcinoma,0,1	PDK2	41	1	NM_002611	exon2	c.C240T	p.S80S	ACCCTCCGTGCAG	.	PASS	Atlas-SNP
B9D1	27077	hgsc.bcm.edu	37	17	19246667	19246667	+	Silent	SNP	A	A	G	rs7212549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	59	0	0.487805	0	A|0.980;G|0.020	0.020	strong	.	B9D1	8	.	NM_015681	exon7	c.T580C	p.L194L	GCCCCAACACACC	.	PASS	Atlas-SNP
ZBED5	58486	hgsc.bcm.edu	37	11	10875701	10875701	+	Silent	SNP	A	A	G	rs2232922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	48	120	0	0.417391	0	A|0.896;G|0.104	0.104	strong	.	ZBED5	50	.	NM_021211	exon3	c.T792C	p.V264V	TCTACAAACAAGC	.	PASS	Atlas-SNP
ZNF34	80778	hgsc.bcm.edu	37	8	145999080	145999080	+	Silent	SNP	G	G	A	rs7845196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	85	144	0	0.52795	0	G|0.927;A|0.073	0.073	strong	.	ZNF34	38	.	NM_030580	exon6	c.C1254T	p.P418P	TTTATAGGGTTTC	.	PASS	Atlas-SNP
LPCAT3	10162	hgsc.bcm.edu	37	12	7125672	7125672	+	Silent	SNP	C	C	G	rs61733160	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	50	93	0	0.462963	0	C|0.950;G|0.050	0.050	strong	.	LPCAT3	33	.	NM_005768	exon1	c.G57C	p.L19L	CGACTGCAGAACC	.	PASS	Atlas-SNP
KRT33A	3883	hgsc.bcm.edu	37	17	39502398	39502398	+	Silent	SNP	A	A	G	rs16966703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	190	142	0	1	0	A|0.854;G|0.146	0.146	strong	.	KRT33A	53	.	NM_004138	exon7	c.T1188C	p.C396C	AGGCCCACACCGA	.	PASS	Atlas-SNP
ANKZF1	55139	hgsc.bcm.edu	37	2	220097257	220097257	+	Missense_Mutation	SNP	G	G	C	rs61747682	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	69	93	0	0.589744	0	G|0.960;C|0.040	0.040	strong	.	ANKZF1	45	.	NM_001042410	exon5	c.G410C	p.S137T	CAGCCAGTGAGGA	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261793	39261793	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	14	115	0	0.184211	0	.	.	none	.	KRTAP4-9	110	.	NM_001146041	exon1	c.G153A	p.R51R	CTGCAGGCCCCAG	.	PASS	Atlas-SNP
ZNF157	7712	hgsc.bcm.edu	37	X	47272970	47272970	+	Missense_Mutation	SNP	A	A	G	rs61736398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	53	150	0	0.381295	0	A|0.984;G|0.016	0.016	strong	.	ZNF157	46	.	NM_003446	exon4	c.A1498G	p.T500A	CGTTGTACAATGA	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2428434	2428434	+	Silent	SNP	G	G	A	rs369339407		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	70	101	0	0.569106	0	.	.	weak	.	TRPM5	86	.	NM_014555	exon20	c.C3033T	p.A1011A	GGGCGGGGCCAGG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941617	22941617	+	Missense_Mutation	SNP	T	T	C	rs58653025	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	39	32	1	1	0.03125	T|0.811;C|0.189	0.189	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon4	c.A1094G	p.E365G	TTCTCTTCAGTAT	.	scavenged	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18735947	18735947	+	Missense_Mutation	SNP	T	T	C	rs7125943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	122	0	1	0	T|0.224;C|0.776	0.776	strong	.	IGSF22	211	.	NM_173588	exon13	c.A1675G	p.M559V	TCTGCATGCCTGG	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55955610	55955610	+	Missense_Mutation	SNP	C	C	T	rs10825269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	34	70	0	0.395349	0	C|0.772;T|0.228	0.228	strong	.	PCDH15	1715	.	NM_001142763	exon12	c.G1153A	p.G385S	GTAGACCGGCAAA	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765627	66765627	+	Silent	SNP	G	G	A	rs6152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	79	0	1	0	G|0.700;A|0.300	0.300	strong	.	AR	249	.	NM_000044	exon1	c.G639A	p.E213E	GAGGGAGGCCTCG	.	PASS	Atlas-SNP
USP33	23032	hgsc.bcm.edu	37	1	78201745	78201745	+	Silent	SNP	G	G	T	rs2296227	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	155	161	0	1	0	G|0.550;T|0.450	0.450	strong	.	USP33	87	.	NM_201626	exon7	c.C543A	p.A181A	ACCTCTGGCCCTA	.	PASS	Atlas-SNP
ZNF613	79898	hgsc.bcm.edu	37	19	52448669	52448669	+	Silent	SNP	G	G	C	rs11880193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	150	168	1	1	0.00595238	G|0.841;C|0.159	0.159	strong	.	ZNF613	62	.	NM_001031721	exon6	c.G1533C	p.P511P	GAGACCGTATGGA	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79030346	79030346	+	Missense_Mutation	SNP	A	A	G	rs16877151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	214	224	0	0.990741	0	A|0.702;G|0.298	0.298	strong	.	CMYA5	643	.	NM_153610	exon2	c.A5758G	p.S1920G	TCCTCTAGCAGCA	.	PASS	Atlas-SNP
OR2S2	56656	hgsc.bcm.edu	37	9	35957728	35957728	+	Missense_Mutation	SNP	C	C	T	rs2233563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	57	103	0	0.57	0	C|0.975;T|0.025	0.025	strong	.	OR2S2	46	.	NM_019897	exon1	c.G368A	p.R123H	ACATAGCGATCAA	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9543622	9543622	+	Missense_Mutation	SNP	C	C	T	rs2297345	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	56	104	0	0.57732	0	C|0.503;T|0.497	0.497	strong	.	PAK7	194	.	NM_177990	exon6	c.G1532A	p.S511N	TAGCTGCTGTACA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268513	1268513	+	Missense_Mutation	SNP	G	G	C	rs2943529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	715	422	476	0	0.59021	0	G|0.497;C|0.503	0.503	strong	.	MUC5B	473	.	NM_002458	exon31	c.G10403C	p.R3468P	CGGTGCGCACAGC	.	PASS	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	37	3	10413715	10413715	+	Silent	SNP	G	G	A	rs2289274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	143	261	1	0.483108	0.00383142	G|0.752;A|0.248	0.248	strong	ATP2B2_ENST00000360273,right_lower_lobe,carcinoma,-1,3	ATP2B2	304	3	NM_001001331	exon12	c.C1437T	p.N479N	TACCAGGTTGTTG	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87696476	87696476	+	Silent	SNP	G	G	A	rs12499471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	69	136	0	0.456954	0	G|0.906;A|0.094	0.094	strong	.	PTPN13	203	.	NM_080685	exon34	c.G5676A	p.T1892T	ACTAACGTGCAAC	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232942251	232942251	+	Silent	SNP	A	A	G	rs12048236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	69	0	1	0	A|0.885;G|0.115	0.115	strong	KIAA1383_ENST00000418460,NS,carcinoma,0,1	.	.	1	NM_019090	exon1	c.A1482G	p.L494L	TTGTCTAAAGCAT	.	PASS	Atlas-SNP
OR14A16	284532	hgsc.bcm.edu	37	1	247978768	247978768	+	Silent	SNP	G	G	A	rs61740923	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	84	191	0	0.413793	0	G|0.986;A|0.014	0.014	strong	.	OR14A16	90	.	NM_001001966	exon1	c.C264T	p.N88N	AATGGAGTTGTTG	.	PASS	Atlas-SNP
GDF5	8200	hgsc.bcm.edu	37	20	34022344	34022344	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	4	97	0	0.0454545	0	.	.	none	.	GDF5	66	.	NM_000557	exon2	c.G869A	p.G290D	TCCCAGCCAGATC	.	PASS	Atlas-SNP
PMS2	5395	hgsc.bcm.edu	37	7	6026787	6026787	+	Missense_Mutation	SNP	C	C	T	rs115052399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	89	0	0.470588	0	C|0.995;T|0.005	0.005	strong	.	PMS2	88	.	NM_000535	exon11	c.G1609A	p.E537K	CTTTCTCCTGAGA	.	PASS	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55183203	55183203	+	Silent	SNP	T	T	C	rs2230772	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	97	170	0	0.507853	0	T|0.554;C|0.446	0.446	strong	.	AKAP1	73	.	NM_001242902	exon3	c.T378C	p.D126D	CAGAGATGACAGT	.	PASS	Atlas-SNP
C4orf40	401137	hgsc.bcm.edu	37	4	71024552	71024552	+	Missense_Mutation	SNP	C	C	G	rs143985138	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	136	325	0	0.448845	0	C|0.987;G|0.013	0.013	strong	.	C4orf40	19	.	NM_214711	exon3	c.C583G	p.P195A	CCTTCACCAGCTG	.	PASS	Atlas-SNP
PARK2	5071	hgsc.bcm.edu	37	6	162475167	162475167	+	Missense_Mutation	SNP	T	T	G	rs9456735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	53	98	0	0.546392	0	T|0.977;G|0.023	0.023	strong	.	PARK2	96	.	NM_004562	exon5	c.A574C	p.M192L	CACTCATCCGGTT	.	PASS	Atlas-SNP
MRPL9	65005	hgsc.bcm.edu	37	1	151735545	151735545	+	Silent	SNP	A	A	G	rs1196455	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	95	208	0	0.489691	0	A|0.908;G|0.092	0.092	strong	.	MRPL9	21	.	NM_031420	exon2	c.T231C	p.H77H	GACGCGATGTCGC	.	PASS	Atlas-SNP
REL	5966	hgsc.bcm.edu	37	2	61148988	61148988	+	Missense_Mutation	SNP	C	C	G	rs34661029	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	132	105	0	1	0	C|0.993;G|0.007	0.007	strong	.	REL	48	.	NM_002908	exon11	c.C1178G	p.P393R	CTGGGCCCATCTC	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1640793	1640793	+	Silent	SNP	C	C	T	rs8077638	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	62	191	0	0.405229	0	C|0.789;T|0.211	0.211	strong	WDR81_ENST00000437219,colon,carcinoma,0,6	WDR81	180	6	NM_001163809	exon10	c.C5640T	p.S1880S	CGGCAGCGAGGTG	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25672955	25672955	+	Missense_Mutation	SNP	C	C	T	rs35450203	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	89	158	0	0.559748	0	C|0.980;T|0.020	0.020	strong	.	IFLTD1	121	.	NM_001145728	exon7	c.G853A	p.A285T	CGTCAGCATCTAA	.	PASS	Atlas-SNP
MB21D1	115004	hgsc.bcm.edu	37	6	74138503	74138503	+	Silent	SNP	G	G	A	rs73754628	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	81	115	0	0.623077	0	G|0.947;A|0.053	0.053	strong	.	MB21D1	33	.	NM_138441	exon4	c.C1146T	p.I382I	CTTTTCGATGTGA	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133789790	133789790	+	Missense_Mutation	SNP	G	G	C	rs200373794	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	46	92	0	0.505495	0	.	.	weak	.	IGSF9B	290	.	NM_014987	exon18	c.C3830G	p.T1277S	GCCAGAGTGGTGA	.	PASS	Atlas-SNP
ZNF280B	140883	hgsc.bcm.edu	37	22	22842484	22842484	+	Missense_Mutation	SNP	C	C	T	rs57235089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	110	286	0	0.413534	0	C|0.973;T|0.027	0.027	strong	.	ZNF280B	67	.	NM_080764	exon4	c.G1240A	p.V414I	CAAAGACCGACGA	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5212380	5212380	+	Silent	SNP	C	C	T	rs1064300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	47	102	0	0.398305	0	C|0.669;T|0.331	0.331	strong	.	PTPRS	169	.	NM_002850	exon31	c.G4737A	p.P1579P	ATCTGGCGGGTTG	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152325456	152325456	+	Silent	SNP	G	G	A	rs73007787	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	399	226	404	1	0.566416	0.00247525	G|0.940;A|0.060	0.060	strong	.	FLG2	431	.	NM_001014342	exon3	c.C4806T	p.A1602A	AGATCCGGCTTGG	.	PASS	Atlas-SNP
CFTR	1080	hgsc.bcm.edu	37	7	117307108	117307108	+	Silent	SNP	G	G	A	rs1800136	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	84	169	0	0.446809	0	G|0.790;A|0.210	0.210	strong	.	CFTR	171	.	NM_000492	exon27	c.G4389A	p.Q1463Q	GCCCCAGATTGCT	.	PASS	Atlas-SNP
MMP2	4313	hgsc.bcm.edu	37	16	55523705	55523705	+	Silent	SNP	T	T	C	rs243849	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	81	0	1	0	T|0.213;C|0.787	0.787	strong	.	MMP2	119	.	NM_004530	exon7	c.T1149C	p.D383D	CGATGATGACCGC	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151970811	151970811	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	801	39	725	0	0.0486891	0	.	.	none	.	MLL3	1564	.	NM_170606	exon7	c.A991G	p.I331V	GGTCAATGTGTTC	.	PASS	Atlas-SNP
EEA1	8411	hgsc.bcm.edu	37	12	93196422	93196422	+	Missense_Mutation	SNP	T	T	G	rs10745623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	70	0	1	0	T|0.364;G|0.636	0.636	strong	.	EEA1	104	.	NM_003566	exon19	c.A2428C	p.K810Q	GGATTTTTTTTTC	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3214939	3214939	+	Missense_Mutation	SNP	C	C	A	rs199766052	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	22	0	0.5	0	.	.	weak	.	PITRM1	109	.	NM_014889	exon1	c.G26T	p.G9V	CACAGGCCCTGCC	.	PASS	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120386922	120386922	+	Splice_Site	SNP	A	A	T	rs12068863	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	40	83	0	0.366972	0	A|0.957;T|0.043	0.043	strong	.	NBPF7	46	.	NM_001047980	exon2	c.235+2T>A	.	GATCTTACTGTAT	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74275174	74275174	+	Silent	SNP	C	C	T	rs73951129	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	65	121	0	0.53719	0	C|0.984;T|0.016	0.016	strong	.	TET3	101	.	NM_144993	exon1	c.C1725T	p.L575L	AGAGCTCATCCGG	.	PASS	Atlas-SNP
RELA	5970	hgsc.bcm.edu	37	11	65422374	65422374	+	Silent	SNP	C	C	T	rs7116571	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	69	131	0	0.463087	0	C|0.965;T|0.035	0.035	strong	.	RELA	44	.	NM_021975	exon11	c.G1131A	p.S377S	CAAGGCCGAGGCC	.	PASS	Atlas-SNP
CHST5	23563	hgsc.bcm.edu	37	16	75563352	75563352	+	Missense_Mutation	SNP	C	C	T	rs7206332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	58	0	0.490909	0	C|0.974;T|0.026	0.026	strong	CHST5,middle_lobe,carcinoma,+1,1	CHST5	47	1	NM_024533	exon3	c.G931A	p.A311T	TGAAGGCGTAGAG	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	148	174	0	0.993289	0	T|0.194;C|0.806	0.806	strong	WWP2,NS,carcinoma,0,1	WWP2	88	1	NM_001270454	exon17	c.T1707C	p.H569H	GTCTCATGAGGTG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	97	175	0	0.477833	0	C|0.803;T|0.197	0.197	strong	FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	NM_025074	exon66	c.C10377T	p.T3459T	TGTAACCGCTGAC	.	PASS	Atlas-SNP
CYTH2	9266	hgsc.bcm.edu	37	19	48977479	48977479	+	Silent	SNP	C	C	T	rs61748773	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	194	158	0	1	0	C|0.937;T|0.063	0.063	strong	.	CYTH2	33	.	NM_017457	exon7	c.C588T	p.N196N	GCTCAACACCAGT	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108143299	108143299	+	Missense_Mutation	SNP	A	A	G	rs3092857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	51	203	0	0.359155	0	A|0.985;G|0.015	0.015	strong	ATM_ENST00000278616,colon,carcinoma,-1,7	ATM	1657	7	NM_000051	exon21	c.A3118G	p.M1040V	GTAAGAATGGCCC	.	PASS	Atlas-SNP
TGFBI	7045	hgsc.bcm.edu	37	5	135392482	135392482	+	Missense_Mutation	SNP	T	T	G	rs200219644	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	117	178	0	0.541667	0	.	.	weak	.	TGFBI	76	.	NM_000358	exon12	c.T1676G	p.L559W	GACTCTTGGGTAA	.	PASS	Atlas-SNP
EXOC3	11336	hgsc.bcm.edu	37	5	453583	453583	+	Silent	SNP	C	C	T	rs6871053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	76	128	0	0.517007	0	C|0.972;T|0.028	0.028	strong	.	EXOC3	54	.	NM_007277	exon4	c.C463T	p.L155L	GACGGGCTGATGT	.	PASS	Atlas-SNP
C2orf44	80304	hgsc.bcm.edu	37	2	24260862	24260862	+	Silent	SNP	A	A	G	rs115270382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	72	126	0	0.461538	0	A|0.992;G|0.008	0.008	strong	.	C2orf44	56	.	NM_025203	exon2	c.T1503C	p.S501S	CAGAGGACTCTGG	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104385646	104385646	+	Silent	SNP	A	A	G	rs138253972	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	121	169	0	0.661202	0	A|1.000;G|0.000	0.000	strong	.	GRIN3A	186	.	NM_133445	exon5	c.T2568C	p.D856D	GTCAGCATCTATT	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73796683	73796683	+	Missense_Mutation	SNP	T	T	C	rs1095423	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	47	97	0	0.465347	0	T|0.951;C|0.049	0.049	strong	.	C2CD3	288	.	NM_015531	exon21	c.A3890G	p.Y1297C	TCATGATAGACAG	.	PASS	Atlas-SNP
ZNF284	342909	hgsc.bcm.edu	37	19	44590753	44590753	+	Silent	SNP	T	T	C	rs114253786	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	74	196	0	0.496644	0	T|0.995;C|0.005	0.005	strong	.	ZNF284	38	.	NM_001037813	exon5	c.T1122C	p.N374N	TTGTAATGTATGT	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617105	183617105	+	Missense_Mutation	SNP	A	A	G	rs1174658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	205	415	0	0.498783	0	A|0.606;G|0.394	0.394	strong	APOBEC4,NS,carcinoma,0,1	APOBEC4	45	1	NM_203454	exon2	c.T812C	p.F271S	TGAAAAAACTGTC	.	PASS	Atlas-SNP
ILK	3611	hgsc.bcm.edu	37	11	6630833	6630833	+	Silent	SNP	G	G	A	rs1043390	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	117	204	0	0.458824	0	G|0.669;A|0.331	0.331	strong	.	ILK	41	.	NM_001014794	exon9	c.G819A	p.P273P	GATGCCGTATGGA	.	PASS	Atlas-SNP
ALOX15	246	hgsc.bcm.edu	37	17	4539171	4539171	+	Silent	SNP	G	G	T	rs11568113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	77	160	0	0.513333	0	G|0.973;T|0.027	0.027	strong	.	ALOX15	70	.	NM_001140	exon8	c.C1044A	p.R348R	AGAGCTGCGCACC	.	PASS	Atlas-SNP
MNT	4335	hgsc.bcm.edu	37	17	2298615	2298615	+	Silent	SNP	T	T	C	rs7213000	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	30	71	0	0.461538	0	T|0.869;C|0.131	0.131	strong	.	MNT	35	.	NM_020310	exon2	c.A207G	p.P69P	AGCCGGTGGAGAC	.	PASS	Atlas-SNP
BCAS1	8537	hgsc.bcm.edu	37	20	52675188	52675188	+	Missense_Mutation	SNP	G	G	T	rs394732	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	30	78	0	0.535714	0	A|0.003;C|0.003	.	strong	.	BCAS1	77	.	NM_003657	exon2	c.C70A	p.Q24K	CTACCTGGTAAGT	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44974966	44974966	+	Missense_Mutation	SNP	G	G	A	rs1959379	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	61	134	0	0.451852	0	G|0.811;A|0.189	0.189	strong	.	FSCB	173	.	NM_032135	exon1	c.C1225T	p.P409S	TAGCTGGGGCCTC	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73727509	73727509	+	Missense_Mutation	SNP	T	T	G	rs177389	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	50	0	1	0	C|0.003;G|0.633;T|0.364	0.633	strong	.	PAPLN	180	.	NM_173462	exon16	c.T1997G	p.M666R	GGGGCATGCCCAG	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43927568	43927568	+	Silent	SNP	C	C	T	rs17031299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	90	171	0	0.520231	0	C|0.973;T|0.027	0.027	strong	.	PLEKHH2	156	.	NM_172069	exon8	c.C1471T	p.L491L	CTTGATCTAGTTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408182	105408182	+	Missense_Mutation	SNP	T	T	G	rs9672139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	180	204	0	0.994475	0	T|0.501;G|0.499	0.499	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A13606C	p.M4536L	CGGGCATGTGGCC	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	37	17	35470031	35470031	+	Silent	SNP	T	T	G	rs55811414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	57	126	0	0.459677	0	G|0.034;T|0.966	0.034	strong	.	ACACA	395	.	NM_198834	exon51	c.A6444C	p.R2148R	GCTTTCTCGGTCA	.	PASS	Atlas-SNP
ARRDC2	27106	hgsc.bcm.edu	37	19	18123738	18123738	+	Missense_Mutation	SNP	T	T	C	rs7259041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	41	0	0.509091	0	T|0.697;C|0.303	0.303	strong	.	ARRDC2	60	.	NM_015683	exon8	c.T1187C	p.L396P	ACCCACTCTTGGG	.	PASS	Atlas-SNP
GIMAP2	26157	hgsc.bcm.edu	37	7	150390255	150390255	+	Missense_Mutation	SNP	T	T	C	rs115945256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	55	119	0	0.436508	0	T|0.995;C|0.005	0.005	strong	.	GIMAP2	39	.	NM_015660	exon3	c.T881C	p.M294T	ACAGCATGTGCAA	.	PASS	Atlas-SNP
RNF122	79845	hgsc.bcm.edu	37	8	33416222	33416222	+	Silent	SNP	C	C	T	rs3735951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	66	70	0	0.985075	0	C|0.357;T|0.643	0.643	strong	.	RNF122	17	.	NM_024787	exon2	c.G93A	p.Q31Q	AAGGTCCTGGAAA	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108487330	108487330	+	Missense_Mutation	SNP	A	A	G	rs7562548	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1647	1227	1693	1	0.744991	0.000590667	G|1.000;|0.000	1.000	weak	RGPD4,NS,carcinoma,0,1	RGPD4	112	1	NM_182588	exon20	c.A2870G	p.N957S	AGAAGAATGGCCG	.	scavenged	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535830	88535830	+	Silent	SNP	T	T	C	rs202057495		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	56	345	0	0.154696	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.T2016C	p.S672S	CAGCAGTGATAGC	.	PASS	Atlas-SNP
C2orf81	388963	hgsc.bcm.edu	37	2	74641624	74641624	+	Silent	SNP	G	G	C	rs2240444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	158	152	0	1	0	G|0.496;C|0.504	0.504	strong	.	C2orf81	23	.	NM_001145054	exon4	c.C1599G	p.P533P	CAACACGGGCTTC	.	PASS	Atlas-SNP
CREB3L1	90993	hgsc.bcm.edu	37	11	46339011	46339011	+	Missense_Mutation	SNP	G	G	A	rs35652107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	33	58	0	0.589286	0	G|0.914;A|0.086	0.086	strong	.	CREB3L1	30	.	NM_052854	exon10	c.G1231A	p.A411T	CTGGCCGCAGACG	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127670412	127670412	+	Silent	SNP	T	T	G	rs28763943	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	30	62	0	0.441176	0	T|0.975;G|0.025	0.025	strong	.	FBN2	858	.	NM_001999	exon31	c.A4098C	p.T1366T	CCTACCTGTACAT	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11725908	11725908	+	Missense_Mutation	SNP	G	G	A	rs6744817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	147	138	0	0.993243	0	G|0.906;A|0.094	0.094	strong	.	GREB1	308	.	NM_148903	exon9	c.G1036A	p.V346M	TCCTGCGTGCCGC	.	PASS	Atlas-SNP
TOR1A	1861	hgsc.bcm.edu	37	9	132585058	132585058	+	Silent	SNP	G	G	A	rs2296793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	63	202	0	0.302885	0	G|0.763;A|0.237	0.237	strong	TOR1A,NS,carcinoma,0,1	TOR1A	36	1	NM_000113	exon2	c.C246T	p.A82A	AAACACGGCATTT	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47545889	47545889	+	Silent	SNP	C	C	G	rs61735829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	86	148	0	0.518072	0	C|0.982;G|0.018	0.018	strong	COL6A2_ENST00000357838,NS,carcinoma,+2,3	COL6A2	351	3	NM_058175	exon26	c.C2160G	p.R720R	CCGGCGCCAGAAG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124369744	124369744	+	Silent	SNP	C	C	T	rs12106716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	22	75	0	0.305556	0	C|0.888;T|0.112	0.112	strong	.	KALRN	556	.	NM_001024660	exon38	c.C5751T	p.N1917N	TAAAAACCCAGAA	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27460968	27460968	+	Silent	SNP	A	A	G	rs1141313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	194	170	0	0.994872	0	A|0.568;G|0.432	0.432	strong	CAD,NS,carcinoma,+1,1	CAD	199	1	NM_004341	exon30	c.A4773G	p.A1591A	TCACGCAGAGCAG	.	PASS	Atlas-SNP
FNDC7	163479	hgsc.bcm.edu	37	1	109270563	109270563	+	Silent	SNP	T	T	C	rs4484951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	105	202	0	0.5	0	T|0.959;C|0.041	0.041	strong	.	FNDC7	113	.	NM_001144937	exon7	c.T1245C	p.N415N	GTGCAATGACACT	.	PASS	Atlas-SNP
SLC17A5	26503	hgsc.bcm.edu	37	6	74354175	74354175	+	Silent	SNP	C	C	T	rs472294	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	61	141	0	0.469231	0	C|0.888;T|0.112	0.112	strong	.	SLC17A5	42	.	NM_012434	exon2	c.G246A	p.A82A	TGGACACGCCTTG	.	PASS	Atlas-SNP
ZNF841	284371	hgsc.bcm.edu	37	19	52569479	52569479	+	Silent	SNP	G	G	A	rs61738706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	21	48	0	0.396226	0	G|0.979;A|0.021	0.021	strong	.	ZNF841	183	.	NM_001136499	exon7	c.C1656T	p.Y552Y	TCCACCGTAATTA	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	62	121	0	0.534483	0	A|0.952;G|0.048	0.048	strong	.	TH	43	.	NM_199292	exon3	c.T303C	p.A101A	GGCCACAGCCTCC	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27250823	27250823	+	Silent	SNP	T	T	C	rs3764108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	39	95	0	0.506494	0	T|0.660;C|0.340	0.340	strong	.	WASF3	68	.	NM_006646	exon7	c.T678C	p.H226H	GTACCATGGAGCG	.	PASS	Atlas-SNP
POLR3D	661	hgsc.bcm.edu	37	8	22107707	22107707	+	Silent	SNP	C	C	T	rs34435413	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	52	97	0	0.464286	0	C|0.993;T|0.007	0.007	strong	.	POLR3D	26	.	NM_001722	exon8	c.C1041T	p.D347D	TCTGGACGTGACC	.	PASS	Atlas-SNP
NECAB3	63941	hgsc.bcm.edu	37	20	32248088	32248088	+	Silent	SNP	C	C	T	rs146604647	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	23	69	0	0.425926	0	C|0.996;T|0.004	0.004	strong	.	NECAB3	27	.	NM_031232	exon6	c.G501A	p.L167L	GGCCTCCAGGGTA	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	37	15	90145118	90145118	+	Silent	SNP	T	T	A	rs202042800	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	80	0	0.486486	0	T|1.000;A|0.000	0.000	strong	.	.	.	.	NM_152259	exon12	c.T2478A	p.P826P	TGTGCCTTTTTTG	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11550413	11550413	+	Silent	SNP	T	T	C	rs61745426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	59	129	0	0.450382	0	T|0.988;C|0.012	0.012	strong	.	DNAH9	695	.	NM_001372	exon12	c.T1995C	p.D665D	TGAGGATTGGTGC	.	PASS	Atlas-SNP
IGSF9	57549	hgsc.bcm.edu	37	1	159900655	159900655	+	Missense_Mutation	SNP	G	G	A	rs140306211	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	71	152	0	0.486301	0	G|0.994;A|0.006	0.006	strong	.	IGSF9	123	.	NM_001135050	exon14	c.C1640T	p.A547V	CGCTTGGCCCTGG	.	PASS	Atlas-SNP
SLC13A1	6561	hgsc.bcm.edu	37	7	122787306	122787306	+	Missense_Mutation	SNP	G	G	A	rs10231144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	79	95	0	0.580882	0	G|0.989;A|0.011	0.011	strong	.	SLC13A1	110	.	NM_022444	exon7	c.C719T	p.T240M	AAACACGTAAGTT	.	PASS	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140802723	140802723	+	Silent	SNP	C	C	T	rs62378456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	84	115	0	0.515337	0	C|0.963;T|0.037	0.037	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.C1929T	p.L643L	GAGCCTCGTGGTG	.	PASS	Atlas-SNP
SGCD	6444	hgsc.bcm.edu	37	5	156184786	156184786	+	Silent	SNP	G	G	A	rs187204080	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	98	201	0	0.451613	0	G|0.998;A|0.002	0.002	strong	.	SGCD	52	.	NM_172244	exon8	c.G770A	p.X257X	CTGGTTGACCTCG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44890817	44890817	+	Silent	SNP	G	G	A	rs73039937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	79	211	0	0.393035	0	G|0.932;A|0.068	0.068	strong	.	ZNF285	86	.	NM_152354	exon4	c.C1590T	p.H530H	TCTGAGGTGAACA	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321686	52321686	+	Missense_Mutation	SNP	C	C	T	rs11985241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	47	52	0	0.701493	0	C|0.853;T|0.147	0.147	strong	.	PXDNL	414	.	NM_144651	exon17	c.G2498A	p.S833N	ACGGAGCTGCACG	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	37	1	57422511	57422511	+	Missense_Mutation	SNP	C	C	T	rs12067507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	63	109	0	0.525	0	C|0.944;T|0.056	0.056	strong	C8B,caecum,carcinoma,0,1	C8B	107	1	NM_000066	exon3	c.G322A	p.E108K	AGTCTTCGACTTC	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89645345	89645345	+	Missense_Mutation	SNP	C	C	A	rs9944362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	58	78	0	0.58	0	C|0.998;A|0.002	0.002	strong	.	CPNE7	56	.	NM_014427	exon3	c.C438A	p.H146Q	TAAGCACTTCCTG	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579068	55579068	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	8	225	0	0.0373832	0	.	.	none	OR5L1,colon,carcinoma,0,3	OR5L1	145	3	NM_001004738	exon1	c.C126T	p.N42N	AGCCAACCTGGGC	.	scavenged	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57077464	57077464	+	Silent	SNP	T	T	C	rs10896602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	92	173	0	0.505495	0	T|0.650;C|0.350	0.350	strong	.	TNKS1BP1	148	.	NM_033396	exon6	c.A2721G	p.Q907Q	CAAATCTTGGCCC	.	PASS	Atlas-SNP
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	131	254	0	0.519841	0	A|0.547;G|0.453	0.453	strong	VAMP8,NS,carcinoma,0,1	VAMP8	10	1	NM_003761	exon3	c.A201G	p.R67R	GGCTCGAAAATTC	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	102	197	0	0.495146	0	C|0.892;G|0.108	0.108	strong	.	FANCA	99	.	NM_000135	exon38	c.G3807C	p.L1269L	TGACGACAGCAGG	.	PASS	Atlas-SNP
PCDHGB7	56099	hgsc.bcm.edu	37	5	140797630	140797630	+	Silent	SNP	G	G	T	rs2015825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	167	146	0	0.982353	0	G|0.500;T|0.500	0.500	strong	.	PCDHGB7	117	.	NM_018927	exon1	c.G204T	p.V68V	GCGAGTGAGCGCG	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106778	55106778	+	Missense_Mutation	SNP	G	G	A	rs10418391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	408	194	402	0	0.47549	0	G|0.857;A|0.143	0.143	strong	LILRA1,NS,malignant_melanoma,+1,2	LILRA1	105	2	NM_006863	exon5	c.G572A	p.R191H	CGAGTCGCAGGTG	.	PASS	Atlas-SNP
CCBL2	56267	hgsc.bcm.edu	37	1	89426956	89426956	+	Silent	SNP	C	C	T	rs12063768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	50	81	0	0.555556	0	C|0.961;T|0.039	0.039	strong	.	CCBL2	138	.	NM_001008661	exon8	c.G681A	p.E227E	CAGTTCCTCTCTG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16769273	16769273	+	Missense_Mutation	SNP	G	G	A	rs11750538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	96	70	0	0.989691	0	G|0.492;A|0.507	0.507	strong	.	MYO10	198	.	NM_012334	exon10	c.C970T	p.R324W	CTTCCCGAACTTC	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36353880	36353880	+	Missense_Mutation	SNP	G	G	A	rs35775934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	65	0	1	0	G|0.959;A|0.041	0.041	strong	KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	NM_199180	exon13	c.G1667A	p.S556N	GCAGCAGCGACGG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	137	206	0	0.590517	0	0|0.015;A|0.479	0.479	strong	.	GPR112	459	.	NM_153834	exon6	c.C3638A	p.T1213N	ATGAGACCACACC	.	PASS	Atlas-SNP
S100A3	6274	hgsc.bcm.edu	37	1	153520203	153520203	+	Silent	SNP	G	G	A	rs41265164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	74	156	0	0.506849	0	A|0.147;C|0.000;G|0.853;T|0.000	0.147	strong	.	S100A3	7	.	NM_002960	exon3	c.C261T	p.H87H	GTACTCGTGGCAG	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031615	32031615	+	Missense_Mutation	SNP	A	A	C	rs13064905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	127	380	0	0.40836	0	A|0.614;C|0.386	0.386	strong	.	ZNF860	96	.	NM_001137674	exon2	c.A1044C	p.E348D	TTGTGAAAAGGCT	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563173	140563173	+	Missense_Mutation	SNP	G	G	T	rs28664170	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	60	120	0	0.472441	0	C|0.000;G|0.818;T|0.182	0.182	strong	.	PCDHB16	159	.	NM_020957	exon1	c.G1039T	p.V347L	CCACAGGTGACCA	.	PASS	Atlas-SNP
ORM2	5005	hgsc.bcm.edu	37	9	117094159	117094159	+	Missense_Mutation	SNP	G	G	A	rs148221879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	152	194	0	0.706977	0	G|0.997;A|0.003	0.003	strong	.	ORM2	13	.	NM_000608	exon5	c.G490A	p.D164N	GCTCTCGACTGCT	.	PASS	Atlas-SNP
CCDC94	55702	hgsc.bcm.edu	37	19	4254375	4254375	+	Silent	SNP	C	C	T	rs11085068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	112	1	1	0.00892857	C|0.632;T|0.368	0.368	strong	CCDC94,NS,carcinoma,0,1	CCDC94	28	1	NM_018074	exon4	c.C294T	p.Y98Y	AGACTACACCATG	.	PASS	Atlas-SNP
CLASRP	11129	hgsc.bcm.edu	37	19	45561014	45561014	+	Silent	SNP	A	A	G	rs76953457	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	29	75	0	0.414286	0	A|0.990;G|0.010	0.010	strong	.	CLASRP	44	.	NM_007056	exon7	c.A471G	p.A157A	GCTGGCAGAGAAG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	73	122	0	0.493243	0	C|0.621;T|0.379	0.379	strong	.	ZNF835	106	.	NM_001005850	exon2	c.G85A	p.E29K	GGTTTTCCTGCAG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940474	144940474	+	Silent	SNP	C	C	T	rs56015972	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	15	164	0	0.0815217	0	C|0.500;T|0.500	0.500	weak	EPPK1,right_lower_lobe,carcinoma,-2,2	EPPK1	199	2	NM_031308	exon1	c.G6948A	p.G2316G	CTGCTGCCCGGTG	.	PASS	Atlas-SNP
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	127	126	0	0.984496	0	G|0.704;A|0.296	0.296	strong	TCN1,NS,carcinoma,0,1	TCN1	64	1	NM_001062	exon6	c.C846T	p.S282S	TGGATTGCTGAAT	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27462076	27462076	+	Silent	SNP	C	C	T	rs3739092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	59	0	0.477612	0	C|0.773;T|0.227	0.227	strong	.	CAD	199	.	NM_004341	exon32	c.C5229T	p.P1743P	CCTGCCCCCGCAG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8175868	8175868	+	Silent	SNP	C	C	T	rs114026601	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	68	91	0	0.623853	0	C|0.988;T|0.012	0.012	strong	.	.	.	.	NM_001080826	exon5	c.G4017A	p.S1339S	CTCCTCCGAGGTG	.	PASS	Atlas-SNP
FBXO41	150726	hgsc.bcm.edu	37	2	73492614	73492614	+	Missense_Mutation	SNP	A	A	T	rs526106	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	10	36	0	0.384615	0	A|0.673;T|0.327	0.327	strong	.	FBXO41	82	.	NM_001080410	exon4	c.T1360A	p.S454T	GCTGGGACCGCTC	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71577169	71577169	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	2	95	0	0.016129	0	.	.	none	ZNF638,caecum,carcinoma,+1,1	ZNF638	179	1	NM_014497	exon2	c.T1085C	p.V362A	CTAACGTACATGT	.	scavenged	Atlas-SNP
CASP8AP2	9994	hgsc.bcm.edu	37	6	90565242	90565242	+	Silent	SNP	A	A	G	rs369328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	75	81	0	1	0	G|0.396;N|0.000	0.396	strong	.	CASP8AP2	108	.	NM_001137667	exon5	c.A279G	p.K93K	GAAAAAATTTAAA	.	PASS	Atlas-SNP
LPIN1	23175	hgsc.bcm.edu	37	2	11913806	11913806	+	Silent	SNP	G	G	A	rs59909741	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	41	90	0	0.445652	0	G|0.937;A|0.063	0.063	strong	.	LPIN1	99	.	NM_001261428	exon6	c.G804A	p.L268L	CTCCCTGGCTGTG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18731905	18731905	+	Silent	SNP	T	T	A	rs114511413	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	53	133	0	0.481818	0	T|0.991;A|0.009	0.009	strong	.	IGSF22	211	.	NM_173588	exon17	c.A2670T	p.P890P	GCTGGATGGCACA	.	PASS	Atlas-SNP
FAM208A	23272	hgsc.bcm.edu	37	3	56658871	56658871	+	Missense_Mutation	SNP	T	T	C	rs2291498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	82	177	0	0.42487	0	T|0.785;C|0.215	0.215	strong	.	FAM208A	113	.	NM_001112736	exon22	c.A4303G	p.I1435V	AGACTATGTGTCG	.	PASS	Atlas-SNP
ZFP28	140612	hgsc.bcm.edu	37	19	57050521	57050521	+	Missense_Mutation	SNP	G	G	A	rs199655023	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	37	0	0.45614	0	.	.	weak	.	ZFP28	99	.	NM_020828	exon1	c.G134A	p.G45E	CCCGGGGAAGGCC	.	PASS	Atlas-SNP
OR2A4	79541	hgsc.bcm.edu	37	6	132021722	132021722	+	Silent	SNP	G	G	A	rs145289654	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	935	254	770	2	0.271658	0.0025974	G|0.995;A|0.005	0.005	strong	.	OR2A4	17	.	NM_030908	exon1	c.C820T	p.L274L	ACAGCAGGAGATA	.	PASS	Atlas-SNP
PRKD3	23683	hgsc.bcm.edu	37	2	37506939	37506939	+	Silent	SNP	A	A	G	rs3770761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	60	111	0	0.5	0	A|0.895;G|0.105	0.105	strong	.	PRKD3	170	.	NM_005813	exon7	c.T1122C	p.D374D	AGATGGATCCAAG	.	PASS	Atlas-SNP
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	26	40	0	0.577778	0	G|0.064;C|0.936	0.064	strong	.	ANAPC16	10	.	NM_001242546	exon5	c.C321G	p.P107P	CACCCCCTCTTCA	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21932598	21932598	+	Silent	SNP	G	G	A	rs150973141	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	50	106	0	0.438596	0	G|0.999;A|0.001	0.001	strong	.	RAP1GAP	119	.	NM_001145658	exon18	c.C1581T	p.F527F	GGGCGCGAAGCTC	.	PASS	Atlas-SNP
STAG3	10734	hgsc.bcm.edu	37	7	99799845	99799845	+	Silent	SNP	T	T	A	rs1043915	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	51	101	0	0.525773	0	T|0.679;A|0.321	0.321	strong	.	STAG3	121	.	NM_012447	exon24	c.T2445A	p.I815I	GATGATTGTTGGG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388757	1388757	+	Missense_Mutation	SNP	T	T	C	rs138170890		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	9	31	1	0.115385	0.0322581	.	.	weak	CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.T458C	p.M153T	TGCCCATGCGGAG	.	scavenged	Atlas-SNP
MRPS9	64965	hgsc.bcm.edu	37	2	105708936	105708936	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	46	81	0	0.511111	0	.	.	none	.	MRPS9	32	.	NM_182640	exon8	c.G729C	p.R243S	GCAGAGGTTTCGA	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17445710	17445710	+	Silent	SNP	C	C	T	rs5992599	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	127	208	1	0.490348	0.00480769	C|0.954;T|0.046	0.046	strong	.	GAB4	95	.	NM_001037814	exon8	c.G1422A	p.T474T	GCTCTGCGTGGAG	.	PASS	Atlas-SNP
USP44	84101	hgsc.bcm.edu	37	12	95927172	95927172	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	66	0	0.460526	0	.	.	none	.	USP44	83	.	NM_032147	exon2	c.T861C	p.V287V	CTGAAGAACAGAA	.	PASS	Atlas-SNP
DEAF1	10522	hgsc.bcm.edu	37	11	653968	653968	+	Silent	SNP	T	T	C	rs10615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	37	61	0	0.521127	0	T|0.726;C|0.274	0.274	strong	.	DEAF1	47	.	NM_021008	exon11	c.A1587G	p.Q529Q	CTTGCGTTGGCAG	.	PASS	Atlas-SNP
SETD9	133383	hgsc.bcm.edu	37	5	56205559	56205559	+	Silent	SNP	C	C	T	rs80198735	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	34	75	0	0.346939	0	C|0.987;T|0.013	0.013	strong	.	.	.	.	NM_153706	exon1	c.C87T	p.S29S	CCTAAGCCACAAC	.	PASS	Atlas-SNP
COCH	1690	hgsc.bcm.edu	37	14	31355096	31355096	+	Missense_Mutation	SNP	C	C	G	rs1045644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	82	169	0	0.503067	0	C|0.529;G|0.471	0.471	strong	.	COCH	54	.	NM_004086	exon11	c.C1055G	p.T352S	TGTGCACTCATGA	.	PASS	Atlas-SNP
RIPPLY2	134701	hgsc.bcm.edu	37	6	84563147	84563147	+	Silent	SNP	G	G	A	rs9353143	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	13	28	0	0.65	0	G|0.692;A|0.308	0.308	strong	RIPPLY2,rectum,carcinoma,0,1	RIPPLY2	17	1	NM_001009994	exon1	c.G12A	p.A4A	GAACGCGGGAGGC	.	PASS	Atlas-SNP
OR11A1	26531	hgsc.bcm.edu	37	6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	rs61978565	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	44	60	0	0.586667	0	A|0.957;G|0.043	0.043	strong	OR11A1,NS,carcinoma,0,1	OR11A1	30	1	NM_013937	exon1	c.T239C	p.M80T	TTTGGCATCACTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	799	460	714	3	0.57572	0.00420168	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.G6891C	p.E2297D	GGAGCTCTCTGCA	.	PASS	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116008497	116008497	+	Missense_Mutation	SNP	G	G	A	rs9664945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	143	208	0	0.576613	0	G|0.764;A|0.236	0.236	strong	.	VWA2	64	.	NM_001272046	exon2	c.G25A	p.A9T	CTGGAAGCCGTCT	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995868	995868	+	Silent	SNP	C	C	T	rs114806891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	18	66	0	0.327273	0	C|0.965;T|0.035	0.035	strong	.	IDUA	33	.	NM_000203	exon7	c.C891T	p.N297N	TTACAACGACGAG	.	PASS	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	94	0	0.490385	0	T|0.620;C|0.380;A|0.000	0.380	strong	.	SUN2	59	.	NM_001199579	exon16	c.A1887G	p.Q629Q	GAAGCCTTGTGGC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186043899	186043899	+	Silent	SNP	T	T	C	rs77026548	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	119	0	0.484127	0	T|0.967;C|0.033	0.033	strong	.	HMCN1	797	.	NM_031935	exon53	c.T8166C	p.N2722N	TGTTAATATTGCT	.	PASS	Atlas-SNP
AKAP11	11215	hgsc.bcm.edu	37	13	42876290	42876290	+	Silent	SNP	A	A	C	rs41288311	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	100	160	0	0.531915	0	A|0.882;C|0.118	0.118	strong	.	AKAP11	146	.	NM_016248	exon8	c.A3408C	p.T1136T	TGCTACACCACCT	.	PASS	Atlas-SNP
KLHL26	55295	hgsc.bcm.edu	37	19	18779728	18779728	+	Silent	SNP	C	C	T	rs73533829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	18	24	0	0.5	0	C|0.988;T|0.012	0.012	strong	.	KLHL26	43	.	NM_018316	exon3	c.C1521T	p.G507G	TGCCGGCGGCCGC	.	PASS	Atlas-SNP
FIGLA	344018	hgsc.bcm.edu	37	2	71012604	71012604	+	Silent	SNP	G	G	A	rs7566541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	189	170	1	0.994737	0.00588235	G|0.225;A|0.774	0.774	strong	.	FIGLA	23	.	NM_001004311	exon3	c.C552T	p.H184H	ACAAGCGTGTGCT	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500117	59500117	+	Silent	SNP	T	T	C	rs61753957	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	63	148	0	0.496063	0	T|0.912;C|0.088	0.088	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.T978C	p.I326I	CATAATTAAGGGC	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15668276	15668276	+	Missense_Mutation	SNP	G	G	A	rs763821	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	71	164	0	0.518248	0	G|0.653;A|0.347	0.347	strong	.	FHAD1	78	.	NM_052929	exon15	c.G1951A	p.G651R	ACTGCAGGAAAAG	.	PASS	Atlas-SNP
PCYT1B	9468	hgsc.bcm.edu	37	X	24637193	24637193	+	Silent	SNP	A	A	C	rs7060616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	78	159	0	0.503226	0	A|0.861;C|0.139	0.139	strong	.	PCYT1B	88	.	NM_004845	exon2	c.T126G	p.T42T	AGGTGCAGTCAGG	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31289396	31289396	+	Missense_Mutation	SNP	T	T	C	rs1143680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	93	136	0	0.611842	0	T|0.871;C|0.129	0.129	strong	.	ITGAM	137	.	NM_000632	exon12	c.T1322C	p.M441T	CTGGCATGTGGGA	.	PASS	Atlas-SNP
ARSH	347527	hgsc.bcm.edu	37	X	2933323	2933323	+	Missense_Mutation	SNP	C	C	T	rs61997197	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	123	273	1	0.437722	0.003663	C|0.952;T|0.048	0.048	strong	.	ARSH	72	.	NM_001011719	exon4	c.C653T	p.T218I	GATTTACTCGACG	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167095163	167095163	+	Missense_Mutation	SNP	G	G	C	rs267745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	47	94	0	0.474747	0	G|0.373;C|0.627	0.627	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G795C	p.E265D	CAATGAGGGCTTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682275	100682275	+	Silent	SNP	A	A	G	rs4386914	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	80	149	0	0.490798	0	A|0.835;G|0.165	0.165	strong	.	MUC17	804	.	NM_001040105	exon3	c.A7578G	p.P2526P	CACGCCAGTGGCC	.	PASS	Atlas-SNP
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12253003	12253003	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	58	76	0	0.527273	0	.	.	none	.	TNFRSF1B	28	.	NM_001066	exon6	c.G635A	p.G212E	CCCCAGGGGCAGT	.	PASS	Atlas-SNP
FOXC1	2296	hgsc.bcm.edu	37	6	1612243	1612243	+	Silent	SNP	T	T	G	rs73406891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	24	43	0	0.393443	0	T|0.963;G|0.037	0.037	strong	.	FOXC1	19	.	NM_001453	exon1	c.T1563G	p.S521S	CAACTCTCCAGTG	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50407162	50407162	+	Silent	SNP	T	T	C	rs6021437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	97	194	0	0.455399	0	T|0.668;C|0.332	0.332	strong	.	SALL4	168	.	NM_020436	exon2	c.A1860G	p.T620T	AATGGATGTGTTG	.	PASS	Atlas-SNP
TBC1D8B	54885	hgsc.bcm.edu	37	X	106083304	106083304	+	Silent	SNP	A	A	G	rs56825776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	318	338	1	1	0.00295858	A|0.923;G|0.077	0.077	strong	.	TBC1D8B	181	.	NM_198881	exon9	c.A1380G	p.S460S	ACAGTCATGGAAA	.	PASS	Atlas-SNP
GATA3	2625	hgsc.bcm.edu	37	10	8100632	8100632	+	Silent	SNP	T	T	C	rs2228254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	27	55	0	0.586957	0	T|0.959;C|0.041	0.041	strong	.	GATA3	182	.	NM_002051	exon3	c.T606C	p.R202R	CTCCCGTGGCAGC	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808465	18808465	+	Silent	SNP	T	T	A	rs3007718	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	45	44	0	1	0	T|0.328;A|0.672	0.672	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.T990A	p.A330A	AGGGGCTGCCTCG	.	PASS	Atlas-SNP
SETD1A	9739	hgsc.bcm.edu	37	16	30978324	30978324	+	Silent	SNP	C	C	A	rs11866157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	54	81	0	0.54	0	C|0.968;A|0.032	0.032	strong	.	SETD1A	143	.	NM_014712	exon9	c.C2625A	p.I875I	GGGCATCGAGGCT	.	PASS	Atlas-SNP
UNC93A	54346	hgsc.bcm.edu	37	6	167719436	167719436	+	Missense_Mutation	SNP	G	G	A	rs2072767	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	82	142	0	0.468571	0	G|0.732;A|0.268	0.268	strong	.	UNC93A	66	.	NM_018974	exon6	c.G874A	p.V292I	CAGTTCGTCGGCT	.	PASS	Atlas-SNP
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	53	112	0	0.449153	0	C|0.746;T|0.254	0.254	strong	.	MSRB2	21	.	NM_012228	exon4	c.C342T	p.S114S	GTTTTCCGAGGCT	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2091765	2091765	+	Missense_Mutation	SNP	C	C	T	rs903160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	113	0	1	0	C|0.626;T|0.374	0.374	strong	.	SMG6	97	.	NM_017575	exon11	c.G2914A	p.A972T	GAGCTGCGGCTTG	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234529552	234529552	+	Silent	SNP	C	C	T	rs2175594	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	61	168	0	0.448529	0	C|0.508;T|0.492	0.492	strong	.	TARBP1	111	.	NM_005646	exon27	c.G4275A	p.A1425A	CCACTCCGCTTGG	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180218668	180218668	+	Missense_Mutation	SNP	A	A	G	rs634501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	127	0	1	0	A|0.273;G|0.727	0.727	strong	MGAT1,NS,carcinoma,0,1	MGAT1	48	1	NM_001114617	exon3	c.T1304C	p.L435P	CACGTCAGTGGGG	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15931975	15931975	+	Silent	SNP	G	G	A	rs28570191	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	58	87	0	0.591837	0	G|0.951;A|0.049	0.049	strong	.	MYH11	520	.	NM_001040114	exon2	c.C135T	p.F45F	TGCCTCGAAGCCC	.	PASS	Atlas-SNP
ZNF497	162968	hgsc.bcm.edu	37	19	58868480	58868480	+	Missense_Mutation	SNP	G	G	T	rs12609654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	120	180	0	0.487805	0	G|0.561;T|0.439	0.439	strong	.	ZNF497	22	.	NM_001207009	exon2	c.C522A	p.H174Q	CTGCGAGTGCGCG	.	PASS	Atlas-SNP
USP29	57663	hgsc.bcm.edu	37	19	57641887	57641887	+	Missense_Mutation	SNP	A	A	G	rs74511605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	74	132	0	0.616667	0	A|0.995;G|0.005	0.005	strong	.	USP29	186	.	NM_020903	exon4	c.A1844G	p.Q615R	CAAGCCAAGAGCA	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053891	95053891	+	Silent	SNP	C	C	T	rs6111	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	36	71	0	0.413793	0	C|0.783;T|0.217	0.217	strong	.	SERPINA5	69	.	NM_000624	exon3	c.C192T	p.S64S	CCAGAGCATCTTC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	710	707	439	0	0.995775	0	A|0.718;G|0.282	0.282	strong	FLG,NS,carcinoma,-2,2	FLG	900	2	NM_002016	exon3	c.T6603C	p.D2201D	AGAGCCATCTCCT	.	PASS	Atlas-SNP
ZBED4	9889	hgsc.bcm.edu	37	22	50279749	50279749	+	Silent	SNP	C	C	T	rs61731524	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	28	61	0	0.388889	0	C|0.998;T|0.002	0.002	strong	.	ZBED4	102	.	NM_014838	exon2	c.C2439T	p.I813I	CAGCATCGGGAAG	.	PASS	Atlas-SNP
CC2D2A	57545	hgsc.bcm.edu	37	4	15516389	15516389	+	Silent	SNP	C	C	T	rs2286976	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	57	140	0	0.456	0	C|0.900;T|0.100	0.100	strong	.	CC2D2A	158	.	NM_001080522	exon10	c.C777T	p.H259H	AGATCACGTGGCT	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110813709	110813709	+	Silent	SNP	G	G	A	rs1133219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	48	0	0.5	0	G|0.664;A|0.336	0.336	strong	.	COL4A1	372	.	NM_001845	exon49	c.C4470T	p.A1490A	GCTGCCGGCCGTG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919913	28919913	+	Missense_Mutation	SNP	G	G	A	rs34302455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	42	142	0	0.388889	0	G|0.894;A|0.106	0.106	strong	DSG1,NS,carcinoma,0,1	DSG1	176	1	NM_001942	exon11	c.G1612A	p.D538N	GCCAAAGATTTGT	.	PASS	Atlas-SNP
SEMG2	6407	hgsc.bcm.edu	37	20	43851101	43851101	+	Silent	SNP	T	T	C	rs2233902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	78	158	0	0.516556	0	T|0.985;C|0.015	0.015	strong	.	SEMG2	92	.	NM_003008	exon2	c.T828C	p.D276D	TCAAGATCAAGAG	.	PASS	Atlas-SNP
PDHX	8050	hgsc.bcm.edu	37	11	34938310	34938310	+	Silent	SNP	T	T	C	rs1049307	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	83	0	1	0	T|0.802;C|0.198	0.198	strong	.	PDHX	40	.	NM_003477	exon1	c.T108C	p.S36S	GTGGTCTGTAAGC	.	PASS	Atlas-SNP
PWWP2B	170394	hgsc.bcm.edu	37	10	134218802	134218802	+	Silent	SNP	G	G	T	rs76160300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	52	116	0	0.55914	0	G|0.993;T|0.007	0.007	strong	.	PWWP2B	33	.	NM_001098637	exon2	c.G798T	p.V266V	AGAGGTGGTCAAG	.	PASS	Atlas-SNP
SFXN5	94097	hgsc.bcm.edu	37	2	73226090	73226090	+	Silent	SNP	G	G	A	rs12233055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	59	87	0	0.522124	0	G|0.682;A|0.318	0.318	strong	SFXN5,NS,carcinoma,-2,1	SFXN5	31	1	NM_144579	exon9	c.C522T	p.A174A	GGAGACGGCGCTG	.	PASS	Atlas-SNP
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	78	139	0	0.609375	0	A|0.858;T|0.142	0.142	strong	C12orf40,fourth_ventricle,glioma,0,1	C12orf40	118	1	NM_001031748	exon11	c.A1403T	p.K468M	CTACTAAGAAAAT	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41627868	41627868	+	Missense_Mutation	SNP	G	G	A	rs80319612	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	204	212	0	0.990291	0	G|0.637;A|0.363	0.363	strong	.	CYP2F1	60	.	NM_000774	exon6	c.G652A	p.D218N	TTGTACGACATCT	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38376804	38376804	+	Missense_Mutation	SNP	T	T	C	rs78748271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	147	284	1	0.491639	0.00352113	T|0.979;C|0.021	0.021	strong	.	WDR87	191	.	NM_031951	exon6	c.A7390G	p.T2464A	ATGGGGTCTTTAA	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21049286	21049286	+	Missense_Mutation	SNP	C	C	T	rs16970832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	60	88	0	0.625	0	C|0.944;T|0.056	0.056	strong	.	DNAH3	1142	.	NM_017539	exon34	c.G4747A	p.V1583I	TCGCAACGATCTT	.	PASS	Atlas-SNP
ACVRL1	94	hgsc.bcm.edu	37	12	52306898	52306898	+	Missense_Mutation	SNP	C	C	T	rs199542304	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	12	24	0	0.285714	0	.	.	weak	.	ACVRL1	60	.	NM_000020	exon3	c.C77T	p.P26L	TGAAGCCGTCTCG	.	PASS	Atlas-SNP
CACNA2D1	781	hgsc.bcm.edu	37	7	81588636	81588636	+	Silent	SNP	G	G	A	rs1229502	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	33	95	0	0.458333	0	G|0.750;A|0.250	0.250	strong	CACNA2D1,NS,carcinoma,0,1	CACNA2D1	191	1	NM_000722	exon38	c.C3114T	p.P1038P	GTATCTGGGTTGC	.	PASS	Atlas-SNP
ACSL3	2181	hgsc.bcm.edu	37	2	223783841	223783841	+	Silent	SNP	G	G	A	rs13000358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	107	184	0	0.475556	0	G|0.963;A|0.037	0.037	strong	.	ACSL3	107	.	NM_203372	exon6	c.G726A	p.P242P	GCCACCGACCTGG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26222454	26222454	+	Missense_Mutation	SNP	C	C	T	rs9624909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	103	238	0	0.476852	0	C|0.835;T|0.165	0.165	strong	.	MYO18B	322	.	NM_032608	exon14	c.C2774T	p.S925L	TGGTCTCACTCAT	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746399	143746399	+	Missense_Mutation	SNP	T	T	C	rs73379623	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	43	89	0	0.472527	0	T|0.992;C|0.008	0.008	strong	.	.	.	.	NM_003724	exon2	c.A1079G	p.N360S	GCATCGTTCATGT	.	PASS	Atlas-SNP
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	101	240	0	0.461187	0	C|0.603;T|0.397	0.397	strong	.	AKR7A3	30	.	NM_012067	exon3	c.G412A	p.V138M	GCTCCACGAACTT	.	PASS	Atlas-SNP
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	100	233	0	0.416667	0	A|0.678;G|0.322	0.322	strong	.	CLEC4D	46	.	NM_080387	exon2	c.A94G	p.S32G	CTTCTCAGTGTCT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40384035	40384035	+	Missense_Mutation	SNP	G	G	A	rs367618328		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	639	130	585	1	0.203443	0.0017094	.	.	weak	FCGBP,NS,haematopoietic_neoplasm,-1,1	FCGBP	416	1	NM_003890	exon21	c.C9575T	p.A3192V	AAACCCGCGTCGC	.	scavenged	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65299766	65299766	+	Silent	SNP	T	T	C	rs55952639	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	55	88	0	0.495495	0	T|0.848;C|0.152	0.152	strong	.	CEP68	69	.	NM_015147	exon3	c.T1536C	p.D512D	TGGGGATATCAAA	.	PASS	Atlas-SNP
ATP8A1	10396	hgsc.bcm.edu	37	4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	rs61755862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	84	206	0	0.442105	0	C|0.975;T|0.025	0.025	strong	ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	NM_001105529	exon14	c.G1285A	p.V429I	AAGCAACTCCCGC	.	PASS	Atlas-SNP
ZNF257	113835	hgsc.bcm.edu	37	19	22256347	22256347	+	Silent	SNP	G	G	A	rs10423157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	26	55	0	0.42623	0	G|0.927;A|0.073	0.073	strong	.	ZNF257	156	.	NM_033468	exon3	c.G207A	p.E69E	ACATGAGATGGTA	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862731	5862731	+	Missense_Mutation	SNP	A	A	G	rs61743084	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	88	188	0	0.435644	0	A|0.622;G|0.378	0.378	strong	OR52E6,NS,carcinoma,+2,2	OR52E6	70	2	NM_001005167	exon1	c.T397C	p.W133R	TGTACCAAAGAGG	.	PASS	Atlas-SNP
KLHL20	27252	hgsc.bcm.edu	37	1	173735378	173735378	+	Silent	SNP	T	T	C	rs7536773	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	135	303	0	0.409091	0	T|0.875;C|0.125	0.125	strong	.	KLHL20	54	.	NM_014458	exon8	c.T1245C	p.L415L	CTTTCTTTATGCT	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7163154	7163154	+	Silent	SNP	G	G	A	rs2963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	68	192	0	0.386364	0	G|0.876;A|0.124	0.124	strong	.	INSR	265	.	NM_000208	exon9	c.C1918T	p.L640L	ACTTCAGAATAAT	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192321	102192321	+	Silent	SNP	A	A	G	rs61745027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	258	331	1	0.996139	0.00302115	A|0.824;G|0.176	0.176	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.A75G	p.V25V	GGACGTAGGCAAG	.	PASS	Atlas-SNP
PARP10	84875	hgsc.bcm.edu	37	8	145058539	145058539	+	Missense_Mutation	SNP	T	T	C	rs80304851	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	24	30	0	0.510638	0	T|0.903;C|0.097	0.097	strong	.	PARP10	57	.	NM_032789	exon6	c.A1519G	p.S507G	TAATGCTGCCCAG	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	37	5	33881385	33881385	+	Missense_Mutation	SNP	G	G	C	rs16891862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	72	130	0	0.439024	0	C|0.011;G|0.989	0.011	strong	.	ADAMTS12	464	.	NM_030955	exon2	c.C328G	p.Q110E	ATCCTTGATTGAC	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101551065	101551065	+	Missense_Mutation	SNP	G	G	A	rs113062899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	67	128	0	0.567797	0	G|0.987;A|0.013	0.013	strong	.	SLC5A8	102	.	NM_145913	exon15	c.C1825T	p.R609C	ACAAACGAGTCCC	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100995721	100995721	+	Missense_Mutation	SNP	A	A	G	rs879369	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	59	77	0	0.584158	0	T|0.000;G|0.439;C|0.000;A|0.561	0.439	strong	.	TBC1D2	70	.	NM_001267571	exon4	c.T758C	p.L253S	GAGGCCAAGGGCT	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122296638	122296638	+	Missense_Mutation	SNP	G	G	A	rs1875272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	68	100	0	0.586207	0	G|0.744;A|0.256	0.256	strong	PARP15_ENST00000464300,NS,carcinoma,0,1	PARP15	115	1	NM_001113523	exon1	c.G124A	p.V42M	GGGAGCGTGCTGC	.	PASS	Atlas-SNP
THEG	51298	hgsc.bcm.edu	37	19	373531	373531	+	Nonsense_Mutation	SNP	C	C	T	rs73489977	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	86	134	0	0.518072	0	C|0.960;T|0.040	0.040	strong	.	THEG	58	.	NM_016585	exon4	c.G504A	p.W168X	AGAGGGCCTGGAA	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744844	23744844	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	7	127	0	0.0614035	0	.	.	none	.	HOMEZ	80	.	NM_020834	exon2	c.G1593A	p.E531E	CTCCTCCTCTTCC	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18729367	18729367	+	Silent	SNP	G	G	T	rs57253324	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	57	0	0.419753	0	G|0.901;T|0.099	0.099	strong	.	IGSF22	211	.	NM_173588	exon20	c.C3264A	p.I1088I	CACATGGATGTCA	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	994452	994452	+	Silent	SNP	C	C	T	rs3755954	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	121	197	0	0.5	0	C|0.784;T|0.216	0.216	strong	.	IDUA	33	.	NM_000203	exon3	c.C352T	p.L118L	GGGTACCTGGACC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628193	33628193	+	Missense_Mutation	SNP	G	G	C	rs9527025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	49	89	0	0.429825	0	G|0.848;C|0.152	0.152	strong	.	KL	106	.	NM_004795	exon2	c.G1109C	p.C370S	CTCTTTGCTTTGG	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	85	150	0	0.515152	0	T|0.782;C|0.218	0.218	strong	.	IQUB	117	.	NM_178827	exon8	c.A1269G	p.Q423Q	AAAAGATTGGTTA	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81589340	81589340	+	Silent	SNP	C	C	T	rs201624502	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	89	176	0	0.514451	0	C|0.999;T|0.001	0.001	strong	.	IL16	254	.	NM_001172128	exon13	c.C1974T	p.A658A	CTCTGCCGGCTGC	.	PASS	Atlas-SNP
MRS2	57380	hgsc.bcm.edu	37	6	24403377	24403377	+	Missense_Mutation	SNP	C	C	T	rs2295651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	59	0	1	0	C|0.961;T|0.039	0.039	strong	.	MRS2	31	.	NM_020662	exon1	c.C103T	p.P35S	GGTCCTCCCGTTG	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	141	223	0	0.64977	0	A|0.421;G|0.579	0.579	strong	OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	NM_001004482	exon1	c.T773C	p.M258T	ATGTACATGAGGA	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73574948	73574948	+	Silent	SNP	C	C	T	rs73277900	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	27	59	0	0.5	0	C|0.984;T|0.016	0.016	strong	.	CDH23	365	.	NM_022124	exon68	c.C9978T	p.N3326N	GCGCAACGCCCGC	.	PASS	Atlas-SNP
YEATS2	55689	hgsc.bcm.edu	37	3	183432983	183432983	+	Silent	SNP	C	C	T	rs3736535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	105	204	0	0.596591	0	C|0.804;T|0.196	0.196	strong	.	YEATS2	111	.	NM_018023	exon2	c.C33T	p.T11T	AGAAACCGACCCT	.	PASS	Atlas-SNP
CDH16	1014	hgsc.bcm.edu	37	16	66945947	66945947	+	Missense_Mutation	SNP	C	C	T	rs61735427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	51	107	0	0.542553	0	C|0.942;T|0.058	0.058	strong	.	CDH16	91	.	NM_004062	exon13	c.G1645A	p.A549T	CCGTGGCGGTGGC	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121251924	121251924	+	Silent	SNP	C	C	T	rs41390550	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	117	317	0	0.45	0	C|0.982;T|0.018	0.018	strong	.	POLQ	273	.	NM_199420	exon6	c.G873A	p.P291P	CAAAAGCGGTACA	.	PASS	Atlas-SNP
COX2	5743	hgsc.bcm.edu	37	MT	8027	8027	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	13	5	0	0.928571	0	.	.	none	.	.	.	.	ENST00000361739	exon1	c.G442A	p.A148T	ATTGAAGCCCCCA	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30915263	30915263	+	Missense_Mutation	SNP	A	A	G	rs10216063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	123	0	1	0	A|0.726;G|0.274	0.274	strong	.	FAM188B	62	.	NM_032222	exon15	c.A1963G	p.M655V	TACAACATGTGCC	.	PASS	Atlas-SNP
C7orf72	100130988	hgsc.bcm.edu	37	7	50173702	50173702	+	Splice_Site	SNP	A	A	G	rs78990563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	29	49	0	0.54717	0	A|0.997;G|0.003	0.003	strong	.	C7orf72	26	.	NM_001161834	exon4	c.729-2A>G	.	CTTCATAGAGCTT	.	PASS	Atlas-SNP
TUBGCP2	10844	hgsc.bcm.edu	37	10	135106718	135106718	+	Silent	SNP	G	G	A	rs3008344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	26	60	0	0.448276	0	G|0.996;A|0.004	0.004	strong	.	TUBGCP2	79	.	NM_001256617	exon8	c.C933T	p.F311F	GTACTCGAAGGAA	.	PASS	Atlas-SNP
HECTD4	283450	hgsc.bcm.edu	37	12	112667675	112667675	+	Silent	SNP	T	T	G	rs1005902	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	113	0	1	0	T|0.381;G|0.619	0.619	strong	.	.	.	.	NM_001109662	exon41	c.A5944C	p.R1982R	GTGCTCTAGACAG	.	PASS	Atlas-SNP
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	158	325	0	0.496855	0	G|0.751;A|0.249	0.249	strong	SLC41A1,colon,carcinoma,0,1	SLC41A1	46	1	NM_173854	exon6	c.C756T	p.N252N	GGCCACGTTGTCT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179571448	179571448	+	Missense_Mutation	SNP	A	A	G	rs4893852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	48	105	0	0.505263	0	A|0.910;G|0.090	0.090	strong	.	TTN	18412	.	NM_001267550	exon102	c.T29153C	p.I9718T	TTTGCAATGAAGG	.	PASS	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	37	16	1664931	1664931	+	Silent	SNP	T	T	C	rs7201813	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	10	0	1	0	T|0.365;C|0.635	0.635	strong	.	CRAMP1L	60	.	NM_020825	exon1	c.T291C	p.D97D	GAAGGATCCTCCG	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	622834	622834	+	Missense_Mutation	SNP	C	C	G	rs146178977	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	36	66	0	0.642857	0	C|0.997;G|0.003	0.003	strong	.	POLRMT	91	.	NM_005035	exon7	c.G1442C	p.R481P	AGCATCCGCACCA	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44058265	44058265	+	Silent	SNP	C	C	A	rs3828151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	26	28	0	1	0	C|0.581;A|0.419	0.419	strong	.	PTPRF	172	.	NM_002840	exon11	c.C1806A	p.A602A	CACAGCCCAGTCC	.	PASS	Atlas-SNP
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833342	27833342	+	Silent	SNP	C	C	T	rs11966705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	122	245	0	0.491935	0	C|0.975;T|0.025	0.025	strong	.	HIST1H2AL	14	.	NM_003511	exon1	c.C210T	p.A70A	CAACGCCGCCCGC	.	PASS	Atlas-SNP
CDC37L1	55664	hgsc.bcm.edu	37	9	4685008	4685008	+	Silent	SNP	C	C	T	rs2295967	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	73	147	0	0.532847	0	C|0.893;T|0.107	0.107	strong	.	CDC37L1	19	.	NM_017913	exon2	c.C264T	p.S88S	TGAGTCCTTGGAT	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609097	32609097	+	Silent	SNP	T	T	C	rs1129738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	160	170	1	1	0.00588235	T|0.743;C|0.257	0.257	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.T93C	p.V31V	CCACGTTGCCTCT	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1122147	1122147	+	Silent	SNP	G	G	A	rs2072280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	32	83	0	0.444444	0	G|0.572;A|0.428	0.428	strong	.	SBNO2	112	.	NM_014963	exon11	c.C1140T	p.F380F	GCCCTCGAAGGCC	.	PASS	Atlas-SNP
SLC26A4	5172	hgsc.bcm.edu	37	7	107342294	107342294	+	Missense_Mutation	SNP	T	T	G	rs17154335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	43	89	0	0.467391	0	T|0.952;G|0.048	0.048	strong	.	SLC26A4	117	.	NM_000441	exon17	c.T1826G	p.V609G	ATGCTGTTTCAAC	.	PASS	Atlas-SNP
CELSR3	1951	hgsc.bcm.edu	37	3	48699134	48699134	+	Silent	SNP	G	G	T	rs76423828	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	46	0	0.485294	0	G|0.995;T|0.005	0.005	strong	.	CELSR3	237	.	NM_001407	exon1	c.C934A	p.R312R	GTGCCCGGTTCGC	.	PASS	Atlas-SNP
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	55	116	0	0.416667	0	A|0.466;G|0.534	0.534	strong	.	ARHGAP26	57	.	NM_015071	exon3	c.A255G	p.R85R	AGCAAGATCTTTG	.	PASS	Atlas-SNP
CCDC101	112869	hgsc.bcm.edu	37	16	28602991	28602991	+	Silent	SNP	A	A	G	rs11401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	44	99	0	0.411215	0	A|0.832;G|0.168	0.168	strong	.	CCDC101	24	.	NM_138414	exon10	c.A846G	p.R282R	TCAGAGATACGTG	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44378009	44378009	+	Silent	SNP	A	A	C	rs74424854	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	36	181	0	0.313043	0	A|0.939;C|0.061	0.061	strong	ZNF404,NS,carcinoma,-1,1	ZNF404	46	1	NM_001033719	exon2	c.T348G	p.P116P	ATGTAGAGGAAGG	.	PASS	Atlas-SNP
LILRA2	11027	hgsc.bcm.edu	37	19	55087313	55087313	+	Missense_Mutation	SNP	T	T	G	rs7249811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	102	184	0	0.554348	0	T|0.876;G|0.124	0.124	strong	.	LILRA2	99	.	NM_001130917	exon6	c.T992G	p.V331G	AGCCGGTCCCCAC	.	PASS	Atlas-SNP
GPR151	134391	hgsc.bcm.edu	37	5	145894896	145894896	+	Missense_Mutation	SNP	G	G	C	rs7709485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	40	90	0	0.5	0	G|0.723;C|0.277	0.277	strong	.	GPR151	35	.	NM_194251	exon1	c.C781G	p.L261V	ACAAGAGAGCAGA	.	PASS	Atlas-SNP
RPP40	10799	hgsc.bcm.edu	37	6	4996543	4996543	+	Missense_Mutation	SNP	C	C	T	rs62385118	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	34	106	0	0.472222	0	C|0.956;T|0.044	0.044	strong	.	RPP40	36	.	NM_006638	exon6	c.G671A	p.S224N	TCGCTGCTCTGCA	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23746269	23746269	+	Silent	SNP	C	C	G	rs1057119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	88	178	0	0.486188	0	C|0.797;G|0.203	0.203	strong	.	HOMEZ	80	.	NM_020834	exon2	c.G168C	p.T56T	TGCTTGCGTCCAC	.	PASS	Atlas-SNP
OR4K13	390433	hgsc.bcm.edu	37	14	20502779	20502779	+	Missense_Mutation	SNP	C	C	T	rs144683363	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	39	107	0	0.453488	0	C|0.985;T|0.015	0.015	strong	.	OR4K13	68	.	NM_001004714	exon1	c.G139A	p.V47M	CAGTCACCAAGAT	.	PASS	Atlas-SNP
DAD1	1603	hgsc.bcm.edu	37	14	23044004	23044004	+	Silent	SNP	C	C	T	rs1051154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	59	107	0	0.472	0	C|0.901;T|0.099	0.099	strong	.	DAD1	8	.	NM_001344	exon2	c.G341A	p.X114X	ATGAGTCAGCCAA	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	883088	883088	+	Missense_Mutation	SNP	G	G	A	rs116520953	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	43	63	0	0.589041	0	G|0.996;A|0.004	0.004	strong	.	SUN1	157	.	NM_001171945	exon7	c.G652A	p.V218M	AAGGACGTGCTCA	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6211183	6211183	+	Silent	SNP	G	G	A	rs9434711	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	77	148	0	0.52381	0	G|0.588;A|0.412	0.412	strong	.	CHD5	267	.	NM_015557	exon7	c.C903T	p.F301F	GCTGTCGAAGTCC	.	PASS	Atlas-SNP
PSKH2	85481	hgsc.bcm.edu	37	8	87060793	87060793	+	Silent	SNP	T	T	A	rs28483271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	69	150	0	0.485915	0	T|0.966;A|0.034	0.034	strong	.	PSKH2	79	.	NM_033126	exon3	c.A1056T	p.G352G	TGCAGATCCAGGA	.	PASS	Atlas-SNP
ORM2	5005	hgsc.bcm.edu	37	9	117093856	117093856	+	Missense_Mutation	SNP	G	G	A	rs142633392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	135	208	0	0.625	0	G|0.995;A|0.005	0.005	strong	.	ORM2	13	.	NM_000608	exon4	c.G338A	p.R113Q	GAGGCCGAGAACA	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82785096	82785096	+	Silent	SNP	G	G	A	rs61744360	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	125	264	1	0.462963	0.00378788	G|0.998;A|0.002	0.002	strong	.	PCLO	1506	.	NM_014510	exon2	c.C861T	p.D287D	TACTATGTCTGCC	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36487412	36487412	+	Silent	SNP	G	G	A	rs111770829	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	92	168	0	0.44878	0	G|0.981;A|0.019	0.019	strong	.	GPR179	170	.	NM_001004334	exon11	c.C2040T	p.D680D	CAGCTCGTCCTGT	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111862074	111862074	+	Silent	SNP	C	C	T	rs2820092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	128	0	1	0	C|0.834;T|0.166	0.166	strong	.	CHIA	115	.	NM_201653	exon11	c.C1161T	p.L387L	GGCCCTCGGCCTG	.	PASS	Atlas-SNP
RPS16	6217	hgsc.bcm.edu	37	19	39923952	39923952	+	Silent	SNP	G	G	A	rs17627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	76	204	0	0.469136	0	G|0.758;A|0.242	0.242	strong	.	RPS16	12	.	NM_001020	exon5	c.C402T	p.G134G	ACCAGGGCCTCCA	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36656001	36656001	+	Silent	SNP	C	C	T	rs3735387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	41	86	0	0.577465	0	C|0.978;T|0.022	0.022	strong	.	AOAH	79	.	NM_001637	exon11	c.G831A	p.A277A	CTGCGACGCTGTG	.	PASS	Atlas-SNP
ABHD12B	145447	hgsc.bcm.edu	37	14	51368610	51368610	+	Missense_Mutation	SNP	A	A	G	rs28564871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	35	117	0	0.388889	0	A|0.765;G|0.235	0.235	strong	ABHD12B_ENST00000337334,colon,carcinoma,-1,5	ABHD12B	53	5	NM_001206673	exon10	c.A844G	p.I282V	AAAATAATCTTTC	.	PASS	Atlas-SNP
ABCC10	89845	hgsc.bcm.edu	37	6	43412935	43412935	+	Silent	SNP	T	T	C	rs2125740	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	103	225	0	0.440171	0	T|0.940;C|0.060	0.060	strong	.	ABCC10	118	.	NM_001198934	exon14	c.T2913C	p.Y971Y	CGTGTATGCGACC	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	50	93	0	0.434783	0	C|0.617;G|0.383	0.383	strong	MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	NM_001145809	exon18	c.C2205G	p.R735R	TGTCCGCTGCATT	.	PASS	Atlas-SNP
PAX2	5076	hgsc.bcm.edu	37	10	102568983	102568983	+	Silent	SNP	A	A	C	rs1800898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	49	0	1	0	A|0.594;C|0.406	0.406	strong	.	PAX2	83	.	NM_003987	exon8	c.A978C	p.P326P	ATACCCAGTTGTG	.	PASS	Atlas-SNP
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	100	0	0.490385	0	G|0.849;A|0.151	0.151	strong	.	KCTD18	44	.	NM_152387	exon7	c.C998T	p.A333V	ACCAGGGCCGTGG	.	PASS	Atlas-SNP
CCT3	7203	hgsc.bcm.edu	37	1	156281999	156281999	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	48	86	0	0.521739	0	.	.	none	.	CCT3	61	.	NM_005998	exon11	c.C988T	p.R330W	CTATCCGGGCCCC	.	PASS	Atlas-SNP
PCDH12	51294	hgsc.bcm.edu	37	5	141331098	141331098	+	Missense_Mutation	SNP	G	G	A	rs115735066	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	45	106	0	0.381356	0	G|0.991;A|0.009	0.009	strong	.	PCDH12	133	.	NM_016580	exon2	c.C2938T	p.H980Y	CTCGGTGGTTTGG	.	PASS	Atlas-SNP
C10orf12	26148	hgsc.bcm.edu	37	10	98742021	98742021	+	Silent	SNP	C	C	T	rs7098255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	26	78	0	0.440678	0	C|0.931;T|0.069	0.069	strong	C10orf12,NS,carcinoma,0,1	C10orf12	94	1	NM_015652	exon1	c.C874T	p.L292L	CCGAACCTGAGCA	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12675690	12675690	+	Missense_Mutation	SNP	G	G	A	rs35385652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	55	93	0	0.504587	0	G|0.972;A|0.028	0.028	strong	.	SCIN	105	.	NM_001112706	exon10	c.G1340A	p.R447Q	CCACACGAGATGA	.	PASS	Atlas-SNP
PHACTR4	65979	hgsc.bcm.edu	37	1	28800380	28800380	+	Missense_Mutation	SNP	C	C	A	rs61785974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	35	50	0	0.625	0	C|0.726;A|0.274	0.274	strong	.	PHACTR4	64	.	NM_023923	exon6	c.C1168A	p.L390I	TTAGATCTACACC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149509048	149509048	+	Silent	SNP	C	C	T	rs115723456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	52	83	0	0.5	0	C|0.989;T|0.011	0.011	strong	.	.	.	.	NM_198455	exon68	c.C9594T	p.S3198S	AGCCTCCTGTGGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680120	100680120	+	Missense_Mutation	SNP	C	C	A	rs147991653	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	10	135	0	0.0487805	0	C|0.975;A|0.025	0.025	strong	MUC17,extremity,malignant_melanoma,0,2	MUC17	804	2	NM_001040105	exon3	c.C5423A	p.T1808N	GAATGACTCCATT	.	scavenged	Atlas-SNP
PLEKHG3	26030	hgsc.bcm.edu	37	14	65197791	65197791	+	Silent	SNP	C	C	A	rs61742295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	73	108	0	0.584	0	C|0.974;A|0.026	0.026	strong	.	PLEKHG3	89	.	NM_015549	exon5	c.C585A	p.G195G	GGATGGCTTTGAG	.	PASS	Atlas-SNP
PIGT	51604	hgsc.bcm.edu	37	20	44052992	44052992	+	Silent	SNP	G	G	A	rs13217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	62	102	0	0.462687	0	G|0.654;A|0.346	0.346	strong	PIGT_ENST00000279036,caecum,carcinoma,0,3	PIGT	85	3	NM_015937	exon10	c.G1371A	p.T457T	GTACACGCCAGAT	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116279880	116279880	+	Silent	SNP	T	T	C	rs35270441	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	60	85	0	0.731707	0	T|0.889;C|0.111	0.111	strong	.	RGS3	251	.	NM_144488	exon17	c.T1734C	p.Y578Y	GCTGTATGAAGGG	.	PASS	Atlas-SNP
MAT1A	4143	hgsc.bcm.edu	37	10	82034854	82034854	+	Silent	SNP	T	T	C	rs10788546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	51	66	0	0.980769	0	T|0.235;C|0.765	0.765	strong	.	MAT1A	52	.	NM_000429	exon7	c.A870G	p.V290V	GCGGTCTACCTTG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573655	140573655	+	Silent	SNP	C	C	T	rs17844572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	395	107	374	0	0.270886	0	C|0.986;T|0.014	0.014	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C1530T	p.N510N	GGACAACGGCCAC	.	PASS	Atlas-SNP
ZAK	0	hgsc.bcm.edu	37	2	174103160	174103160	+	Silent	SNP	T	T	C	rs3739103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	64	154	0	0.441379	0	T|0.850;C|0.150	0.150	strong	.	ZAK	62	.	NM_016653	exon15	c.T1263C	p.I421I	ACTAATTAAGGTA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238277573	238277573	+	Silent	SNP	C	C	A	rs2645774	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	45	70	0	0.432692	0	C|0.757;A|0.243	0.243	strong	.	COL6A3	608	.	NM_004369	exon10	c.G4533T	p.G1511G	TGGGGACCCCCCT	.	PASS	Atlas-SNP
SATB2	23314	hgsc.bcm.edu	37	2	200233357	200233357	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	2	105	0	0.0185185	0	.	.	none	SATB2,colon,carcinoma,+1,1	SATB2	134	1	NM_015265	exon7	c.G671A	p.R224K	TACCATCTCCCAA	.	scavenged	Atlas-SNP
TTC38	55020	hgsc.bcm.edu	37	22	46664431	46664431	+	Silent	SNP	C	C	G	rs9627359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	51	0	0.459459	0	C|0.912;G|0.088	0.088	strong	.	TTC38	40	.	NM_017931	exon2	c.C54G	p.L18L	GAGGCTCCCGCTC	.	PASS	Atlas-SNP
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	20	32	0	0.434783	0	T|0.951;C|0.049	0.049	strong	.	AIRE	61	.	NM_000383	exon10	c.T1203C	p.P401P	TCCGCCTTCTGCA	.	PASS	Atlas-SNP
DENND2A	27147	hgsc.bcm.edu	37	7	140244560	140244560	+	Missense_Mutation	SNP	C	C	T	rs2293177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	26	86	0	0.305882	0	C|0.758;T|0.242	0.242	strong	.	DENND2A	132	.	NM_015689	exon12	c.G2185A	p.E729K	ACAGTTCGATCAC	.	PASS	Atlas-SNP
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	55	106	0	0.426357	0	C|0.977;T|0.023	0.023	strong	.	MSH2	198	.	NM_000251	exon3	c.C573T	p.L191L	TCTCCTCATCCAG	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117870257	117870257	+	Silent	SNP	C	C	T	rs146193205	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	30	67	0	0.566038	0	C|0.999;T|0.001	0.001	strong	.	IL10RA	46	.	NM_001558	exon7	c.C1638T	p.A546A	CCTTGCCCCTCTA	.	PASS	Atlas-SNP
PTTG2	10744	hgsc.bcm.edu	37	4	37962186	37962186	+	Missense_Mutation	SNP	G	G	C	rs6811863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	223	188	0	1	0	G|0.275;C|0.725	0.725	strong	.	PTTG2	15	.	NM_006607	exon1	c.G131C	p.R44P	TAACACGACGTTT	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890064	7890064	+	Silent	SNP	A	A	G	rs12023156	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	135	98	0	0.478723	0	A|0.714;G|0.286	0.286	strong	.	PER3	95	.	NM_016831	exon18	c.A3030G	p.T1010T	GTCCACAGGATCG	.	PASS	Atlas-SNP
SCNN1B	6338	hgsc.bcm.edu	37	16	23379279	23379279	+	Silent	SNP	C	C	T	rs250563	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	81	144	0	0.522581	0	C|0.894;T|0.106	0.106	strong	.	SCNN1B	81	.	NM_000336	exon5	c.C879T	p.F293F	TGAATTCGGTGAG	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	171969077	171969077	+	Missense_Mutation	SNP	C	C	G	rs7652177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	104	141	0	0.971963	0	C|0.384;G|0.616	0.616	strong	FNDC3B,NS,carcinoma,0,1	FNDC3B	118	1	NM_001135095	exon6	c.C536G	p.T179S	TGTCAACCTACAT	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	99027137	99027137	+	Silent	SNP	T	T	C	rs2865979	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	50	122	0	0.454545	0	T|0.607;C|0.393	0.393	strong	.	.	.	.	NM_174952	exon5	c.A579G	p.L193L	TTCATATAGTCGT	.	PASS	Atlas-SNP
HSD17B4	3295	hgsc.bcm.edu	37	5	118861713	118861713	+	Missense_Mutation	SNP	A	A	G	rs11205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	74	166	0	0.496644	0	A|0.591;G|0.409	0.409	strong	HSD17B4,NS,carcinoma,0,1	HSD17B4	63	1	NM_001199291	exon20	c.A1750G	p.I584V	AAGGCAATTAAGG	.	PASS	Atlas-SNP
AADACL3	126767	hgsc.bcm.edu	37	1	12779560	12779560	+	Silent	SNP	T	T	C	rs3010876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	130	158	0	1	0	T|0.148;C|0.852	0.852	strong	.	AADACL3	84	.	NM_001103170	exon2	c.T81C	p.D27D	GTATGATCCCGAT	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151165106	151165106	+	Missense_Mutation	SNP	T	T	G	rs35491609	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	348	156	324	0	0.448276	0	T|0.992;G|0.008	0.008	strong	IGSF10,NS,carcinoma,-1,1	IGSF10	279	1	NM_178822	exon4	c.A2663C	p.Q888P	GAATGTTGATTGG	.	PASS	Atlas-SNP
ZNF516	9658	hgsc.bcm.edu	37	18	74091235	74091235	+	Silent	SNP	G	G	C	rs621265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	47	0	0.490909	0	G|0.898;C|0.102	0.102	strong	.	ZNF516	102	.	NM_014643	exon4	c.C2835G	p.A945A	GCTATTGGCCGAG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20876253	20876253	+	Missense_Mutation	SNP	A	A	G	rs1760897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	84	199	0	0.459016	0	A|0.635;G|0.365	0.365	strong	.	TEP1	224	.	NM_007110	exon2	c.T346C	p.S116P	GACTAGAGAGGGT	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7885907	7885907	+	Missense_Mutation	SNP	C	C	G	rs10064631	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	92	176	0	0.467005	0	C|0.948;G|0.052	0.052	strong	.	MTRR	74	.	NM_024010	exon7	c.C1078G	p.L360V	CTGCAGCTTGAAG	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107578478	107578478	+	Silent	SNP	C	C	T	rs2230807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	87	148	0	0.550633	0	T|0.049;G|0.134	0.049	strong	.	ABCA1	244	.	NM_005502	exon25	c.G3684A	p.R1228R	TGAGAGCCGGTCA	.	PASS	Atlas-SNP
ACHE	43	hgsc.bcm.edu	37	7	100490077	100490077	+	Silent	SNP	G	G	A	rs7636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	42	84	0	0.415842	0	G|0.887;A|0.113	0.113	strong	.	ACHE	80	.	NM_000665	exon3	c.C1431T	p.P477P	GCCGTGGGGCACC	.	PASS	Atlas-SNP
SETD3	84193	hgsc.bcm.edu	37	14	99927594	99927594	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	4	147	0	0.0240964	0	.	.	none	SETD3,colon,carcinoma,+2,1	SETD3	56	1	NM_032233	exon4	c.G280A	p.E94K	AACCCTCGACAGA	.	scavenged	Atlas-SNP
USP45	85015	hgsc.bcm.edu	37	6	99893938	99893938	+	Silent	SNP	T	T	C	rs4504482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	36	40	0	0.972973	0	T|0.693;C|0.307	0.307	strong	.	USP45	56	.	NM_001080481	exon14	c.A1710G	p.G570G	TTGATCTCCAGTT	.	PASS	Atlas-SNP
ARMCX2	9823	hgsc.bcm.edu	37	X	100912065	100912065	+	Silent	SNP	C	C	T	rs78189978	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	46	116	0	0.621622	0	C|0.981;T|0.019	0.019	strong	.	ARMCX2	75	.	NM_014782	exon5	c.G510A	p.A170A	AGTCTCCGCTTCT	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27442336	27442336	+	Silent	SNP	G	G	A	rs3736312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	75	182	0	0.46875	0	G|0.828;A|0.172	0.172	strong	.	SLC4A7	119	.	NM_003615	exon16	c.C2319T	p.N773N	GCTGGGGTTTGGA	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	21	61	0	0.375	0	G|0.931;A|0.069	0.069	strong	.	MYO18B	322	.	NM_032608	exon43	c.G7537A	p.G2513S	TCCTCCGGCTCCA	.	PASS	Atlas-SNP
NMU	10874	hgsc.bcm.edu	37	4	56466734	56466734	+	Missense_Mutation	SNP	G	G	T	rs12108463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	91	230	0	0.42723	0	G|0.960;T|0.040	0.040	strong	.	NMU	17	.	NM_006681	exon8	c.C444A	p.F148L	ACTTTGGAATTCT	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280162	39280162	+	Silent	SNP	A	A	G	rs28515113	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	116	0	1	0	A|0.891;G|0.109	0.109	strong	KRTAP4-12,colon,carcinoma,0,3	KRTAP4-12	32	3	NM_031854	exon1	c.T213C	p.C71C	GGTCCTACAGCAG	.	scavenged	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133898949	133898949	+	Silent	SNP	C	C	T	rs61741629	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	42	48	0	0.617647	0	C|0.971;T|0.029	0.029	strong	.	TG	416	.	NM_003235	exon9	c.C1332T	p.I444I	AGCCATCCGAGCA	.	PASS	Atlas-SNP
VAMP8	8673	hgsc.bcm.edu	37	2	85806266	85806266	+	Silent	SNP	C	C	T	rs3731828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	30	53	0	0.526316	0	C|0.698;T|0.302	0.302	strong	VAMP8,NS,carcinoma,0,1	VAMP8	10	1	NM_003761	exon2	c.C138T	p.N46N	CCGCAACAAGACA	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184764351	184764351	+	Silent	SNP	G	G	A	rs35543943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	44	104	0	0.44898	0	A|0.101;C|0.000;G|0.899;T|0.000	0.101	strong	.	FAM129A	98	.	NM_052966	exon14	c.C2547T	p.D849D	GATGGGGTCAGAA	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7577260	7577260	+	Silent	SNP	C	C	T	rs2064217	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	71	170	0	0.482993	0	C|0.737;T|0.263	0.263	strong	DSP,NS,carcinoma,0,1	DSP	306	1	NM_004415	exon20	c.C2862T	p.C954C	ACTTTGCGCCAAT	.	PASS	Atlas-SNP
ZNF746	155061	hgsc.bcm.edu	37	7	149174758	149174758	+	Silent	SNP	G	G	A	rs61746598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	47	69	0	0.552941	0	G|0.960;A|0.040	0.040	strong	.	ZNF746	68	.	NM_001163474	exon5	c.C609T	p.G203G	CTCCACGCCCAGG	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152326516	152326516	+	Missense_Mutation	SNP	T	T	C	rs16833974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	175	271	0	0.501433	0	T|0.932;C|0.068	0.068	strong	.	FLG2	431	.	NM_001014342	exon3	c.A3746G	p.H1249R	TGGCTATGTCTAG	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	39	93	0	0.423913	0	T|0.874;C|0.126	0.126	strong	.	FANCA	99	.	NM_000135	exon37	c.A3654G	p.P1218P	GGGTGCTGGGGAG	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232940953	232940953	+	Missense_Mutation	SNP	T	T	C	rs10797593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	100	251	1	0.485437	0.00398406	T|0.893;C|0.107	0.107	strong	KIAA1383_ENST00000418460,NS,carcinoma,0,1	.	.	1	NM_019090	exon1	c.T184C	p.S62P	GCATTATCATCAA	.	PASS	Atlas-SNP
RBM34	23029	hgsc.bcm.edu	37	1	235324298	235324298	+	Silent	SNP	T	T	C	rs2295815	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	58	0	1	0	T|0.850;C|0.150	0.150	strong	.	RBM34	41	.	NM_001161533	exon2	c.A138G	p.E46E	ATGGTGTTCGCCG	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86940673	86940673	+	Silent	SNP	C	C	T	rs1367647	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	67	183	0	0.39881	0	C|0.912;T|0.088	0.088	strong	.	AGBL1	151	.	NM_152336	exon17	c.C2313T	p.T771T	GGGTACCTTGGAG	.	PASS	Atlas-SNP
VPS25	84313	hgsc.bcm.edu	37	17	40931054	40931054	+	Silent	SNP	T	T	C	rs3744239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	86	181	0	0.547771	0	T|0.877;C|0.123	0.123	strong	.	VPS25	11	.	NM_032353	exon6	c.T498C	p.T166T	CATCACTGTCAGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100683053	100683053	+	Missense_Mutation	SNP	A	A	G	rs200821451	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	26	116	0	0.149425	0	A|0.999;G|0.001	0.001	weak	.	MUC17	804	.	NM_001040105	exon3	c.A8356G	p.T2786A	ACTTCTACTGAAG	.	PASS	Atlas-SNP
ADAM30	11085	hgsc.bcm.edu	37	1	120436751	120436751	+	Missense_Mutation	SNP	T	T	C	rs35273427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	384	213	350	1	0.554688	0.00285714	T|0.878;C|0.122	0.122	strong	.	ADAM30	88	.	NM_021794	exon1	c.A2209G	p.T737A	TTTTTGTTTTAGA	.	PASS	Atlas-SNP
IL12RB2	3595	hgsc.bcm.edu	37	1	67787286	67787286	+	Silent	SNP	T	T	C	rs2307147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	56	0	0.448718	0	T|0.926;C|0.074	0.074	strong	.	IL12RB2	94	.	NM_001559	exon3	c.T78C	p.D26D	TGCAGATGCGTGC	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27802457	27802457	+	Silent	SNP	T	T	C	rs12329054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	59	96	0	0.578431	0	T|0.986;C|0.014	0.014	strong	.	C2orf16	357	.	NM_032266	exon1	c.T3018C	p.G1006G	CAATGGTATATCC	.	PASS	Atlas-SNP
CDH9	1007	hgsc.bcm.edu	37	5	26988424	26988424	+	Missense_Mutation	SNP	T	T	C	rs2288467	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	39	92	0	0.448276	0	C|0.447;N|0.000	0.447	strong	.	CDH9	305	.	NM_016279	exon2	c.A17G	p.Y6C	GGTATATAATGGT	.	PASS	Atlas-SNP
TMEM30A	55754	hgsc.bcm.edu	37	6	75994151	75994151	+	Silent	SNP	A	A	G	rs240374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	67	0	1	0	A|0.828;G|0.172	0.172	strong	.	TMEM30A	40	.	NM_001143958	exon1	c.T204C	p.I68I	GACAAAAATGCCA	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	37	17	80039481	80039481	+	Silent	SNP	G	G	A	rs1140616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	39	69	0	0.58209	0	G|0.632;A|0.368	0.368	strong	.	FASN	154	.	NM_004104	exon37	c.C6402T	p.I2134I	ACCCAGGATGTGT	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16259497	16259497	+	Missense_Mutation	SNP	G	G	T	rs60707953	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	88	0	0.452381	0	G|0.992;T|0.008	0.008	strong	.	ABCC6	110	.	NM_001171	exon23	c.C3289A	p.L1097I	CGTAGAGGAGAAA	.	PASS	Atlas-SNP
IQCF1	132141	hgsc.bcm.edu	37	3	51930850	51930850	+	Missense_Mutation	SNP	T	T	C	rs57859638	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	62	142	0	0.394904	0	T|0.851;C|0.149	0.149	strong	IQCF1,tonsil,carcinoma,0,1	IQCF1	26	1	NM_152397	exon3	c.A169G	p.K57E	ATACTTTTTCTGA	.	PASS	Atlas-SNP
DLK1	8788	hgsc.bcm.edu	37	14	101200514	101200514	+	Missense_Mutation	SNP	G	G	T	rs116078181	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	54	126	0	0.606742	0	G|0.981;T|0.019	0.019	strong	.	DLK1	57	.	NM_003836	exon5	c.G433T	p.V145L	ACCTGCGTGGATG	.	PASS	Atlas-SNP
AQP12A	375318	hgsc.bcm.edu	37	2	241631616	241631616	+	Silent	SNP	T	T	C	rs11889147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	62	123	1	0.469697	0.00813008	T|0.958;C|0.042	0.042	strong	AQP12A,NS,carcinoma,0,1	AQP12A	32	1	NM_198998	exon2	c.T249C	p.T83T	CCCCACTGTGTCC	.	scavenged	Atlas-SNP
DDX43	55510	hgsc.bcm.edu	37	6	74125283	74125283	+	Silent	SNP	T	T	C	rs138615882	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	61	0	0.551282	0	T|0.997;C|0.003	0.003	strong	.	DDX43	69	.	NM_018665	exon15	c.T1809C	p.I603I	ATTGATTAATATT	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	210	234	2	1	0.00854701	G|0.727;A|0.273	0.273	strong	.	SEC16B	92	.	NM_033127	exon7	c.C922T	p.L308L	TGTGCAGTTCAAC	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	32	41	0	0.516129	0	G|0.838;C|0.000;A|0.162	0.162	strong	.	DEK	31	.	NM_003472	exon2	c.C9T	p.A3A	GGCCGAGGCGGAC	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	37	12	94976084	94976084	+	Silent	SNP	T	T	C	rs3747552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	82	147	0	0.5125	0	T|0.335;C|0.665	0.665	strong	.	TMCC3	63	.	NM_020698	exon2	c.A309G	p.A103A	CTTGTCTGCGTTG	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13679203	13679203	+	Silent	SNP	G	G	A	rs1061375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	123	208	0	0.527897	0	G|0.494;A|0.506	0.506	strong	.	FBLN2	137	.	NM_001004019	exon18	c.G3480A	p.T1160T	CTTCACGGGGGAC	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68023989	68023989	+	Missense_Mutation	SNP	G	G	C	rs149253165	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	52	81	0	0.565217	0	G|0.993;C|0.007	0.007	strong	.	PLEKHH1	118	.	NM_020715	exon4	c.G193C	p.G65R	CAGGTGGGTGTCA	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122419151	122419151	+	Missense_Mutation	SNP	G	G	A	rs201474464	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	32	79	0	0.415584	0	.	.	weak	PARP14_ENST00000474629,caecum,carcinoma,-2,2	PARP14	242	2	NM_017554	exon6	c.G1750A	p.A584T	TCTGAAGCCCTGT	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241973223	241973223	+	Silent	SNP	C	C	T	rs61746865	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	332	165	322	0	0.496988	0	C|0.940;T|0.060	0.060	strong	.	SNED1	76	.	NM_001080437	exon3	c.C573T	p.I191I	GTCCATCGTGTGG	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134042164	134042164	+	Missense_Mutation	SNP	C	C	T	rs61742878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	49	106	0	0.395161	0	C|0.995;T|0.005	0.005	strong	TG,NS,carcinoma,0,4	TG	416	4	NM_003235	exon41	c.C7135T	p.R2379C	CCTCGGCGCGTGT	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45786709	45786709	+	Missense_Mutation	SNP	G	G	A	rs45544142	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	33	51	0	0.507692	0	G|0.962;A|0.038	0.038	strong	.	TRPM2	196	.	NM_003307	exon4	c.G496A	p.V166I	CTGGACGTCCCCA	.	PASS	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	52	105	0	0.464286	0	G|0.696;A|0.304	0.304	strong	OR6K3,NS,carcinoma,0,1	OR6K3	101	1	NM_001005327	exon1	c.C682T	p.P228S	AAGAGGGAATCCT	.	PASS	Atlas-SNP
SLC2A14	144195	hgsc.bcm.edu	37	12	7967071	7967071	+	Silent	SNP	G	G	A	rs78504893		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	47	114	0	0.427273	0	.	.	weak	.	SLC2A14	78	.	NM_153449	exon12	c.C1404T	p.A468A	GGTAAAGGCCAAG	.	PASS	Atlas-SNP
ZNF398	57541	hgsc.bcm.edu	37	7	148851273	148851273	+	Missense_Mutation	SNP	G	G	C	rs3801979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	46	122	0	0.403509	0	G|0.925;C|0.075	0.075	strong	ZNF398,colon,carcinoma,+2,1	ZNF398	54	1	NM_170686	exon2	c.G261C	p.E87D	TACCGAGCTTGGG	.	PASS	Atlas-SNP
MBLAC1	255374	hgsc.bcm.edu	37	7	99725466	99725466	+	Missense_Mutation	SNP	G	G	T	rs78225840	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	27	32	0	0.55102	0	G|0.980;T|0.020	0.020	strong	.	MBLAC1	13	.	NM_203397	exon2	c.G448T	p.G150C	GGGCTGGGTGAGG	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	37	3	14755617	14755617	+	Missense_Mutation	SNP	C	C	G	rs6790129	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	71	164	0	0.525926	0	C|0.582;G|0.418	0.418	strong	.	C3orf20	109	.	NM_032137	exon8	c.C1264G	p.L422V	CTGGCCCTATTCA	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs7776775	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	44	119	0	0.346457	0	.	.	weak	.	TYW1	71	.	NM_018264	exon14	c.G1785A	p.G595G	CCTGGGGAATCCT	.	PASS	Atlas-SNP
TTLL11	158135	hgsc.bcm.edu	37	9	124633018	124633018	+	Silent	SNP	C	C	T	rs16911064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	67	159	0	0.507576	0	C|0.983;T|0.017	0.017	strong	.	TTLL11	67	.	NM_001139442	exon7	c.G1761A	p.Q587Q	TTCAAGCTGCTGA	.	PASS	Atlas-SNP
ZNF385B	151126	hgsc.bcm.edu	37	2	180311444	180311444	+	Missense_Mutation	SNP	T	T	C	rs2271761	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	91	177	0	0.494565	0	T|0.937;C|0.063	0.063	strong	.	ZNF385B	68	.	NM_152520	exon7	c.A724G	p.S242G	AGCCACTTTCAGA	.	PASS	Atlas-SNP
IL17RA	23765	hgsc.bcm.edu	37	22	17589983	17589983	+	Missense_Mutation	SNP	G	G	A	rs189025188	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	12	10	0	0.75	0	G|0.999;A|0.001	0.001	strong	.	IL17RA	62	.	NM_014339	exon13	c.G1874A	p.R625H	TGGTGCGCGAGCC	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	150911405	150911405	+	Silent	SNP	T	T	C	rs3732755	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	49	98	0	0.505155	0	T|0.896;C|0.104	0.104	strong	.	MED12L	271	.	NM_053002	exon14	c.T2097C	p.Y699Y	TAATTATGACCTC	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5085247	5085247	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	16	155	0	0.163265	0	.	.	none	.	ZNF594	89	.	NM_032530	exon2	c.A2305G	p.T769A	GGAAGGTCCTACT	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118166195	118166195	+	Silent	SNP	C	C	T	rs10923359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	56	135	0	0.4375	0	C|0.979;T|0.021	0.021	strong	.	FAM46C	25	.	NM_017709	exon2	c.C705T	p.N235N	CAAGAACCCAGAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412259	105412259	+	Missense_Mutation	SNP	G	G	C	rs2819426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	393	392	393	0	0.997455	0	G|0.657;C|0.343	0.343	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C9529G	p.L3177V	GGCTCAGGTCGGC	.	PASS	Atlas-SNP
FAM194B	220081	hgsc.bcm.edu	37	13	46170898	46170898	+	Silent	SNP	C	C	T	rs78950901	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	163	340	0	0.488024	0	C|0.987;T|0.013	0.013	strong	.	FAM194B	42	.	NM_182542	exon3	c.G243A	p.K81K	TTCCTCCTTCAAG	.	PASS	Atlas-SNP
PIF1	80119	hgsc.bcm.edu	37	15	65108939	65108939	+	Missense_Mutation	SNP	A	A	G	rs138069301	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	84	175	0	0.482759	0	A|1.000;G|0.000	0.000	weak	.	PIF1	43	.	NM_025049	exon12	c.T1700C	p.I567T	AGAGAAATCTCCA	.	PASS	Atlas-SNP
SLC35D3	340146	hgsc.bcm.edu	37	6	137245567	137245567	+	Missense_Mutation	SNP	C	C	A	rs116512494	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	59	88	0	0.561905	0	C|0.988;A|0.012	0.012	strong	.	SLC35D3	33	.	NM_001008783	exon2	c.C984A	p.D328E	TGGAGACCAGCTG	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108677821	108677821	+	Silent	SNP	C	C	A	rs2197737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	76	0	0.483516	0	C|0.656;A|0.344	0.344	strong	MORC1,NS,carcinoma,0,1	MORC1	211	1	NM_014429	exon28	c.G2946T	p.S982S	ATTTTCCGAAGTC	.	PASS	Atlas-SNP
EPOR	2057	hgsc.bcm.edu	37	19	11489049	11489049	+	Missense_Mutation	SNP	G	G	C	rs35423344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	19	32	0	0.558824	0	G|0.941;C|0.059	0.059	strong	.	EPOR	26	.	NM_000121	exon8	c.C1138G	p.P380A	TGGGCGGGTTCCG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536451	88536451	+	Silent	SNP	C	C	T	rs141946550		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	35	283	1	0.10479	0.00353357	.	.	weak	DSPP,colon,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.C2637T	p.S879S	TGACAGCAGTGAT	.	scavenged	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102477395	102477395	+	Missense_Mutation	SNP	A	A	G	rs1784423	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	81	204	0	0.532895	0	G|0.400;N|0.000	0.400	strong	.	MMP20	52	.	NM_004771	exon6	c.T824C	p.V275A	AGGAATACTTTCC	.	PASS	Atlas-SNP
SCOC	60592	hgsc.bcm.edu	37	4	141294814	141294814	+	Missense_Mutation	SNP	G	G	C	rs2271430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	62	81	0	0.53913	0	G|0.887;C|0.113	0.113	strong	SCOC_ENST00000394201,NS,carcinoma,0,1	SCOC	11	1	NM_001153484	exon1	c.G124C	p.V42L	GTCCAAGTGTCCC	.	PASS	Atlas-SNP
CES4A	283848	hgsc.bcm.edu	37	16	67037054	67037054	+	Missense_Mutation	SNP	A	A	C	rs61744399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	66	128	0	0.425806	0	A|0.791;C|0.209	0.209	strong	.	CES4A	24	.	NM_173815	exon6	c.A772C	p.S258R	ATCACTAGTAACC	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39871135	39871135	+	Silent	SNP	C	C	T	rs2001923	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	56	121	0	0.434109	0	C|0.932;T|0.068	0.068	strong	IDO2_ENST00000502986,trunk,malignant_melanoma,+1,1	IDO2	78	1	NM_194294	exon10	c.C810T	p.S270S	AGTTTCCCAAGAG	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140222534	140222534	+	Missense_Mutation	SNP	C	C	A	rs6889154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	29	55	0	0.508772	0	C|0.978;A|0.022	0.022	strong	PCDHA8_ENST00000531613,NS,carcinoma,-1,6	PCDHA8	366	6	NM_031856	exon1	c.C1628A	p.P543Q	GCGTGCCGCCTCT	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129289752	129289752	+	Silent	SNP	C	C	T	rs2285365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	151	327	0	0.505017	0	C|0.857;T|0.143	0.143	strong	.	PLXND1	149	.	NM_015103	exon19	c.G3627A	p.Q1209Q	GTGACTCTGGAGC	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55111273	55111273	+	Silent	SNP	C	C	T	rs2296128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	61	121	0	0.544643	0	C|0.937;T|0.063	0.063	strong	.	.	.	.	NM_001013646	exon2	c.C295T	p.L99L	ACTCCACTAAAGA	.	PASS	Atlas-SNP
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	71	0	1	0	C|0.503;A|0.003	.	strong	TTLL2,NS,carcinoma,0,1	TTLL2	82	1	NM_031949	exon3	c.C1314T	p.D438D	CATCGACGCTGCA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017307	1017307	+	Missense_Mutation	SNP	G	G	A	rs372717767	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1352	173	1136	14	0.127959	0.0123239	.	.	weak	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.C5494T	p.P1832S	TGTGAGGGTGTGA	.	scavenged	Atlas-SNP
GDF15	9518	hgsc.bcm.edu	37	19	18499151	18499151	+	Silent	SNP	C	C	T	rs1059022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	62	92	0	0.48062	0	C|0.799;T|0.201	0.201	strong	GDF15,NS,carcinoma,0,1	GDF15	31	1	NM_004864	exon2	c.C333T	p.P111P	CCTTCCCGAGGGG	.	PASS	Atlas-SNP
NUDCD1	84955	hgsc.bcm.edu	37	8	110302047	110302047	+	Missense_Mutation	SNP	T	T	G	rs2980619	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	370	370	346	0	1	0	G|0.634;N|0.000	0.634	strong	.	NUDCD1	58	.	NM_032869	exon5	c.A756C	p.L252F	AAATGTTAAAGAC	.	PASS	Atlas-SNP
CLUH	23277	hgsc.bcm.edu	37	17	2604698	2604698	+	Silent	SNP	G	G	A	rs115717445	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	53	95	0	0.609195	0	G|0.993;A|0.007	0.007	strong	.	.	.	.	NM_015229	exon6	c.C747T	p.V249V	GATGCTGACTTGC	.	PASS	Atlas-SNP
DPP8	54878	hgsc.bcm.edu	37	15	65772698	65772698	+	Silent	SNP	T	T	C	rs352461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	54	0	0.485294	0	T|0.871;C|0.129	0.129	strong	.	DPP8	78	.	NM_197960	exon11	c.A1206G	p.L402L	TATCTGTAGGCGA	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16918972	16918972	+	Silent	SNP	A	A	G	rs1801241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	38	84	0	0.422222	0	A|0.814;G|0.186	0.186	strong	CUBN,NS,carcinoma,0,1	CUBN	515	1	NM_001081	exon57	c.T9030C	p.A3010A	CGGCCCAGCGATG	.	PASS	Atlas-SNP
MXRA8	54587	hgsc.bcm.edu	37	1	1290408	1290408	+	Silent	SNP	A	A	G	rs147996767	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	7	11	0	0.5	0	A|0.939;G|0.061	0.061	strong	.	MXRA8	28	.	NM_032348	exon5	c.T603C	p.A201A	CTGTTGAGCCTCC	.	PASS	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1555589	1555589	+	Missense_Mutation	SNP	A	A	G	rs2248128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	101	1	1	0.00990099	A|0.561;G|0.439	0.439	strong	.	TELO2	44	.	NM_016111	exon16	c.A2021G	p.Q674R	AGACCCAGCGGCT	.	PASS	Atlas-SNP
ZSCAN10	84891	hgsc.bcm.edu	37	16	3140601	3140601	+	Silent	SNP	C	C	T	rs140690870	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	11	41	0	0.366667	0	C|0.991;T|0.009	0.009	strong	.	ZSCAN10	63	.	NM_032805	exon5	c.G669A	p.E223E	TTTGGGCTCTTCT	.	PASS	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	37	19	12772165	12772165	+	Missense_Mutation	SNP	G	G	A	rs1054487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	67	153	0	0.432258	0	T|0.000;G|0.602;A|0.398	0.398	strong	MAN2B1,NS,adenoma,0,1	MAN2B1	91	1	NM_001173498	exon7	c.C935T	p.T312I	ATCACAGTGTGGT	.	PASS	Atlas-SNP
TRMT12	55039	hgsc.bcm.edu	37	8	125463544	125463544	+	Silent	SNP	T	T	C	rs11556913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	78	113	0	0.573529	0	A|0.000;C|0.268;G|0.000;T|0.731	0.268	strong	.	TRMT12	28	.	NM_017956	exon1	c.T376C	p.L126L	GCCGAGTTGGAGG	.	PASS	Atlas-SNP
SNTG2	54221	hgsc.bcm.edu	37	2	1168781	1168781	+	Missense_Mutation	SNP	C	C	A	rs28505970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	48	105	0	0.475248	0	C|0.822;A|0.178	0.178	strong	SNTG2,NS,carcinoma,0,1	SNTG2	125	1	NM_018968	exon8	c.C503A	p.S168Y	CAGGGTCCCCAGG	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	118	253	1	0.608247	0.00395257	T|0.824;G|0.176	0.176	strong	.	DYNC2H1	246	.	NM_001080463	exon67	c.T10185G	p.T3395T	TGTTACTGAGGTT	.	PASS	Atlas-SNP
OR1L1	26737	hgsc.bcm.edu	37	9	125424164	125424164	+	Missense_Mutation	SNP	C	C	T	rs111803762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	151	155	0	0.668142	0	C|0.987;T|0.013	0.013	strong	OR1L1,caecum,carcinoma,0,1	OR1L1	54	1	NM_001005236	exon1	c.C170T	p.T57M	TCCAGACGCCCAT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124270467	124270467	+	Silent	SNP	C	C	T	rs116310078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	30	27	0	0.5	0	C|0.994;T|0.006	0.006	strong	.	DNAH10	888	.	NM_207437	exon9	c.C1222T	p.L408L	GTCAACCTGCGGA	.	PASS	Atlas-SNP
PCDHA5	56143	hgsc.bcm.edu	37	5	140202821	140202821	+	Silent	SNP	C	C	G	rs80008076	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	145	258	0	0.525362	0	C|0.983;G|0.017	0.017	strong	PCDHA5_ENST00000529859,NS,carcinoma,0,2	PCDHA5	361	2	NM_018908	exon1	c.C1461G	p.A487A	GAACGCCCTGGTG	.	PASS	Atlas-SNP
ITGAX	3687	hgsc.bcm.edu	37	16	31382464	31382464	+	Silent	SNP	G	G	C	rs2230426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	36	68	0	0.467532	0	G|0.961;C|0.039	0.039	strong	.	ITGAX	198	.	NM_000887	exon15	c.G1770C	p.G590G	GAGCGGGGGTCAA	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75899300	75899300	+	Missense_Mutation	SNP	T	T	G	rs75535959	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	50	74	0	0.549451	0	T|0.984;G|0.016	0.016	strong	.	COL12A1	385	.	NM_004370	exon6	c.A626C	p.K209T	GGAATTTTTTTTA	.	PASS	Atlas-SNP
LGI2	55203	hgsc.bcm.edu	37	4	25005193	25005193	+	Silent	SNP	G	G	A	rs2232028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	72	148	0	0.441718	0	G|0.332;A|0.668	0.668	strong	.	LGI2	62	.	NM_018176	exon8	c.C1518T	p.Y506Y	CTGCACGTAAATC	.	PASS	Atlas-SNP
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987526	154987526	+	Silent	SNP	C	C	T	rs11264295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	100	73	0	1	0	C|0.487;T|0.513	0.513	strong	ZBTB7B,NS,carcinoma,0,1	ZBTB7B	69	1	NM_001252406	exon4	c.C492T	p.I164I	GGAGATCCCGTGT	.	PASS	Atlas-SNP
APC	324	hgsc.bcm.edu	37	5	112175240	112175240	+	Missense_Mutation	SNP	G	G	C	rs1801166	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	54	171	0	0.333333	0	G|0.992;C|0.008	0.008	strong	APC,bladder,carcinoma,0,14	APC	4158	14	NM_001127510	exon17	c.G3949C	p.E1317Q	TCAGCTGAAGATC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678013	100678013	+	Missense_Mutation	SNP	G	G	A	rs75312831	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	379	65	166	2	0.171504	0.0120482	A|0.022;G|0.978	0.022	strong	MUC17,NS,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.G3316A	p.V1106M	ACAAGTGTGCCTG	.	scavenged	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	37035866	37035866	+	Silent	SNP	G	G	T	rs36048308	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	67	121	0	0.523438	0	G|0.925;T|0.075	0.075	strong	.	VIT	138	.	NM_053276	exon15	c.G1641T	p.T547T	GGACACGCGCATC	.	PASS	Atlas-SNP
PRDM8	56978	hgsc.bcm.edu	37	4	81124596	81124596	+	Silent	SNP	G	G	C	rs12780	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	61	102	0	0.521368	0	G|0.671;C|0.329	0.329	strong	PRDM8,colon,carcinoma,0,1	PRDM8	44	1	NM_001099403	exon4	c.G1980C	p.R660R	GAAGCGGCGGCGA	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	26	65	0	0.541667	0	T|0.749;C|0.251	0.251	strong	.	ATP10A	270	.	NM_024490	exon21	c.A4449G	p.Q1483Q	TGGCCCTTGAAGT	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200967687	200967687	+	Silent	SNP	C	C	G	rs61740473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	36	77	0	0.537313	0	C|0.920;G|0.080	0.080	strong	.	KIF21B	208	.	NM_017596	exon14	c.G1902C	p.A634A	CAGGTCCGCCTGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408030	105408030	+	Silent	SNP	A	A	G	rs9671643	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	181	195	0	1	0	A|0.469;G|0.531	0.531	strong	AHNAK2_ENST00000333244,caecum,carcinoma,-2,1	AHNAK2	719	1	NM_138420	exon7	c.T13758C	p.D4586D	CTCCACATCGGGG	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229772932	229772932	+	Missense_Mutation	SNP	A	A	G	rs3811474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	74	136	0	0.45679	0	A|0.836;G|0.164	0.164	strong	.	URB2	152	.	NM_014777	exon4	c.A2572G	p.K858E	TTTGCAAAAGCTG	.	PASS	Atlas-SNP
EIF4G1	1981	hgsc.bcm.edu	37	3	184045410	184045410	+	Missense_Mutation	SNP	T	T	C	rs2230570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	89	178	0	0.511494	0	T|0.960;C|0.040	0.040	strong	.	EIF4G1	151	.	NM_001194946	exon26	c.T3719C	p.L1240P	GCCCCCTGAAGGC	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55594869	55594869	+	Missense_Mutation	SNP	G	G	A	rs56711116	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	149	261	0	0.526502	0	G|0.901;A|0.099	0.099	strong	OR5L2,colon,carcinoma,0,2	OR5L2	135	2	NM_001004739	exon1	c.G175A	p.V59M	ACCCCCGTGTACT	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464934	39464934	+	Missense_Mutation	SNP	G	G	A	rs150797223	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	86	162	0	0.452632	0	G|0.995;A|0.005	0.005	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C572T	p.P191L	AGGACAGGCTGGC	.	PASS	Atlas-SNP
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	108	241	2	0.467532	0.00829876	T|0.652;C|0.348	0.348	strong	MAP9,NS,carcinoma,0,1	MAP9	79	1	NM_001039580	exon11	c.A1496G	p.K499R	GTTTTCTTCTTGT	.	scavenged	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17923043	17923043	+	Silent	SNP	G	G	A	rs9322		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	66	123	0	0.528	0	G|1.000;|0.000	.	weak	.	SNX5	38	.	NM_014426	exon13	c.C1173T	p.V391V	AAGGGAGACATTG	.	PASS	Atlas-SNP
DENND2A	27147	hgsc.bcm.edu	37	7	140227184	140227184	+	Silent	SNP	C	C	T	rs76760136	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	113	243	0	0.54067	0	C|0.995;T|0.005	0.005	strong	.	DENND2A	132	.	NM_015689	exon13	c.G2439A	p.P813P	GGGCGTCGGCGAG	.	PASS	Atlas-SNP
ATP2C1	27032	hgsc.bcm.edu	37	3	130698205	130698205	+	Silent	SNP	C	C	T	rs114319700	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	87	122	0	0.59589	0	C|0.995;T|0.005	0.005	strong	.	ATP2C1	94	.	NM_001199181	exon18	c.C1785T	p.A595A	CATTGCCTCAGGA	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408555	29408555	+	Missense_Mutation	SNP	C	C	A	rs17177674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	67	189	0	0.370166	0	C|0.946;A|0.054	0.054	strong	.	OR10C1	58	.	NM_013941	exon1	c.C763A	p.L255I	ACCGCACTCTTTA	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955961	38955961	+	Missense_Mutation	SNP	G	G	A	rs4624233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	33	77	0	0.445946	0	G|0.752;A|0.248	0.248	strong	.	KRT28	65	.	NM_181535	exon1	c.C185T	p.A62V	CCACCAGCATGGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	63	240	0	0.216495	0	.	.	none	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.T3444C	p.S1148S	CAGCAGTGAAAGC	.	PASS	Atlas-SNP
UBE3C	9690	hgsc.bcm.edu	37	7	157000176	157000176	+	Silent	SNP	T	T	C	rs2301914	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	161	172	0	1	0	T|0.498;C|0.502	0.502	strong	.	UBE3C	124	.	NM_014671	exon12	c.T1503C	p.Y501Y	CTTTTATCTTTTT	.	PASS	Atlas-SNP
RSL1D1	26156	hgsc.bcm.edu	37	16	11940390	11940390	+	Silent	SNP	T	T	C	rs8052900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	100	84	1	0.990099	0.0119048	T|0.271;C|0.729	0.729	strong	RSL1D1,NS,carcinoma,0,1	RSL1D1	40	1	NM_015659	exon5	c.A603G	p.T201T	TAAGACTGTTCCA	.	scavenged	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038162	22038162	+	Silent	SNP	A	A	C	rs17197261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	81	129	0	0.468208	0	A|0.916;C|0.084	0.084	strong	.	OR10G3	40	.	NM_001005465	exon1	c.T714G	p.A238A	TGAAAAAGCCCGG	.	PASS	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	37	1	38188736	38188736	+	Missense_Mutation	SNP	G	G	A	rs146568133	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	128	0	0.483051	0	G|0.999;A|0.001	0.001	strong	.	EPHA10	120	.	NM_001099439	exon10	c.C1937T	p.T646M	TCCAGCGTGACGC	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27279877	27279877	+	Missense_Mutation	SNP	T	T	C	rs11965377	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	39	93	0	0.410526	0	T|0.968;C|0.032	0.032	strong	.	POM121L2	61	.	NM_033482	exon1	c.A73G	p.R25G	TGGGCCTCTCGGG	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	212	1255	0	0.959276	0	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	NM_001144013	exon20	c.A3851G	p.H1284R	TCAAAGTGGAAAA	.	scavenged	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120744349	120744349	+	Missense_Mutation	SNP	T	T	C	rs956748	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	116	1	1	0.00862069	T|0.823;C|0.177	0.177	strong	.	TAF2	204	.	NM_003184	exon26	c.A3415G	p.T1139A	AGGCTGTAGATTC	.	PASS	Atlas-SNP
LTV1	84946	hgsc.bcm.edu	37	6	144183376	144183376	+	Silent	SNP	T	T	C	rs56155985	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	27	57	0	0.586957	0	T|0.936;C|0.064	0.064	strong	.	LTV1	48	.	NM_032860	exon8	c.T1059C	p.I353I	ATCTATTTGTAGT	.	PASS	Atlas-SNP
EVI5L	115704	hgsc.bcm.edu	37	19	7914022	7914022	+	Silent	SNP	C	C	T	rs554853	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	34	65	0	0.465753	0	C|0.984;T|0.016	0.016	strong	.	EVI5L	43	.	NM_001159944	exon3	c.C543T	p.N181N	CTTCAACGTCATG	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	69	109	0	0.5	0	G|0.784;A|0.216	0.216	strong	.	SMOC1	61	.	NM_001034852	exon2	c.G126A	p.Q42Q	CCCACAGTGCAAC	.	PASS	Atlas-SNP
UBA1	7317	hgsc.bcm.edu	37	X	47070261	47070261	+	Silent	SNP	G	G	A	rs2230147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	94	177	0	0.522222	0	0|0.004;A|0.126	0.126	strong	.	UBA1	89	.	NM_153280	exon19	c.G2220A	p.P740P	AGCGCCGTTCTGG	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503278	140503278	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	24	61	1	0.369231	0.0163934	.	.	none	PCDHB4,NS,carcinoma,+1,1	PCDHB4	177	1	NM_018938	exon1	c.T1698C	p.N566N	GCAGAATGGCTCC	.	scavenged	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31256905	31256905	+	Missense_Mutation	SNP	T	T	C	rs1046458	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	63	149	0	0.463235	0	T|0.458;C|0.542	0.542	strong	.	DDX11	188	.	NM_001257144	exon27	c.T2851C	p.C951R	CCAGAGTGCTGCC	.	PASS	Atlas-SNP
IL5RA	3568	hgsc.bcm.edu	37	3	3139957	3139957	+	Missense_Mutation	SNP	T	T	C	rs2290610	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	78	158	0	0.52	0	T|0.610;C|0.390	0.390	strong	.	IL5RA	55	.	NM_001243099	exon6	c.A385G	p.I129V	TCACAATTGAGGT	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24533539	24533539	+	Missense_Mutation	SNP	C	C	A	rs10146906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	24	57	0	0.5	0	C|0.593;A|0.407	0.407	strong	.	LRRC16B	120	.	NM_138360	exon32	c.C3064A	p.L1022M	AGGGTCCTGGAGG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40364011	40364011	+	Silent	SNP	G	G	A	rs78835791	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	65	146	0	0.445205	0	G|0.988;A|0.012	0.012	strong	.	FCGBP	416	.	NM_003890	exon31	c.C14631T	p.S4877S	GGAGCAGGAGCCA	.	PASS	Atlas-SNP
RGMA	56963	hgsc.bcm.edu	37	15	93588657	93588657	+	Silent	SNP	G	G	A	rs61733836	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	77	0	0.452381	0	G|0.994;A|0.006	0.006	strong	.	RGMA	49	.	NM_001166283	exon4	c.C948T	p.D316D	CTGGCTGTCCCAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411852	105411852	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	7	264	0	0.0234899	0	.	.	none	AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.A9936G	p.K3312K	CTTGAATTTGGGC	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149485059	149485059	+	Missense_Mutation	SNP	T	T	C	rs709060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	26	43	0	0.509804	0	T|0.893;C|0.107	0.107	strong	.	.	.	.	NM_198455	exon26	c.T3814C	p.S1272P	CTCTGCTGTGAGT	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7514235	7514235	+	Missense_Mutation	SNP	C	C	G	rs6952195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	48	0	1	0	C|0.712;G|0.288	0.288	strong	COL28A1,NS,carcinoma,0,1	COL28A1	113	1	NM_001037763	exon15	c.G1299C	p.E433D	TACCTTCTCCCCT	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871055	170871055	+	Silent	SNP	G	G	A	rs112928724		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	3	78	0	0.046875	0	G|0.500;A|0.500	0.500	weak	TBP,colon,carcinoma,0,2	TBP	58	2	NM_003194	exon3	c.G231A	p.Q77Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
LRRC52	440699	hgsc.bcm.edu	37	1	165532746	165532746	+	Missense_Mutation	SNP	T	T	A	rs17407838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	23	58	0	0.410714	0	T|0.917;A|0.083	0.083	strong	.	LRRC52	50	.	NM_001005214	exon2	c.T627A	p.D209E	AGATGATCTAAAT	.	PASS	Atlas-SNP
SLC6A16	28968	hgsc.bcm.edu	37	19	49793620	49793620	+	Silent	SNP	C	C	T	rs34817563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	68	134	0	0.511278	0	C|0.989;T|0.011	0.011	strong	.	SLC6A16	62	.	NM_014037	exon12	c.G1971A	p.P657P	TGCCCACGGTGGG	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	109	199	0	0.436	0	0|0.003;T|0.145	0.145	strong	.	KIF4A	118	.	NM_012310	exon15	c.C1656T	p.P552P	GCAGCCCATTCAG	.	PASS	Atlas-SNP
LYPLA1	10434	hgsc.bcm.edu	37	8	54967638	54967638	+	Missense_Mutation	SNP	A	A	C	rs76859468	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	108	212	0	0.484305	0	A|0.983;C|0.017	0.017	strong	.	LYPLA1	15	.	NM_006330	exon6	c.T342G	p.I114M	TCCCAAAATAATT	.	PASS	Atlas-SNP
TACSTD2	4070	hgsc.bcm.edu	37	1	59042181	59042181	+	Missense_Mutation	SNP	G	G	T	rs14008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	53	79	0	0.557895	0	G|0.865;T|0.135	0.135	strong	.	TACSTD2	6	.	NM_002353	exon1	c.C648A	p.D216E	ATCCACGTCACCG	.	PASS	Atlas-SNP
WWC3	55841	hgsc.bcm.edu	37	X	10106971	10106971	+	Missense_Mutation	SNP	C	C	T	rs377116582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	16	10	0	0.842105	0	.	.	weak	.	WWC3	142	.	NM_015691	exon21	c.C3079T	p.R1027W	GCCGAGCGGCAGG	.	PASS	Atlas-SNP
TACSTD2	4070	hgsc.bcm.edu	37	1	59041940	59041940	+	Missense_Mutation	SNP	T	T	C	rs114373153	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	61	103	0	0.580952	0	T|0.965;C|0.035	0.035	strong	.	TACSTD2	6	.	NM_002353	exon1	c.A889G	p.I297V	TGGTGATCACCAG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89401825	89401825	+	Silent	SNP	T	T	C	rs35676128	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	31	67	0	0.584906	0	T|0.985;C|0.015	0.015	strong	.	ACAN	220	.	NM_001135	exon12	c.T6009C	p.Y2003Y	TCCATATTTTAGT	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	72	165	1	0.426035	0.00606061	C|0.671;A|0.329	0.329	strong	TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G764T	p.R255L	TTTGGTCGCATCT	.	scavenged	Atlas-SNP
C2orf83	56918	hgsc.bcm.edu	37	2	228493211	228493211	+	Missense_Mutation	SNP	G	G	A	rs28739019	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	69	136	0	0.413174	0	G|0.709;A|0.291	0.291	strong	C2orf83,NS,carcinoma,0,1	C2orf83	15	1	NM_020161	exon2	c.C134T	p.S45L	TTTGGCGAGGGCT	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100468284	100468284	+	Silent	SNP	A	A	G	rs1054391	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	183	165	0	1	0	A|0.482;G|0.518	0.518	strong	TRIP6,colon,carcinoma,0,1	TRIP6	45	1	NM_003302	exon6	c.A918G	p.V306V	CTTTGTATGTTCT	.	PASS	Atlas-SNP
MACROD2	140733	hgsc.bcm.edu	37	20	14066276	14066276	+	Missense_Mutation	SNP	C	C	T	rs2990505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	44	129	1	0.40367	0.00775194	C|0.749;T|0.251	0.251	strong	C20orf133,NS,carcinoma,0,1	MACROD2	34	1	NM_080676	exon3	c.C173T	p.T58I	AAAATACTCAGGA	.	scavenged	Atlas-SNP
MRPS27	23107	hgsc.bcm.edu	37	5	71519664	71519664	+	Missense_Mutation	SNP	C	C	T	rs3209157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	59	101	2	0.508621	0.019802	T|0.258;G|0.146	0.258	strong	MRPS27,NS,neuroblastoma,-1,1	MRPS27	23	1	NM_015084	exon10	c.G851A	p.G284D	ACTGCACCCAGCA	.	scavenged	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078409	2078409	+	Silent	SNP	A	A	G	rs2074893	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	32	70	0	0.533333	0	A|0.578;G|0.422	0.422	strong	.	.	.	.	NM_130807	exon3	c.T151C	p.L51L	GGGGCAACTGCAC	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117146319	117146319	+	Silent	SNP	C	C	T	rs61730486	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	105	197	1	0.525	0.00507614	C|0.965;T|0.035	0.035	strong	.	IGSF3	294	.	NM_001542	exon7	c.G1611A	p.V537V	TGCCCGCACCCAT	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152518847	152518847	+	Silent	SNP	G	G	A	rs77547727	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	63	119	0	0.492188	0	G|0.971;A|0.029	0.029	strong	.	NEB	1697	.	NM_004543	exon46	c.C5772T	p.Y1924Y	AGCCTTGTACTGA	.	PASS	Atlas-SNP
TEX2	55852	hgsc.bcm.edu	37	17	62291105	62291105	+	Missense_Mutation	SNP	G	G	A	rs28605685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	68	128	0	0.475524	0	G|0.937;A|0.063	0.063	strong	.	TEX2	89	.	NM_018469	exon2	c.C473T	p.T158I	GAACTGGTTTTCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679754	100679754	+	Missense_Mutation	SNP	C	C	G	rs4992073	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	39	124	0	0.327731	0	C|0.973;G|0.027	0.027	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5057G	p.T1686S	CTTATACTGAAGG	.	PASS	Atlas-SNP
ATHL1	80162	hgsc.bcm.edu	37	11	293188	293188	+	Silent	SNP	T	T	C	rs12801980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	30	80	0	0.461538	0	C|0.344;N|0.000	0.344	strong	.	ATHL1	88	.	NM_025092	exon8	c.T1296C	p.H432H	GTACCATTCAGGG	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8790473	8790473	+	Silent	SNP	G	G	A	rs61761067	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	109	173	0	0.542289	0	G|0.969;A|0.031	0.031	strong	.	PIK3R5	79	.	NM_001142633	exon12	c.C1845T	p.D615D	CCAGGGGTCCAGC	.	PASS	Atlas-SNP
RIMBP3C	150221	hgsc.bcm.edu	37	22	21742598	21742598	+	Missense_Mutation	SNP	G	G	A	rs468931	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	988	205	911	0	0.20749	0	G|0.250;A|0.750	0.750	weak	RIMBP3B,NS,carcinoma,0,3	RIMBP3C	6	3	NM_001128633	exon1	c.G4451A	p.R1484K	AGAAAAGGCAGTT	.	scavenged	Atlas-SNP
ASXL1	171023	hgsc.bcm.edu	37	20	31022480	31022480	+	Silent	SNP	C	C	T	rs79865730	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	33	29	0	0.611111	0	C|0.993;T|0.007	0.007	strong	.	ASXL1	1114	.	NM_015338	exon12	c.C1965T	p.T655T	GGCCACCGATGAG	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026122	+	Silent	SNP	C	C	T	rs3797464		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	26	101	22	0.254902	0.217822	.	.	weak	GPRIN1,rectum,carcinoma,-1,2	GPRIN1	77	2	NM_052899	exon2	c.G714A	p.L238L	CTTTCTCAAAGAC	.	scavenged	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17204187	17204187	+	Missense_Mutation	SNP	G	G	A	rs11254413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	34	118	0	0.354167	0	G|0.579;A|0.421	0.421	strong	.	TRDMT1	46	.	NM_004412	exon4	c.C301T	p.H101Y	GAATATGTAAGAA	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42585099	42585099	+	Missense_Mutation	SNP	A	A	G	rs16973015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	99	177	0	0.582353	0	A|0.989;G|0.011	0.011	strong	.	GANC	57	.	NM_198141	exon5	c.A496G	p.I166V	CTACAGATTCTTC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410183	105410183	+	Missense_Mutation	SNP	T	T	C	rs10438246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	254	248	1	1	0.00403226	T|0.456;C|0.544	0.544	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A11605G	p.M3869V	GTTTCATGTCCAC	.	PASS	Atlas-SNP
NUP98	4928	hgsc.bcm.edu	37	11	3714489	3714489	+	Silent	SNP	C	C	T	rs1875	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	29	77	0	0.381579	0	C|0.757;N|0.000	.	strong	.	NUP98	149	.	NM_016320	exon27	c.G4284A	p.A1428A	GCTGAGCGCCCTA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149486367	149486367	+	Missense_Mutation	SNP	C	C	A	rs855692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	47	81	0	0.54023	0	C|0.968;A|0.032	0.032	strong	.	.	.	.	NM_198455	exon30	c.C4343A	p.P1448Q	ATGAGCCGAGCTA	.	PASS	Atlas-SNP
NIM1	0	hgsc.bcm.edu	37	5	43245922	43245922	+	Silent	SNP	C	C	T	rs13176855	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	75	159	0	0.487013	0	C|0.645;T|0.355	0.355	strong	.	.	.	.	NM_153361	exon2	c.C45T	p.H15H	CCCCCACTATGCC	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786748	75786748	+	Missense_Mutation	SNP	C	C	T	rs112332186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	26	18	0	0.577778	0	C|0.516;T|0.484	0.484	strong	.	ZNF717	160	.	NM_001128223	exon5	c.G2026A	p.D676N	TTACATCCATACG	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549511	158549511	+	Missense_Mutation	SNP	A	A	G	rs863363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	121	1	0.992754	0.00826446	A|0.470;G|0.529	0.529	strong	.	OR10X1	96	.	NM_001004477	exon1	c.T179C	p.I60T	ATGATGATCAGAT	.	PASS	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53636000	53636000	+	Silent	SNP	G	G	A	rs4784320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	77	124	0	0.546099	0	G|0.889;A|0.111	0.111	strong	RPGRIP1L,colon,carcinoma,0,1	RPGRIP1L	118	1	NM_015272	exon27	c.C3936T	p.D1312D	CTCCAAGTCATCT	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27573968	27573968	+	Silent	SNP	T	T	C	rs140674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	68	159	0	0.435897	0	T|0.896;C|0.104	0.104	strong	.	GABRG3	115	.	NM_001270873	exon5	c.T507C	p.A169A	CAATGCTGAGTGC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79455714	79455714	+	Silent	SNP	C	C	G	rs4975070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	51	133	0	0.455357	0	C|0.485;G|0.515	0.515	strong	.	FRAS1	779	.	NM_025074	exon71	c.C11037G	p.P3679P	GGATCCCAATACA	.	PASS	Atlas-SNP
AFP	174	hgsc.bcm.edu	37	4	74316461	74316461	+	Silent	SNP	C	C	T	rs115622472	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	70	145	0	0.434783	0	C|0.994;T|0.006	0.006	strong	.	AFP	60	.	NM_001134	exon11	c.C1419T	p.G473G	CTGTGGCGAGGGA	.	PASS	Atlas-SNP
CRY1	1407	hgsc.bcm.edu	37	12	107395106	107395106	+	Silent	SNP	A	A	G	rs8192440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	128	244	1	0.479401	0.00409836	A|0.264;G|0.736	0.736	strong	CRY1,NS,carcinoma,-2,1	CRY1	74	1	NM_004075	exon5	c.T636C	p.G212G	TTCTCCACCTGGC	.	PASS	Atlas-SNP
FAM83B	222584	hgsc.bcm.edu	37	6	54805074	54805074	+	Missense_Mutation	SNP	C	C	G	rs9475076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	54	80	0	0.490909	0	C|0.945;G|0.055	0.055	strong	.	FAM83B	186	.	NM_001010872	exon5	c.C1305G	p.S435R	TGTAAGCCACCAC	.	PASS	Atlas-SNP
KERA	11081	hgsc.bcm.edu	37	12	91449990	91449990	+	Silent	SNP	C	C	T	rs2735333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	40	97	0	0.588235	0	C|0.364;T|0.636	0.636	strong	.	KERA	62	.	NM_007035	exon2	c.G69A	p.V23V	CTGCCTCACACTT	.	PASS	Atlas-SNP
SLCO5A1	81796	hgsc.bcm.edu	37	8	70588878	70588878	+	Silent	SNP	T	T	C	rs10448034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	51	91	0	0.476636	0	T|0.864;C|0.136	0.136	strong	.	SLCO5A1	142	.	NM_030958	exon9	c.A2055G	p.A685A	TCCCAGTGCAAAA	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26468319	26468319	+	Silent	SNP	C	C	T	rs3734541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	59	146	0	0.464567	0	C|0.870;T|0.130	0.130	strong	.	BTN2A1	118	.	NM_007049	exon8	c.C1126T	p.L376L	TGTGTCCTAGGCC	.	PASS	Atlas-SNP
KIAA0319	9856	hgsc.bcm.edu	37	6	24551729	24551729	+	Silent	SNP	T	T	C	rs807535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	245	257	0	1	0	A|0.006;C|0.112	0.112	strong	.	KIAA0319	117	.	NM_001168375	exon20	c.A2973G	p.K991K	TGTTTTTTTCCTG	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	337	159	342	0	0.47181	0	T|0.707;C|0.293	0.293	strong	.	LRIG1	138	.	NM_015541	exon14	c.A1843G	p.M615V	GGGCCATGGTGGT	.	PASS	Atlas-SNP
NCLN	56926	hgsc.bcm.edu	37	19	3207422	3207422	+	Silent	SNP	T	T	C	rs3816054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	44	117	0	0.463158	0	T|0.820;C|0.180	0.180	strong	.	NCLN	27	.	NM_020170	exon14	c.T1587C	p.A529A	CCTGGCTGTTGGC	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151082923	151082923	+	Silent	SNP	T	T	C	rs1463725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	58	129	0	0.446154	0	T|0.856;C|0.144	0.144	strong	.	MED12L	271	.	NM_053002	exon20	c.T3009C	p.N1003N	TGACAATGCGGCC	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536114	1536114	+	Silent	SNP	C	C	A	rs79788206	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	37	76	0	0.445783	0	C|0.976;A|0.024	0.024	strong	.	PTX4	46	.	NM_001013658	exon3	c.G1248T	p.V416V	GCTCCCCACGAAG	.	PASS	Atlas-SNP
ZFPL1	7542	hgsc.bcm.edu	37	11	64854812	64854812	+	Missense_Mutation	SNP	G	G	A	rs35251366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	68	171	0	0.441558	0	G|0.966;A|0.034	0.034	strong	.	ZFPL1	25	.	NM_006782	exon7	c.G653A	p.R218Q	ATACGCGGGATGA	.	PASS	Atlas-SNP
CERCAM	51148	hgsc.bcm.edu	37	9	131196704	131196704	+	Silent	SNP	G	G	A	rs7259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	78	0	1	0	G|0.673;A|0.327	0.327	strong	.	CERCAM	104	.	NM_016174	exon11	c.G1347A	p.K449K	ACGGAAGCAGGTG	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57071167	57071167	+	Silent	SNP	G	G	A	rs137919442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	23	62	0	0.343284	0	G|0.998;A|0.002	0.002	strong	.	NLRC5	186	.	NM_032206	exon14	c.G2772A	p.A924A	GAGTGCGTGCTGG	.	PASS	Atlas-SNP
OR2M3	127062	hgsc.bcm.edu	37	1	248366792	248366792	+	Silent	SNP	T	T	C	rs12562957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	416	206	423	0	0.495192	0	T|0.828;C|0.172	0.172	strong	.	OR2M3	116	.	NM_001004689	exon1	c.T423C	p.C141C	AATTTGTGGACTT	.	PASS	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	94	0	0.517241	0	A|0.525;G|0.475	0.475	strong	.	USP34	334	.	NM_014709	exon80	c.T10386C	p.A3462A	TTCCTCAGCTAGG	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Missense_Mutation	SNP	T	T	C	rs7258015	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	129	0	1	0	T|0.809;C|0.191	0.191	strong	ICAM3,colon,carcinoma,0,1	ICAM3	29	1	NM_002162	exon2	c.A343G	p.R115G	ACTCACTGTACAC	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90281452	90281452	+	Missense_Mutation	SNP	G	G	A	rs35389334	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	72	105	0	0.553846	0	G|0.977;A|0.023	0.023	strong	WDR93,colon,carcinoma,+1,1	WDR93	63	1	NM_020212	exon16	c.G1946A	p.R649H	GTGAGCGTTTCCT	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9122926	9122926	+	Silent	SNP	C	C	T	rs6894626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	77	203	0	0.409574	0	C|0.837;T|0.163	0.163	strong	.	SEMA5A	236	.	NM_003966	exon14	c.G1623A	p.G541G	AAAGTGCCCATCC	.	PASS	Atlas-SNP
IL4I1	259307	hgsc.bcm.edu	37	19	50393743	50393743	+	Silent	SNP	A	A	G	rs61740372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	40	63	0	0.526316	0	A|0.982;G|0.018	0.018	strong	.	IL4I1	50	.	NM_172374	exon10	c.T954C	p.D318D	GTGCACATCGTGC	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	37	17	80887123	80887123	+	Missense_Mutation	SNP	G	G	T	rs8072406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	53	119	0	0.477477	0	G|0.974;T|0.026	0.026	strong	.	TBCD	94	.	NM_005993	exon31	c.G2828T	p.G943V	ACCGAGGAGAACT	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44386281	44386281	+	Silent	SNP	C	C	T	rs7587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	53	95	0	0.514563	0	T|0.178;G|0.125	0.178	strong	.	SAMM50	30	.	NM_015380	exon14	c.C1359T	p.G453G	GACAGGCGACAGG	.	PASS	Atlas-SNP
DDX5	1655	hgsc.bcm.edu	37	17	62499163	62499163	+	Silent	SNP	C	C	T	rs56025355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	68	153	0	0.402367	0	C|0.993;T|0.007	0.007	strong	.	DDX5	101	.	NM_004396	exon8	c.G864A	p.Q288Q	AGCAAGCTGTCTT	.	PASS	Atlas-SNP
PCDHA5	56143	hgsc.bcm.edu	37	5	140202132	140202132	+	Missense_Mutation	SNP	A	A	G	rs61730633	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	52	130	0	0.412698	0	A|0.993;G|0.007	0.007	strong	.	PCDHA5	361	.	NM_018908	exon1	c.A772G	p.T258A	AGTGGGACATTAG	.	PASS	Atlas-SNP
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524649	6524649	+	Silent	SNP	T	T	C	rs35137293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	50	131	0	0.454545	0	T|0.978;C|0.022	0.022	strong	.	TNFRSF25	22	.	NM_148966	exon4	c.A426G	p.L142L	GCAGTCTAGGCAT	.	PASS	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960655	22960655	+	Silent	SNP	C	C	T	rs374790272	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	77	0	0.487805	0	.	.	alt	.	TNFRSF10C	30	.	NM_003841	exon1	c.C21T	p.T7T	CAAGACCCTAAAG	.	PASS	Atlas-SNP
BPIFA3	128861	hgsc.bcm.edu	37	20	31812923	31812923	+	Missense_Mutation	SNP	G	G	A	rs3818222	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	137	133	0	1	0	G|0.380;A|0.620	0.620	strong	.	.	.	.	NM_178466	exon4	c.G406A	p.V136I	AACATCGTAAAGA	.	PASS	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	42	108	0	0.4375	0	A|0.634;G|0.366	0.366	strong	.	ZNF879	41	.	NM_001136116	exon5	c.A334G	p.T112A	GATGGCACATTTG	.	PASS	Atlas-SNP
APEX2	27301	hgsc.bcm.edu	37	X	55033238	55033238	+	Silent	SNP	A	A	G	rs6651872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	140	238	0	0.544747	0	A|0.975;0|0.005	.	strong	.	APEX2	50	.	NM_014481	exon6	c.A927G	p.A309A	GGGTGCAGTCTTG	.	PASS	Atlas-SNP
FAM181B	220382	hgsc.bcm.edu	37	11	82443672	82443672	+	Missense_Mutation	SNP	C	C	G	rs6592081	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	45	53	0	1	0	C|0.402;G|0.598	0.598	strong	.	FAM181B	14	.	NM_175885	exon1	c.G1100C	p.R367P	TGGCCCCGCCCGT	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22847072	22847072	+	Missense_Mutation	SNP	G	G	C	rs71236900	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	465	341	531	2	0.733333	0.00376648	G|0.500;C|0.500	0.500	strong	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G601C	p.E201Q	TGCGAAGAGTGTG	.	scavenged	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112406862	112406862	+	Silent	SNP	G	G	A	rs2227950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	229	236	1	0.991342	0.00423729	T|0.062;G|0.554;C|0.125;A|0.259	0.259	strong	MCC_ENST00000408903,colon,carcinoma,-1,4	MCC	234	4	NM_001085377	exon12	c.C1854T	p.A618A	CCTCTCGGCATTG	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73151970	73151970	+	Silent	SNP	C	C	T	rs3739776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	187	189	0	1	0	C|0.427;T|0.573	0.573	strong	.	TRPM3	700	.	NM_001007471	exon25	c.G4023A	p.S1341S	ATTGACCGAATAG	.	PASS	Atlas-SNP
ENPP1	5167	hgsc.bcm.edu	37	6	132211534	132211534	+	Silent	SNP	A	A	G	rs1804025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	71	148	0	0.486301	0	A|0.915;G|0.085	0.085	strong	ENPP1,larynx,carcinoma,+2,1	ENPP1	108	1	NM_006208	exon25	c.A2661G	p.A887A	CAGAGCACGGATC	.	PASS	Atlas-SNP
PAX8	7849	hgsc.bcm.edu	37	2	113994191	113994191	+	Silent	SNP	G	G	A	rs112872760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	35	52	0	0.507246	0	G|0.999;A|0.001	0.001	strong	.	PAX8	42	.	NM_013952	exon8	c.C885T	p.Y295Y	CACGGGGTAGGTC	.	PASS	Atlas-SNP
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	67	132	0	0.455782	0	C|0.741;A|0.259	0.259	strong	.	NLRP12	236	.	NM_144687	exon1	c.A116T	p.K39M	CCTTCTCCCAGCT	.	PASS	Atlas-SNP
TRPC7	57113	hgsc.bcm.edu	37	5	135692575	135692575	+	Silent	SNP	G	G	A	rs2546661	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	76	100	0	0.580153	0	G|0.723;A|0.277	0.277	strong	.	TRPC7	126	.	NM_001167576	exon2	c.C501T	p.P167P	GATGATGGGCGTG	.	PASS	Atlas-SNP
ZSCAN12	9753	hgsc.bcm.edu	37	6	28359170	28359170	+	Silent	SNP	A	A	G	rs2859348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	192	189	1	1	0.00529101	A|0.407;G|0.593	0.593	strong	.	ZSCAN12	35	.	NM_001163391	exon4	c.T897C	p.D299D	GGGTCTATCTCCA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467647	10467647	+	Missense_Mutation	SNP	G	G	C	rs200373757	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	12	192	0	0.0638298	0	G|0.966;C|0.034	0.034	strong	RP1L1,NS,haematopoietic_neoplasm,0,1	RP1L1	453	1	NM_178857	exon4	c.C3961G	p.Q1321E	CTAACTGCACCGC	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	372157	372157	+	Missense_Mutation	SNP	C	C	T	rs34063493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	42	95	0	0.392523	0	A|0.000;C|0.629;G|0.000;T|0.371	0.371	strong	.	B4GALNT4	83	.	NM_178537	exon2	c.C200T	p.A67V	ACGCTGCGCCATC	.	PASS	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39468128	39468128	+	Missense_Mutation	SNP	A	A	T	rs73605945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	125	289	0	0.446429	0	A|0.964;T|0.036	0.036	strong	.	ADAM18	169	.	NM_001190956	exon6	c.A425T	p.Q142L	TTTATCAAATGAA	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	107	164	0	0.514423	0	G|0.729;A|0.271	0.271	strong	.	PTCRA	24	.	NM_138296	exon2	c.G316A	p.V106I	CCTTTGGTCTGCC	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	175	161	0	0.994318	0	C|0.779;A|0.221	0.221	strong	ATP10D,NS,carcinoma,0,1	ATP10D	168	1	NM_020453	exon12	c.C2307A	p.I769I	ACACATCCTGCCC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	68	169	0	0.412121	0	T|0.784;C|0.216	0.216	strong	PSME4,NS,carcinoma,0,1	PSME4	247	1	NM_014614	exon26	c.A2934G	p.S978S	ACTGTATGAACTT	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49698695	49698695	+	Silent	SNP	T	T	C	rs149210839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	70	163	0	0.454545	0	T|0.998;C|0.002	0.002	strong	.	BSN	272	.	NM_003458	exon6	c.T9417C	p.R3139R	TAGCCGTGCCCCA	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708793	168708793	+	Silent	SNP	C	C	G	rs10945500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	15	46	0	0.555556	0	C|0.753;G|0.247	0.247	strong	.	DACT2	46	.	NM_214462	exon4	c.G1644C	p.R548R	TGGCCTCCGCTGG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4510850	4510850	+	Missense_Mutation	SNP	G	G	A	rs145519622	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	22	52	0	0.52381	0	G|0.988;A|0.012	0.012	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C3080T	p.A1027V	CCTGTCGCCACGT	.	PASS	Atlas-SNP
CACNA2D2	9254	hgsc.bcm.edu	37	3	50418547	50418547	+	Silent	SNP	G	G	T	rs56287038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	26	105	0	0.313253	0	G|0.887;T|0.113	0.113	strong	.	CACNA2D2	82	.	NM_001174051	exon7	c.C663A	p.I221I	ATTGAGGATGACA	.	PASS	Atlas-SNP
LGI4	163175	hgsc.bcm.edu	37	19	35617639	35617639	+	Silent	SNP	C	C	G	rs1687998	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	20	23	0	1	0	C|0.694;G|0.306	0.306	strong	.	LGI4	32	.	NM_139284	exon8	c.G834C	p.P278P	GAGGCTCGGGCCC	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179363114	179363114	+	Missense_Mutation	SNP	G	G	C	rs139341288	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	33	75	0	0.417722	0	G|0.997;C|0.003	0.003	strong	.	AXDND1	142	.	NM_144696	exon10	c.G940C	p.V314L	CAGCGAGTGATGG	.	PASS	Atlas-SNP
ZNF699	374879	hgsc.bcm.edu	37	19	9415754	9415754	+	Silent	SNP	T	T	C	rs73504761	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	36	111	0	0.433735	0	T|0.975;C|0.025	0.025	strong	.	ZNF699	67	.	NM_198535	exon1	c.A42G	p.R14R	CTGTATTCTATTT	.	PASS	Atlas-SNP
OR10K1	391109	hgsc.bcm.edu	37	1	158435573	158435573	+	Silent	SNP	C	C	G	rs76205582	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	474	205	489	1	0.432489	0.00204499	C|0.966;G|0.034	0.034	strong	.	OR10K1	80	.	NM_001004473	exon1	c.C222G	p.T74T	CTATACCTTTGTC	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101720300	101720300	+	Silent	SNP	T	T	G	rs1289556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	126	119	1	0.992126	0.00840336	T|0.558;G|0.442	0.442	strong	.	NALCN	431	.	NM_052867	exon39	c.A4416C	p.I1472I	CCATATTATTTGA	.	PASS	Atlas-SNP
ARPC5	10092	hgsc.bcm.edu	37	1	183599638	183599638	+	Silent	SNP	C	C	T	rs2231240	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	47	76	0	0.474747	0	C|0.918;T|0.082	0.082	strong	.	ARPC5	6	.	NM_001270439	exon3	c.G360A	p.P120P	GTCAGACGGGCTC	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42221418	42221418	+	Missense_Mutation	SNP	G	G	A	rs75927810	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	91	142	0	0.52907	0	G|0.985;A|0.015	0.015	strong	CEACAM5,NS,carcinoma,-2,1	CEACAM5	84	1	NM_004363	exon5	c.G1003A	p.V335M	AACCCCGTGGAGG	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	37	12	53189428	53189428	+	Silent	SNP	C	C	A	rs184322044	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	38	159	0	0.219653	0	C|0.888;A|0.112	0.112	strong	.	KRT3	65	.	NM_057088	exon1	c.G399T	p.G133G	ACCAGCCCCTCCA	.	PASS	Atlas-SNP
MPRIP	23164	hgsc.bcm.edu	37	17	17030129	17030129	+	Silent	SNP	G	G	A	rs140002644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	52	160	0	0.382353	0	G|0.998;A|0.002	0.002	strong	.	MPRIP	87	.	NM_015134	exon4	c.G381A	p.E127E	GAAGGAGCATTTC	.	PASS	Atlas-SNP
OPRL1	4987	hgsc.bcm.edu	37	20	62729843	62729843	+	Silent	SNP	A	A	G	rs34874539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	114	190	0	0.508929	0	A|0.979;G|0.021	0.021	strong	.	OPRL1	47	.	NM_000913	exon4	c.A804G	p.V268V	GGTGGTAGTGGCT	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8825399	8825399	+	Silent	SNP	C	C	T	rs16954339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	68	133	0	0.5	0	C|0.905;T|0.095	0.095	strong	.	.	.	.	NM_015210	exon15	c.C3891T	p.S1297S	CTGCTCCGGCCCT	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186101539	186101539	+	Missense_Mutation	SNP	A	A	G	rs10911825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	113	111	0	1	0	A|0.569;G|0.431	0.431	strong	.	HMCN1	797	.	NM_031935	exon86	c.A13310G	p.Q4437R	CTCTGCAAAGTAA	.	PASS	Atlas-SNP
NUP155	9631	hgsc.bcm.edu	37	5	37299007	37299007	+	Silent	SNP	G	G	A	rs216400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	40	87	0	0.37037	0	G|0.967;A|0.033	0.033	strong	.	NUP155	116	.	NM_153485	exon32	c.C3756T	p.G1252G	AATTTTGCCAAGG	.	PASS	Atlas-SNP
GSDMD	79792	hgsc.bcm.edu	37	8	144641514	144641514	+	Silent	SNP	G	G	T	rs7840446	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	48	74	0	0.607595	0	G|0.971;T|0.029	0.029	strong	.	GSDMD	28	.	NM_001166237	exon5	c.G9T	p.S3S	GGGGTCGGCCTTT	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16281007	16281007	+	Missense_Mutation	SNP	A	A	G	rs12931472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	35	76	0	0.555556	0	A|0.599;G|0.400	0.400	strong	.	ABCC6	110	.	NM_001171	exon14	c.T1841C	p.V614A	TCTACGACACCAG	.	PASS	Atlas-SNP
ZNF461	92283	hgsc.bcm.edu	37	19	37134737	37134737	+	Missense_Mutation	SNP	T	T	C	rs10419469	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	18	47	0	0.382979	0	T|0.892;C|0.108	0.108	strong	.	ZNF461	73	.	NM_153257	exon5	c.A260G	p.N87S	AAATTATTGTGAA	.	PASS	Atlas-SNP
BMP15	9210	hgsc.bcm.edu	37	X	50659280	50659280	+	Silent	SNP	C	C	T	rs17003221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	62	175	0	0.427586	0	C|0.811;0|0.015	.	strong	.	BMP15	62	.	NM_005448	exon2	c.C852T	p.S284S	ACATAGCGGGCCT	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	104513156	104513156	+	Silent	SNP	C	C	A	rs78505067	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	80	0	0.494737	0	C|0.994;A|0.006	0.006	strong	.	RIMS2	1357	.	NM_001100117	exon1	c.C42A	p.I14I	TCCCATCCCGGCG	.	PASS	Atlas-SNP
KIF12	113220	hgsc.bcm.edu	37	9	116859631	116859631	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	4	215	0	0.0176991	0	.	.	none	KIF12,NS,carcinoma,-1,1	KIF12	35	1	NM_138424	exon4	c.G182A	p.R61Q	ACCACCCGCAGCT	.	scavenged	Atlas-SNP
C11orf53	341032	hgsc.bcm.edu	37	11	111156523	111156523	+	Missense_Mutation	SNP	G	G	T	rs74649813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	34	75	0	0.607143	0	G|0.961;T|0.039	0.039	strong	C11orf53,NS,haematopoietic_neoplasm,-1,1	C11orf53	17	1	NM_198498	exon4	c.G455T	p.W152L	CAAGCTGGGGGTC	.	PASS	Atlas-SNP
ZNF846	162993	hgsc.bcm.edu	37	19	9868764	9868764	+	Missense_Mutation	SNP	C	C	G	rs60387559	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	39	105	0	0.4875	0	C|0.992;G|0.007;T|0.000	0.007	strong	ZNF846,NS,carcinoma,0,3	ZNF846	61	3	NM_001077624	exon6	c.G989C	p.R330P	TGAATTCGCATGT	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60813954	60813954	+	Silent	SNP	A	A	G	rs8068372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	71	186	0	0.435583	0	A|0.952;G|0.048	0.048	strong	.	MARCH10	102	.	NM_001100875	exon6	c.T1275C	p.I425I	CACAGAAATACAA	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167164187	167164187	+	Silent	SNP	A	A	G	rs2272138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	27	50	0	1	0	A|0.775;G|0.225	0.225	strong	.	SERPINI2	85	.	NM_001012303	exon9	c.T1164C	p.N388N	TGTTGGATTATGC	.	PASS	Atlas-SNP
GPRIN3	285513	hgsc.bcm.edu	37	4	90170015	90170015	+	Missense_Mutation	SNP	C	C	A	rs114960901	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	95	172	0	0.5	0	C|0.991;A|0.009	0.009	strong	GPRIN3,colon,carcinoma,+1,1	GPRIN3	90	1	NM_198281	exon2	c.G1247T	p.G416V	AGGACCCCACCTG	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370660	26370660	+	Missense_Mutation	SNP	G	G	A	rs12205731	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	113	196	0	0.518349	0	G|0.927;A|0.073	0.073	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.G544A	p.A182T	AGCAACGCCAAGG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176770	8176770	+	Missense_Mutation	SNP	C	C	T	rs28533138	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	44	93	0	0.458333	0	C|0.982;T|0.018	0.018	strong	.	.	.	.	NM_001080826	exon5	c.G3115A	p.V1039M	CGGGCACGGACGG	.	PASS	Atlas-SNP
TMEM57	55219	hgsc.bcm.edu	37	1	25757607	25757607	+	Silent	SNP	C	C	T	rs114403991	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	34	36	0	0.618182	0	C|0.992;T|0.008	0.008	strong	.	TMEM57	72	.	NM_018202	exon1	c.C18T	p.A6A	GAACGCCGACTGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535878	88535878	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	36	339	0	0.104348	0	.	.	none	.	DSPP	174	.	NM_014208	exon5	c.T2064C	p.D688D	CAGTGATAGTAGT	.	PASS	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48140682	48140682	+	Silent	SNP	C	C	T	rs5628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	108	148	0	0.519231	0	C|0.897;T|0.103	0.103	strong	PTGIS,NS,carcinoma,0,1	PTGIS	60	1	NM_000961	exon6	c.G768A	p.L256L	ACTCTCCAGCCAT	.	PASS	Atlas-SNP
CCDC91	55297	hgsc.bcm.edu	37	12	28603112	28603112	+	Missense_Mutation	SNP	A	A	G	rs1133028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	51	131	0	0.46789	0	A|0.875;G|0.125	0.125	strong	.	CCDC91	63	.	NM_018318	exon8	c.A781G	p.M261V	CTTGAAATGCTAG	.	PASS	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158368915	158368915	+	Silent	SNP	G	G	T	rs56704148	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	74	134	0	0.503401	0	G|0.989;T|0.011	0.011	strong	.	OR10T2	76	.	NM_001004475	exon1	c.C342A	p.L114L	AATGAGGAGGCAG	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217824488	217824488	+	Silent	SNP	T	T	C	rs143446051	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	104	191	0	0.479263	0	T|0.998;C|0.002	0.002	strong	.	SPATA17	59	.	NM_138796	exon3	c.T208C	p.L70L	AGTTTCTTAGGCA	.	PASS	Atlas-SNP
RRP7A	27341	hgsc.bcm.edu	37	22	42910142	42910142	+	Missense_Mutation	SNP	C	C	T	rs61731241	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	49	0	0.466667	0	C|0.958;T|0.042	0.042	strong	.	RRP7A	25	.	NM_015703	exon6	c.G727A	p.A243T	GCCAGGCGTAGAA	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114154419	114154419	+	Silent	SNP	G	G	A	rs2260159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	76	137	0	0.490323	0	G|0.796;A|0.204	0.204	strong	.	TMCO3	77	.	NM_017905	exon4	c.G771A	p.K257K	GACCAAGCCCAGA	.	PASS	Atlas-SNP
WDR63	126820	hgsc.bcm.edu	37	1	85594466	85594466	+	Missense_Mutation	SNP	G	G	A	rs709783	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	95	188	0	0.502645	0	G|0.780;A|0.220	0.220	strong	WDR63,colon,carcinoma,0,1	WDR63	91	1	NM_145172	exon21	c.G2393A	p.R798H	TAAGTCGCCCTTC	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220427347	220427347	+	Silent	SNP	G	G	T	rs10804275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	58	110	0	0.483333	0	C|0.000;G|0.794;T|0.206	0.206	strong	.	OBSL1	120	.	NM_001173431	exon8	c.C2730A	p.A910A	GCGCACGGCTGCC	.	PASS	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124090655	124090655	+	Silent	SNP	C	C	T	rs7973689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	56	93	0	0.533333	0	C|0.929;T|0.071	0.071	strong	.	DDX55	51	.	NM_020936	exon3	c.C195T	p.I65I	TGTCATCCCCATC	.	PASS	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45432870	45432870	+	Missense_Mutation	SNP	G	G	C	rs3825629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	15	19	0	0.652174	0	G|0.836;C|0.164	0.164	strong	.	FAM179B	115	.	NM_015091	exon1	c.G1246C	p.E416Q	ACACTTGAAGTCC	.	PASS	Atlas-SNP
TBX18	9096	hgsc.bcm.edu	37	6	85446965	85446965	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	4	237	0	0.0144928	0	.	.	none	TBX18,colon,carcinoma,0,1	TBX18	131	1	NM_001080508	exon8	c.C1262T	p.A421V	GAGCGGGCACAGG	.	scavenged	Atlas-SNP
NCF1	653361	hgsc.bcm.edu	37	7	74193718	74193718	+	Silent	SNP	C	C	T	rs79234723	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	76	396	0	0.209945	0	C|0.500;T|0.500	0.500	weak	NCF1,NS,carcinoma,0,1	NCF1	26	1	NM_000265	exon4	c.C345T	p.L115L	CCTCCTCGACTTC	.	scavenged	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107756510	107756510	+	Missense_Mutation	SNP	A	A	G	rs35644375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	41	92	0	0.405941	0	A|0.908;G|0.092	0.092	strong	.	LAMB4	253	.	NM_007356	exon3	c.T131C	p.M44T	GAAGCCATAAGCT	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs78694969		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	6	88	0	0.1	0	T|1.000;|0.000	1.000	weak	PRAMEF11,NS,carcinoma,0,7	PRAMEF11	72	7	NM_001146344	exon4	c.C822A	p.L274L	CTGGGAGAGATGC	.	scavenged	Atlas-SNP
FANCI	55215	hgsc.bcm.edu	37	15	89849413	89849413	+	Silent	SNP	C	C	A	rs114810692	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	32	66	0	0.470588	0	C|0.994;A|0.006	0.006	strong	.	FANCI	129	.	NM_001113378	exon32	c.C3525A	p.A1175A	TACAGCCCTTGTC	.	PASS	Atlas-SNP
TMEM218	219854	hgsc.bcm.edu	37	11	124972114	124972114	+	Silent	SNP	G	G	A	rs7114520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	43	88	0	0.544304	0	G|0.946;A|0.054	0.054	strong	.	TMEM218	14	.	NM_001258243	exon4	c.C129T	p.V43V	CGCACCGACTCCG	.	PASS	Atlas-SNP
SCN3B	55800	hgsc.bcm.edu	37	11	123516316	123516316	+	Silent	SNP	G	G	A	rs115752338	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	68	145	0	0.607143	0	G|0.990;A|0.010	0.010	strong	.	SCN3B	53	.	NM_018400	exon2	c.C198T	p.P66P	GCCCTCGGGCCTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	364	330	399	0	0.906593	0	C|0.615;G|0.385	0.385	strong	.	FLG	900	.	NM_002016	exon3	c.G10307C	p.G3436A	GGGTGTCCACGAA	.	PASS	Atlas-SNP
MED15	51586	hgsc.bcm.edu	37	22	20909389	20909389	+	Silent	SNP	G	G	A	rs147554746	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	24	47	0	0.45283	0	G|1.000;A|0.000	0.000	strong	.	MED15	68	.	NM_015889	exon5	c.G405A	p.G135G	CTCGGGGATGGCC	.	PASS	Atlas-SNP
ZNF292	23036	hgsc.bcm.edu	37	6	87969341	87969341	+	Silent	SNP	G	G	A	rs16878809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	55	100	0	0.495495	0	G|0.910;A|0.090	0.090	strong	.	ZNF292	479	.	NM_015021	exon8	c.G5994A	p.P1998P	TGTGCCGGCCTCA	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037580	33037580	+	Missense_Mutation	SNP	T	T	G	rs2308911	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	139	167	0	0.992857	0	T|0.716;G|0.284	0.284	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.A184C	p.M62L	AGAACATCTCATC	.	PASS	Atlas-SNP
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	54	99	0	0.509434	0	C|0.847;T|0.153	0.153	strong	SLC26A3,caecum,carcinoma,0,1	SLC26A3	120	1	NM_000111	exon11	c.G1299A	p.A433A	TAGAGGCGCCAGG	.	PASS	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66700273	66700273	+	Silent	SNP	G	G	A	rs12227179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	33	84	0	0.39759	0	G|0.966;A|0.034	0.034	strong	.	HELB	90	.	NM_033647	exon3	c.G756A	p.P252P	ACATCCGTGGAAA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114358449	114358449	+	Silent	SNP	C	C	T	rs79120696	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	58	102	0	0.537037	0	C|0.917;T|0.083	0.083	strong	.	RBM19	117	.	NM_001146699	exon19	c.G2352A	p.P784P	TTGCTCCGGCTTC	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117127551	117127551	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	4	75	0	0.0454545	0	.	.	none	.	GPRC6A	152	.	NM_148963	exon3	c.C1317T	p.N439N	AAAGGCGTTGGGG	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220315970	220315970	+	Silent	SNP	G	G	A	rs10932806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	47	112	0	0.54023	0	G|0.544;A|0.456	0.456	strong	.	SPEG	272	.	NM_005876	exon5	c.G2226A	p.K742K	GCTCAAGTGTATC	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179504043	179504043	+	Missense_Mutation	SNP	C	C	G	rs6658180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	116	243	0	0.491525	0	C|0.671;G|0.329	0.329	strong	.	AXDND1	142	.	NM_144696	exon25	c.C2977G	p.Q993E	GAACAACAAGAAG	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2435956	2435956	+	Missense_Mutation	SNP	C	C	T	rs4929982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	22	17	0	1	0	C|0.459;T|0.541	0.541	strong	.	TRPM5	86	.	NM_014555	exon11	c.G1733A	p.R578Q	GCCAGCCGCTCGT	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39134528	39134528	+	Missense_Mutation	SNP	G	G	A	rs16968862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	28	68	0	0.337349	0	G|0.870;A|0.130	0.130	strong	.	KRT40	27	.	NM_182497	exon9	c.C1217T	p.S406L	GTGGTCGAACATG	.	PASS	Atlas-SNP
GRAMD3	65983	hgsc.bcm.edu	37	5	125696124	125696124	+	Missense_Mutation	SNP	T	T	A	rs79046516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	82	184	0	0.381395	0	T|0.975;A|0.025	0.025	strong	.	GRAMD3	30	.	NM_001146319	exon1	c.T101A	p.V34E	GAGAAGTGAAGCC	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107790417	107790417	+	Missense_Mutation	SNP	C	C	T	rs74708699	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	93	214	0	0.531429	0	C|0.990;T|0.010	0.010	strong	.	NRCAM	267	.	NM_001037132	exon30	c.G3853A	p.A1285T	CTTCAGCCGGCTC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74287594	74287594	+	Missense_Mutation	SNP	G	G	A	rs2279054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	105	111	0	0.614035	0	G|0.615;A|0.385	0.385	strong	QRICH2,colon,carcinoma,0,1	QRICH2	143	1	NM_032134	exon4	c.C2716T	p.H906Y	CTGGGTGTGTAGA	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553917	140553917	+	Missense_Mutation	SNP	G	G	A	rs17844455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	118	254	0	0.427536	0	G|0.825;A|0.175	0.175	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G1501A	p.A501T	CCCCTCGCCTCCC	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643252	1643252	+	Silent	SNP	A	A	G	rs190925107	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	343	72	216	1	0.209913	0.00462963	A|0.950;G|0.050	0.050	strong	KRTAP5-4,NS,carcinoma,0,6	KRTAP5-4	78	6	NM_001012709	exon1	c.T72C	p.C24C	AGAGCCACAGCCC	.	scavenged	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	52	168	0	0.403101	0	C|0.744;T|0.256	0.256	strong	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	NM_001135099	exon6	c.G589A	p.V197M	AGTACACCTGAAG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157959870	157959870	+	Silent	SNP	G	G	T	rs112343839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	33	76	0	0.52381	0	G|0.985;T|0.015	0.015	strong	.	PTPRN2	243	.	NM_130843	exon6	c.C663A	p.L221L	CTGGCCGAGGGTC	.	PASS	Atlas-SNP
SLC6A14	11254	hgsc.bcm.edu	37	X	115568993	115568993	+	Silent	SNP	T	T	A	rs12720074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	55	61	0	0.705128	0	0|0.018;A|0.063	0.063	strong	.	SLC6A14	56	.	NM_007231	exon2	c.T84A	p.G28G	TGTTGGTGAAAAT	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104066461	104066461	+	Missense_Mutation	SNP	A	A	G	rs2615542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	41	77	0	0.455556	0	A|0.848;G|0.152	0.152	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon32	c.T4603C	p.F1535L	TATTAAATTGTTC	.	PASS	Atlas-SNP
KMO	8564	hgsc.bcm.edu	37	1	241755348	241755348	+	Missense_Mutation	SNP	C	C	T	rs1053230	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	72	0	0.476744	0	C|0.853;T|0.147	0.147	strong	KMO,NS,adenoma,0,1	KMO	69	1	NM_003679	exon15	c.C1354T	p.R452C	TTCCTCCGCTTGA	.	PASS	Atlas-SNP
PPP1R1B	84152	hgsc.bcm.edu	37	17	37791894	37791894	+	Silent	SNP	A	A	G	rs34257414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	43	76	0	0.467391	0	A|0.979;G|0.021	0.021	strong	.	PPP1R1B	9	.	NM_032192	exon6	c.A480G	p.E160E	TCTGGAAGGGCCC	.	PASS	Atlas-SNP
SLC9A8	23315	hgsc.bcm.edu	37	20	48472098	48472098	+	Silent	SNP	A	A	G	rs35137210	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	85	164	0	0.52795	0	A|0.994;G|0.006	0.006	strong	.	SLC9A8	63	.	NM_001260491	exon8	c.A741G	p.A247A	CGATGCAGTCTCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	483	480	564	0	0.993789	0	G|0.716;C|0.284	0.284	strong	FLG,colon,carcinoma,-1,1	FLG	900	1	NM_002016	exon3	c.C10736G	p.T3579R	TGGGACGTGGGGT	.	scavenged	Atlas-SNP
SLC19A3	80704	hgsc.bcm.edu	37	2	228566993	228566993	+	Silent	SNP	G	G	A	rs34080459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	78	0	0.478873	0	G|0.982;A|0.018	0.018	strong	.	SLC19A3	62	.	NM_025243	exon2	c.C42T	p.Y14Y	AGTGGGGTAAATC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47920345	47920345	+	Silent	SNP	G	G	A	rs62447081	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	57	119	0	0.395833	0	G|0.645;A|0.355	0.355	strong	.	PKD1L1	328	.	NM_138295	exon21	c.C3501T	p.Y1167Y	CAGGACGTACGTC	.	PASS	Atlas-SNP
ROBO1	6091	hgsc.bcm.edu	37	3	78676701	78676701	+	Silent	SNP	T	T	C	rs116125749	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	120	268	0	0.491803	0	T|0.991;C|0.009	0.009	strong	.	ROBO1	833	.	NM_002941	exon26	c.A3645G	p.P1215P	GGGACATGGCATT	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147480080	147480080	+	Missense_Mutation	SNP	G	G	A	rs2303064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	65	100	0	0.488722	0	G|0.688;A|0.312	0.312	strong	.	SPINK5	245	.	NM_001127699	exon13	c.G1156A	p.D386N	GAGAACGATCCTA	.	PASS	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50824619	50824619	+	Missense_Mutation	SNP	G	G	A	rs3810950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	84	0	0.478873	0	G|0.762;A|0.237	0.237	strong	CHAT,NS,carcinoma,-1,1	CHAT	162	1	NM_020549	exon2	c.G358A	p.A120T	AAGATGGCAGCAA	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188023	140188023	+	Silent	SNP	C	C	T	rs7702779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	151	268	0	0.511864	0	C|0.944;T|0.056	0.056	strong	.	PCDHA4	419	.	NM_031500	exon1	c.C1251T	p.S417S	CGAGAGCGTGTCA	.	PASS	Atlas-SNP
AMACR	23600	hgsc.bcm.edu	37	5	34008100	34008100	+	Missense_Mutation	SNP	C	C	T	rs3195676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	58	104	0	0.5	0	C|0.609;T|0.391	0.391	strong	AMACR,NS,carcinoma,0,3	AMACR	38	3	NM_014324	exon1	c.G25A	p.V9M	GCTCCACGACCGA	.	PASS	Atlas-SNP
TRIM39	56658	hgsc.bcm.edu	37	6	30297529	30297529	+	Silent	SNP	T	T	C	rs2057727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	65	143	0	0.474453	0	T|0.696;C|0.304	0.304	strong	.	TRIM39	56	.	NM_172016	exon3	c.T435C	p.D145D	GGACGATGCTACA	.	PASS	Atlas-SNP
GATAD2B	57459	hgsc.bcm.edu	37	1	153788927	153788927	+	Silent	SNP	G	G	A	rs114813239	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	144	289	0	0.469055	0	G|0.987;A|0.013	0.013	strong	.	GATAD2B	62	.	NM_020699	exon7	c.C1038T	p.A346A	TGAGTTGGCAGCA	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	111	99	0	0.991071	0	T|0.483;A|0.517	0.517	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T1900A	p.F634I	TCTAGGTTTAAAA	.	PASS	Atlas-SNP
ND4L	0	hgsc.bcm.edu	37	MT	10586	10586	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	8	14	0	1	0	.	.	none	.	.	.	.	ENST00000361335	exon1	c.G117A	p.S39S	ACTATCGCTGTTC	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	57	0	0.490196	0	G|0.613;C|0.387	0.387	strong	.	SYMPK	104	.	NM_004819	exon26	c.C3381G	p.A1127A	GGCCGGGGCCAAG	.	PASS	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34824555	34824555	+	Missense_Mutation	SNP	G	G	T	rs1048944	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	38	58	0	0.612903	0	A|0.004;C|0.007	.	strong	.	RAI14	100	.	NM_001145525	exon17	c.G2617T	p.A873S	AGATACGCTGAGA	.	PASS	Atlas-SNP
WDR34	89891	hgsc.bcm.edu	37	9	131398633	131398633	+	Silent	SNP	C	C	T	rs61744155	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	30	92	0	0.272727	0	C|0.978;T|0.022	0.022	strong	.	WDR34	29	.	NM_052844	exon4	c.G630A	p.P210P	GGCCGACGGCTGC	.	PASS	Atlas-SNP
DCAF11	80344	hgsc.bcm.edu	37	14	24587639	24587639	+	Missense_Mutation	SNP	G	G	A	rs3825584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	77	155	0	0.458333	0	G|0.685;A|0.315	0.315	strong	.	.	.	.	NM_025230	exon7	c.G620A	p.R207H	GTTTCCGTAAATT	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143816869	143816869	+	Missense_Mutation	SNP	G	G	A	rs151156975		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	66	109	0	0.55	0	G|1.000;A|0.000	0.000	weak	.	FUCA2	28	.	NM_032020	exon7	c.C1379T	p.A460V	GCTAGAGCCCAGC	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595116	55595116	+	Missense_Mutation	SNP	G	G	C	rs75822385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	128	292	0	0.447552	0	A|0.002;C|0.069;G|0.929	0.069	strong	OR5L2,NS,carcinoma,+1,1	OR5L2	135	1	NM_001004739	exon1	c.G422C	p.R141P	AGCTGCGTGTGGA	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978128	45978128	+	Silent	SNP	G	G	A	rs186210430	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	99	149	0	0.52381	0	G|0.992;A|0.008	0.008	strong	.	KRTAP10-3	17	.	NM_198696	exon1	c.C471T	p.S157S	GGACACGGAGGAG	.	PASS	Atlas-SNP
CSTB	1476	hgsc.bcm.edu	37	21	45196136	45196136	+	Silent	SNP	C	C	A	rs4533	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	16	13	0	0.571429	0	C|0.988;A|0.012	0.012	strong	.	CSTB	3	.	NM_000100	exon1	c.G15T	p.A5A	GGAGGGCGCCCCG	.	PASS	Atlas-SNP
TRIML1	339976	hgsc.bcm.edu	37	4	189061010	189061010	+	Missense_Mutation	SNP	A	A	G	rs111308948	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	73	134	0	0.467949	0	A|0.962;G|0.038	0.038	strong	.	TRIML1	126	.	NM_178556	exon1	c.A298G	p.T100A	ATGCCCACCACTG	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77211764	77211764	+	Silent	SNP	T	T	C	rs15350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	36	73	0	0.48	0	T|0.727;C|0.273	0.273	strong	.	NFATC1	105	.	NM_172390	exon6	c.T1851C	p.S617S	CCTGTCTGGCCAC	.	PASS	Atlas-SNP
HERC3	8916	hgsc.bcm.edu	37	4	89625427	89625427	+	Missense_Mutation	SNP	G	G	C	rs1804080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	97	177	0	0.527174	0	G|0.801;C|0.199	0.199	strong	.	HERC3	82	.	NM_014606	exon24	c.G2836C	p.E946Q	GAACTGGAAGAGG	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18757501	18757501	+	Silent	SNP	G	G	C	rs3902946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	419	206	338	0	0.491647	0	G|0.689;C|0.311	0.311	strong	.	NT5C1B	72	.	NM_001199087	exon9	c.C1509G	p.L503L	TTTGTCGAGCCCA	.	PASS	Atlas-SNP
CPN2	1370	hgsc.bcm.edu	37	3	194062821	194062821	+	Missense_Mutation	SNP	G	G	A	rs146126834	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	77	124	0	0.542253	0	G|0.996;A|0.004	0.004	strong	CPN2,NS,carcinoma,0,1	CPN2	56	1	NM_001080513	exon2	c.C611T	p.A204V	GAGAGCGCGTTGT	.	PASS	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61433919	61433919	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	101	0	0.449438	0	.	.	none	.	USP34	334	.	NM_014709	exon71	c.A9022G	p.T3008A	GGCGTGTAGACTT	.	PASS	Atlas-SNP
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005458	118005458	+	Silent	SNP	C	C	T	rs35809332	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	94	205	0	0.472362	0	C|0.987;T|0.013	0.013	strong	.	TRAM1L1	55	.	NM_152402	exon1	c.G1092A	p.R364R	CTCTTTCCTCTTT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	853	103	475	0	0.12075	0	C|0.972;T|0.028	0.028	strong	LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	NM_024318	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	scavenged	Atlas-SNP
EXT2	2132	hgsc.bcm.edu	37	11	44129386	44129386	+	Missense_Mutation	SNP	A	A	G	rs4755779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	98	188	0	0.480392	0	A|0.981;G|0.019	0.019	strong	.	EXT2	129	.	NM_000401	exon2	c.A223G	p.M75V	ACTGGCATGTTTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228504486	228504486	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	60	65	0	0.606061	0	.	.	none	.	OBSCN	2142	.	NM_001271223	exon62	c.G16233A	p.T5411T	CTGCACGCTCAGC	.	PASS	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40453430	40453430	+	Silent	SNP	G	G	T	rs7168394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	74	126	0	0.544118	0	G|0.922;T|0.078	0.078	strong	.	BUB1B	71	.	NM_001211	exon1	c.G9T	p.A3A	GGCGGCGGTGAAG	.	PASS	Atlas-SNP
NACA2	342538	hgsc.bcm.edu	37	17	59668275	59668275	+	Silent	SNP	T	T	A	rs61739271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	134	310	0	0.521401	0	T|0.957;A|0.043	0.043	strong	.	NACA2	33	.	NM_199290	exon1	c.A267T	p.T89T	AACTCCTGTAACC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88495021	88495021	+	Silent	SNP	C	C	A	rs74032864	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	53	32	0	1	0	C|0.956;A|0.044	0.044	strong	.	ZNF469	121	.	NM_001127464	exon1	c.C1143A	p.P381P	CCTTCCCGAAAGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679752	100679752	+	Silent	SNP	T	T	C	rs4992072	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	38	127	0	0.319328	0	T|0.980;C|0.020	0.020	strong	.	MUC17	804	.	NM_001040105	exon3	c.T5055C	p.Y1685Y	AACTTATACTGAA	.	PASS	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238453	71238453	+	Missense_Mutation	SNP	G	G	C	rs147685834	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	164	334	0	0.454294	0	G|0.807;C|0.193	0.193	strong	KRTAP5-7,NS,carcinoma,0,1	KRTAP5-7	23	1	NM_001012503	exon1	c.G107C	p.C36S	GCTGCTGTGTGCC	.	PASS	Atlas-SNP
TAS2R30	259293	hgsc.bcm.edu	37	12	11286688	11286688	+	Silent	SNP	C	C	T	rs375822837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	357	187	305	1	0.52381	0.00327869	.	.	weak	.	TAS2R30	28	.	NM_001097643	exon1	c.G156A	p.A52A	GGAGACCGCCAGA	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493200	33493200	+	Missense_Mutation	SNP	G	G	A	rs200623446	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	5	185	1	0.0248756	0.00540541	G|0.935;A|0.065	0.065	strong	RHPN2,caecum,carcinoma,-1,17	RHPN2	107	17	NM_033103	exon9	c.C1058T	p.A353V	AGGGCCGCGTAGT	.	scavenged	Atlas-SNP
SUPT16H	11198	hgsc.bcm.edu	37	14	21841524	21841524	+	Silent	SNP	A	A	G	rs75576875	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	84	126	0	0.494118	0	A|0.985;G|0.015	0.015	strong	.	SUPT16H	84	.	NM_007192	exon2	c.T132C	p.I44I	ATAAACAATTTCT	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65392695	65392695	+	Silent	SNP	C	C	T	rs1205259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	43	63	0	0.511905	0	C|0.733;T|0.267	0.267	strong	.	PCNXL3	140	.	NM_032223	exon17	c.C2973T	p.L991L	TGGCCTCCTGGTG	.	PASS	Atlas-SNP
NCEH1	57552	hgsc.bcm.edu	37	3	172365832	172365832	+	Missense_Mutation	SNP	T	T	G	rs2302815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	80	145	0	0.606061	0	T|0.868;G|0.132	0.132	strong	NCEH1,NS,adenoma,0,1	NCEH1	63	1	NM_020792	exon2	c.A307C	p.K103Q	TTTTTTTGCCAAA	.	PASS	Atlas-SNP
ZCCHC9	84240	hgsc.bcm.edu	37	5	80608363	80608363	+	Missense_Mutation	SNP	A	A	C	rs144053491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	54	116	0	0.504673	0	A|0.998;C|0.002	0.002	strong	.	ZCCHC9	26	.	NM_001131036	exon6	c.A698C	p.E233A	TTACAGAGCGAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507851	195507851	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	142	473	1	0.586777	0.00211416	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G10600C	p.A3534P	GCGTGGCGTGACC	.	PASS	Atlas-SNP
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	69	106	0	0.5	0	G|0.778;A|0.222	0.222	strong	.	SNX9	43	.	NM_016224	exon8	c.G774A	p.R258R	TCCCAGGAAAGGC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	21	46	0	0.512195	0	A|0.648;T|0.352	0.352	strong	.	COL27A1	200	.	NM_032888	exon3	c.A1831T	p.I611F	TATTCGATCTTCC	.	PASS	Atlas-SNP
FKTN	2218	hgsc.bcm.edu	37	9	108380355	108380355	+	Silent	SNP	C	C	A	rs17309806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	159	256	0	0.676596	0	C|0.750;A|0.250	0.250	strong	.	FKTN	47	.	NM_006731	exon8	c.C1026A	p.L342L	TCCGCTCAAACAC	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	123	0	1	0	A|0.837;G|0.163	0.163	strong	ELSPBP1,NS,NS,+1,1	ELSPBP1	29	1	NM_022142	exon4	c.A303G	p.S101S	GTGCTCAGTCACC	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493201	33493201	+	Missense_Mutation	SNP	C	C	T	rs201601538	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	5	183	1	0.0246305	0.00546448	C|0.929;T|0.070	0.070	strong	RHPN2,caecum,carcinoma,0,17	RHPN2	107	17	NM_033103	exon9	c.G1057A	p.A353T	GGGCCGCGTAGTG	.	scavenged	Atlas-SNP
MRC1	4360	hgsc.bcm.edu	37	10	17891705	17891705	+	Missense_Mutation	SNP	A	A	G	rs34039386		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	263	460	0	0.996212	0	.	.	weak	.	MRC1	13	.	NM_002438	exon7	c.A1186G	p.S396G	GAAGGCAGTGACC	.	PASS	Atlas-SNP
CHD1L	9557	hgsc.bcm.edu	37	1	146757092	146757092	+	Missense_Mutation	SNP	A	A	C	rs13374920	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	95	176	0	0.519126	0	A|0.976;C|0.024	0.024	strong	CHD1L,right_upper_lobe,carcinoma,+1,1	CHD1L	72	1	NM_004284	exon17	c.A1946C	p.E649A	GACAAGAAGCAGC	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117560058	117560058	+	Missense_Mutation	SNP	C	C	G	rs17235773	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	86	122	0	0.502924	0	C|0.944;G|0.056	0.056	strong	.	CD101	95	.	NM_001256109	exon5	c.C1575G	p.S525R	TCTGAGCTGGACT	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20435314	20435314	+	Missense_Mutation	SNP	C	C	T	rs73545426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	77	150	0	0.509934	0	C|0.938;T|0.062	0.062	strong	.	ACSM5	101	.	NM_017888	exon6	c.C844T	p.L282F	TGGACTCTCTTCT	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002393	36002393	+	Missense_Mutation	SNP	C	C	T	rs11667007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	42	92	0	0.442105	0	C|0.691;T|0.309	0.309	strong	.	DMKN	116	.	NM_001126058	exon5	c.G838A	p.G280S	TGCTGCCGCCACT	.	PASS	Atlas-SNP
DNAJC11	55735	hgsc.bcm.edu	37	1	6705874	6705874	+	Missense_Mutation	SNP	G	G	C	rs200454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	135	1	1	0.00740741	G|0.786;C|0.214	0.214	strong	.	DNAJC11	93	.	NM_018198	exon8	c.C869G	p.T290S	TGGCTGGTTTTAG	.	PASS	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	75	0	0.505882	0	T|0.840;C|0.160	0.160	strong	.	FAHD1	18	.	NM_031208	exon1	c.T264C	p.A88A	CGAGGCTGCGGCC	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50752258	50752258	+	Silent	SNP	G	G	A	rs115446109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	59	97	0	0.468254	0	G|0.984;A|0.016	0.016	strong	.	.	.	.	NM_001001794	exon14	c.C1188T	p.L396L	CCGTTTGAGCAGC	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167095768	167095768	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	13	83	0	0.132653	0	.	.	none	DUSP27,NS,carcinoma,0,2	DUSP27	235	2	NM_001080426	exon5	c.G1400A	p.R467H	GGCGCCGCGCAGA	.	PASS	Atlas-SNP
TNPO2	30000	hgsc.bcm.edu	37	19	12812169	12812169	+	Silent	SNP	A	A	G	rs16978628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	27	81	0	0.402985	0	A|0.843;G|0.157	0.157	strong	.	TNPO2	108	.	NM_001136196	exon24	c.T2685C	p.Y895Y	GACCCCATAGAAA	.	PASS	Atlas-SNP
WWP1	11059	hgsc.bcm.edu	37	8	87414308	87414308	+	Silent	SNP	A	A	G	rs74884162		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	104	216	1	0.530612	0.00462963	.	.	weak	.	WWP1	97	.	NM_007013	exon8	c.A600G	p.Q200Q	AGTCCAAAACTCA	.	PASS	Atlas-SNP
PRAMEF12	390999	hgsc.bcm.edu	37	1	12835868	12835868	+	Missense_Mutation	SNP	T	T	C	rs1812242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	388	387	401	0	0.997423	0	T|0.256;G|0.003	.	strong	.	PRAMEF12	69	.	NM_001080830	exon2	c.T470C	p.M157T	ATGGGATGCTGGA	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173552703	173552703	+	Silent	SNP	G	G	A	rs16828416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	98	212	0	0.485149	0	G|0.910;A|0.090	0.090	strong	.	.	.	.	NM_178527	exon6	c.C582T	p.I194I	TGATGCGATGCTA	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31477442	31477442	+	Silent	SNP	T	T	C	rs116201073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	56	1	1	0.0178571	T|0.974;C|0.026	0.026	strong	ARMC5,NS,carcinoma,0,1	ARMC5	94	1	NM_001105247	exon6	c.T2040C	p.G680G	GGGTGGTCTCCGG	.	scavenged	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	37	19	7692132	7692132	+	Silent	SNP	G	G	A	rs4134824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	24	29	0	0.615385	0	G|0.990;A|0.010	0.010	strong	.	XAB2	69	.	NM_020196	exon4	c.C519T	p.L173L	CACCTTGAGGAAG	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55523685	55523685	+	Missense_Mutation	SNP	C	C	T	rs12303066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	107	203	0	0.521951	0	C|0.679;T|0.321	0.321	strong	OR9K2,NS,carcinoma,0,2	OR9K2	63	2	NM_001005243	exon1	c.C133T	p.R45C	AGGGTACGCCCAG	.	PASS	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	37	19	12760200	12760200	+	Silent	SNP	G	G	A	rs35880640	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	130	193	0	0.53719	0	G|0.975;A|0.025	0.025	strong	MAN2B1,colon,carcinoma,-1,1	MAN2B1	91	1	NM_000528	exon19	c.C2310T	p.P770P	TGCCACGGGCTCC	.	PASS	Atlas-SNP
ZNF510	22869	hgsc.bcm.edu	37	9	99521150	99521150	+	Silent	SNP	T	T	C	rs61735521	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	103	148	0	0.635802	0	T|0.970;C|0.030	0.030	strong	.	ZNF510	59	.	NM_014930	exon6	c.A1962G	p.K654K	ATAAGATTTCTCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100676409	100676409	+	Missense_Mutation	SNP	C	C	T	rs34834039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	72	147	0	0.464516	0	C|0.880;T|0.120	0.120	strong	.	MUC17	804	.	NM_001040105	exon3	c.C1712T	p.P571L	GCACTCCATTAAC	.	PASS	Atlas-SNP
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	66	0	1	0	A|0.558;G|0.442	0.442	strong	.	SETMAR	30	.	NM_006515	exon3	c.A1335G	p.R445R	CGTTCGACATTTG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20849169	20849169	+	Silent	SNP	G	G	A	rs2228039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	64	114	0	0.528926	0	G|0.935;A|0.065	0.065	strong	.	TEP1	224	.	NM_007110	exon33	c.C4683T	p.F1561F	GGTAAGGAACTTC	.	PASS	Atlas-SNP
KRT24	192666	hgsc.bcm.edu	37	17	38859664	38859664	+	Silent	SNP	G	G	A	rs61237409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	28	67	0	0.5	0	G|0.969;A|0.031	0.031	strong	.	KRT24	60	.	NM_019016	exon1	c.C282T	p.G94G	GACCCCGCCAAAG	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74921129	74921129	+	Silent	SNP	C	C	T	rs34056052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	53	106	0	0.495327	0	C|0.932;T|0.068	0.068	strong	MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	NM_198955	exon8	c.C1140T	p.H380H	CTACCACGGCCTG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592284	1592284	+	Missense_Mutation	SNP	G	G	A	rs1135196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	58	139	0	0.33526	0	G|0.420;A|0.580	0.580	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.C152T	p.T51I	TGCAGAGTGGCCG	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17211545	17211545	+	Missense_Mutation	SNP	C	C	T	rs7200466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	90	165	0	0.494505	0	C|0.934;T|0.066	0.066	strong	.	XYLT1	147	.	NM_022166	exon11	c.G2515A	p.V839I	GCGCAACGAGGAA	.	PASS	Atlas-SNP
TRMT44	152992	hgsc.bcm.edu	37	4	8472839	8472839	+	Silent	SNP	C	C	T	rs17202499	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	54	103	0	0.606742	0	C|0.977;T|0.023	0.023	strong	.	TRMT44	7	.	NM_152544	exon10	c.C1956T	p.N652N	AGCCAACGAGCTG	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167051726	167051726	+	Silent	SNP	A	A	G	rs10936530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	117	0	1	0	A|0.557;G|0.443	0.443	strong	ZBBX_ENST00000455345,NS,carcinoma,-2,2	ZBBX	299	2	NM_024687	exon10	c.T576C	p.F192F	CTTTATAAACTGA	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87696623	87696623	+	Silent	SNP	C	C	T	rs148059206	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	141	0	0.482517	0	C|0.999;T|0.001	0.001	strong	.	PTPN13	203	.	NM_080685	exon35	c.C5724T	p.S1908S	TGACAGCCTTTAT	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149759201	149759201	+	Missense_Mutation	SNP	C	C	T	rs114689020	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	75	170	0	0.528169	0	C|0.979;T|0.021	0.021	strong	.	TCOF1	154	.	NM_001135243	exon17	c.C2765T	p.S922L	GGCCTTCGGCTGC	.	PASS	Atlas-SNP
MVP	9961	hgsc.bcm.edu	37	16	29856082	29856082	+	Missense_Mutation	SNP	G	G	A	rs35916172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	55	0	0.490196	0	G|0.985;A|0.015	0.015	strong	.	MVP	80	.	NM_017458	exon11	c.G1903A	p.V635I	CTGGTGGTCAGCA	.	PASS	Atlas-SNP
CD72	971	hgsc.bcm.edu	37	9	35612978	35612978	+	Missense_Mutation	SNP	G	G	A	rs34791102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	113	0	1	0	G|0.929;A|0.071	0.071	strong	.	CD72	20	.	NM_001782	exon6	c.C701T	p.P234L	CCCGACGGACAGC	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192885	102192885	+	Silent	SNP	G	G	A	rs7876193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	111	266	0	0.358065	0	G|0.981;A|0.019	0.019	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.G639A	p.P213P	GCTCCCGCTCCCC	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156878531	156878531	+	Silent	SNP	T	T	C	rs11264580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	75	0	0.42	0	T|0.780;C|0.220	0.220	strong	PEAR1,colon,carcinoma,0,1	PEAR1	118	1	NM_001080471	exon10	c.T1200C	p.H400H	CACGCATGGGCCA	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123775824	123775824	+	Missense_Mutation	SNP	T	T	C	rs16999334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	56	155	0	0.352201	0	0|0.018;C|0.053	0.053	strong	.	.	.	.	NM_001163278	exon11	c.A1894G	p.M632V	AACACATTGGGTC	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170062078	170062078	+	Silent	SNP	G	G	C	rs13397109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	54	121	1	0.514286	0.00826446	G|0.878;C|0.122	0.122	strong	LRP2,NS,carcinoma,-2,1	LRP2	751	1	NM_004525	exon41	c.C7626G	p.R2542R	GGGTACGCGGAAG	.	scavenged	Atlas-SNP
SLC30A5	64924	hgsc.bcm.edu	37	5	68417643	68417643	+	Silent	SNP	C	C	T	rs164578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	122	262	0	0.458647	0	C|0.589;T|0.411	0.411	strong	.	SLC30A5	54	.	NM_022902	exon13	c.C1692T	p.H564H	TTCACACCATATG	.	PASS	Atlas-SNP
AKAP7	9465	hgsc.bcm.edu	37	6	131490324	131490324	+	Missense_Mutation	SNP	C	C	T	rs115301121	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	104	188	0	0.495238	0	C|0.993;T|0.007	0.007	strong	.	AKAP7	61	.	NM_016377	exon5	c.C500T	p.P167L	CTTTGCCCTTTCA	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	90	221	0	0.542169	0	G|0.598;T|0.402	0.402	strong	.	MMP20	52	.	NM_004771	exon6	c.C842A	p.T281N	GGCAGAGTGGGCT	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33684221	33684221	+	Missense_Mutation	SNP	C	C	T	rs140868444	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	14	64	0	0.291667	0	C|0.996;T|0.004	0.004	strong	.	STARD13	100	.	NM_178006	exon12	c.G2836A	p.D946N	TCCCGTCGCCCAC	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	45	126	0	0.412844	0	A|0.692;G|0.308	0.308	strong	.	HBS1L	75	.	NM_006620	exon17	c.T1977C	p.F659F	CTCTTTAAAGTCT	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25959298	25959298	+	Missense_Mutation	SNP	T	T	C	rs141928852	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	58	0	0.428571	0	T|0.997;C|0.003	0.003	strong	.	ATP10A	270	.	NM_024490	exon10	c.A1867G	p.S623G	TGCTGCTGCAGCC	.	PASS	Atlas-SNP
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	71	186	0	0.356784	0	C|0.543;T|0.457	0.457	strong	.	NACC2	16	.	NM_144653	exon5	c.G1164A	p.T388T	GGCCAGCGTGTTC	.	PASS	Atlas-SNP
TTC5	91875	hgsc.bcm.edu	37	14	20757804	20757804	+	Silent	SNP	C	C	A	rs3737220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	76	0	0.521277	0	C|0.873;A|0.127	0.127	strong	TTC5,NS,carcinoma,-1,3	TTC5	34	3	NM_138376	exon10	c.G1305T	p.S435S	TGGTCGCGATGCC	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21231524	21231524	+	Missense_Mutation	SNP	G	G	A	rs676210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	170	269	1	0.548387	0.00371747	G|0.731;A|0.269	0.269	strong	.	APOB	761	.	NM_000384	exon26	c.C8216T	p.P2739L	AATTCTGGTATGT	.	PASS	Atlas-SNP
MAD1L1	8379	hgsc.bcm.edu	37	7	2257612	2257612	+	Silent	SNP	G	G	A	rs6951493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	263	322	0	1	0	G|0.639;A|0.361	0.361	strong	.	MAD1L1	81	.	NM_003550	exon7	c.C663T	p.H221H	CTGCTCGTGGTCT	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20850093	20850093	+	Missense_Mutation	SNP	C	C	T	rs1713456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	45	83	0	0.463918	0	C|0.754;A|0.001	.	strong	TEP1,NS,carcinoma,+1,1	TEP1	224	1	NM_007110	exon30	c.G4403A	p.C1468Y	ACGAGGCAGGCAA	.	PASS	Atlas-SNP
CCAR1	55749	hgsc.bcm.edu	37	10	70549579	70549579	+	Silent	SNP	G	G	A	rs11594683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	69	178	0	0.415663	0	G|0.947;A|0.053	0.053	strong	.	CCAR1	118	.	NM_018237	exon24	c.G3300A	p.S1100S	GATTTCGGAAAAC	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48180311	48180311	+	Missense_Mutation	SNP	T	T	G	rs16945901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	63	133	0	0.492188	0	T|0.955;G|0.045	0.045	strong	.	ABCC12	190	.	NM_033226	exon1	c.A25C	p.I9L	CTGAGATAAGGTA	.	PASS	Atlas-SNP
PPEF2	5470	hgsc.bcm.edu	37	4	76788564	76788564	+	Missense_Mutation	SNP	C	C	T	rs34155925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	66	127	0	0.485294	0	C|0.877;T|0.123	0.123	strong	.	PPEF2	108	.	NM_006239	exon14	c.G1658A	p.R553K	TCCACTCTGCTAA	.	PASS	Atlas-SNP
TATDN2	9797	hgsc.bcm.edu	37	3	10312113	10312113	+	Missense_Mutation	SNP	T	T	C	rs61730105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	87	134	0	0.540373	0	T|0.957;C|0.043	0.043	strong	.	TATDN2	59	.	NM_014760	exon4	c.T1247C	p.M416T	GCCGCATGAGTGA	.	PASS	Atlas-SNP
CAMK2D	817	hgsc.bcm.edu	37	4	114438740	114438740	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	4	66	0	0.0470588	0	.	.	none	.	CAMK2D	55	.	NM_172128	exon9	c.G675A	p.Q225Q	CTTGATCTGCTGA	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249183	71249183	+	Missense_Mutation	SNP	T	T	C	rs55921335	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	101	258	0	0.429787	0	T|0.650;C|0.350	0.350	strong	KRTAP5-8,colon,carcinoma,0,1	KRTAP5-8	28	1	NM_021046	exon1	c.T82C	p.C28R	TCTAGCTGCTGTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511524	195511524	+	Silent	SNP	G	G	A	rs201351734	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	20	126	0	0.175439	0	G|0.967;A|0.033	0.033	strong	MUC4_ENST00000463781,NS,carcinoma,-1,5	MUC4	1505	5	NM_018406	exon2	c.C6927T	p.D2309D	GGAAGCGTCGGTG	.	scavenged	Atlas-SNP
C17orf53	78995	hgsc.bcm.edu	37	17	42225250	42225250	+	Missense_Mutation	SNP	G	G	A	rs35879996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	68	0	0.493333	0	G|0.983;A|0.017	0.017	strong	.	C17orf53	59	.	NM_001171251	exon3	c.G79A	p.A27T	GAGGATGCAGAGA	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1642736	1642736	+	Missense_Mutation	SNP	C	C	T	rs61747868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	47	105	0	0.439252	0	C|0.992;T|0.008	0.008	strong	.	PXDN	255	.	NM_012293	exon21	c.G4088A	p.G1363E	TGTTCCCCCTGTC	.	PASS	Atlas-SNP
OR2Z1	284383	hgsc.bcm.edu	37	19	8841461	8841461	+	Missense_Mutation	SNP	G	G	A	rs61746162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	109	207	0	0.567708	0	G|0.984;A|0.016	0.016	strong	.	OR2Z1	53	.	NM_001004699	exon1	c.G71A	p.R24H	GATCACGCCAGCT	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109617728	109617728	+	Missense_Mutation	SNP	A	A	G	rs16940029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	110	231	0	0.521327	0	A|0.917;G|0.083	0.083	strong	.	ACACB	330	.	NM_001093	exon10	c.A1654G	p.I552V	TGTGCCATCCGCC	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125488404	125488404	+	Silent	SNP	C	C	T	rs17140116	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	29	99	0	0.386667	0	C|0.878;T|0.122	0.122	strong	.	STT3A	52	.	NM_152713	exon16	c.C1911T	p.C637C	CAACTGCCTCATG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34726524	34726524	+	Missense_Mutation	SNP	G	G	A	rs1810820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	73	0	0.506667	0	G|0.815;A|0.185	0.185	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C713T	p.T238M	CTCTGCGTCATCT	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952189	14952189	+	Silent	SNP	G	G	T	rs114596415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	74	137	0	0.486842	0	G|0.980;T|0.020	0.020	strong	OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	NM_001005190	exon1	c.C501A	p.P167P	ACAAAAGGGCAGT	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1531701	1531701	+	Silent	SNP	C	C	T	rs11553056	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	448	211	404	1	0.470982	0.00247525	C|0.981;T|0.019	0.019	strong	.	ASMTL	56	.	NM_004192	exon12	c.G1569A	p.L523L	CCGGCACAGGACG	.	PASS	Atlas-SNP
ATP1A4	480	hgsc.bcm.edu	37	1	160129273	160129273	+	Silent	SNP	G	G	A	rs61734686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	72	176	0	0.48	0	G|0.992;A|0.008	0.008	strong	.	ATP1A4	167	.	NM_144699	exon6	c.G735A	p.L245L	CCCTCTGGAGACC	.	PASS	Atlas-SNP
TM9SF3	56889	hgsc.bcm.edu	37	10	98287792	98287792	+	Silent	SNP	G	G	T	rs12779720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	79	142	0	0.523179	0	G|0.783;T|0.217	0.217	strong	.	TM9SF3	45	.	NM_020123	exon12	c.C1537A	p.R513R	ACCACCGGTAATC	.	PASS	Atlas-SNP
FLNA	2316	hgsc.bcm.edu	37	X	153581214	153581214	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	41	167	0	0.225275	0	.	.	none	.	FLNA	373	.	NM_001110556	exon39	c.G6305T	p.C2102F	ACCCTGCACGTCC	.	PASS	Atlas-SNP
FBF1	85302	hgsc.bcm.edu	37	17	73913827	73913827	+	Silent	SNP	G	G	T	rs150139322	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	85	161	0	0.459459	0	G|0.997;T|0.003	0.003	strong	.	FBF1	48	.	NM_001080542	exon22	c.C2446A	p.R816R	GCAGCCGGCTCTG	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56389732	56389732	+	Missense_Mutation	SNP	T	T	C	rs9913145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	53	114	0	0.495327	0	T|0.850;C|0.150	0.150	strong	.	BZRAP1	287	.	NM_004758	exon17	c.A2450G	p.Q817R	TCCACTTGCTCAG	.	PASS	Atlas-SNP
LRAT	9227	hgsc.bcm.edu	37	4	155665820	155665820	+	Silent	SNP	G	G	A	rs17031981	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	42	87	0	0.5	0	G|0.910;A|0.090	0.090	strong	.	LRAT	29	.	NM_004744	exon2	c.G342A	p.E114E	AGTGGAGGACTTC	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595115	55595115	+	Missense_Mutation	SNP	C	C	T	rs71490506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	127	294	0	0.450355	0	C|0.913;G|0.000;T|0.087	0.087	strong	OR5L2,NS,carcinoma,0,1	OR5L2	135	1	NM_001004739	exon1	c.C421T	p.R141C	AAGCTGCGTGTGG	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257836	110257836	+	Silent	SNP	T	T	C	rs67757008	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	577	284	537	2	0.492201	0.00372439	CAAATC|0.500;TAAACT|0.500	.	alt	GSTM5,brain,glioma,0,4	GSTM5	89	4	NM_000851	exon7	c.T541C	p.L181L	CTAAACTTGAAGG	.	PASS	Atlas-SNP
CPVL	54504	hgsc.bcm.edu	37	7	29070320	29070320	+	Missense_Mutation	SNP	C	C	T	rs1052200	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	109	171	0	0.521531	0	C|0.836;T|0.163	0.163	strong	.	CPVL	60	.	NM_019029	exon12	c.G1193A	p.R398H	AAGGAGCGCTCTG	.	PASS	Atlas-SNP
DBNL	28988	hgsc.bcm.edu	37	7	44099664	44099664	+	Silent	SNP	T	T	C	rs11552797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	225	214	0	1	0	T|0.715;C|0.285	0.285	strong	DBNL,NS,carcinoma,0,1	DBNL	26	1	NM_001122956	exon12	c.T1092C	p.A364A	AGGTGCTGGCTCT	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65242044	65242044	+	Silent	SNP	C	C	T	rs184528	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	78	133	0	0.513158	0	C|0.642;T|0.358	0.358	strong	.	SPTB	378	.	NM_001024858	exon22	c.G4641A	p.A1547A	CTCCGCCGCCTCC	.	PASS	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59283299	59283299	+	Missense_Mutation	SNP	T	T	C	rs79922105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	26	69	0	0.313253	0	T|0.980;C|0.020	0.020	strong	.	OR4D9	47	.	NM_001004711	exon1	c.T914C	p.L305P	GACGGCTAGGACA	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193120627	193120627	+	Silent	SNP	C	C	T	rs61733355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	63	128	0	0.431507	0	C|0.982;T|0.018	0.018	strong	.	ATP13A4	154	.	NM_032279	exon30	c.G3405A	p.L1135L	CATCCACAGGGCT	.	PASS	Atlas-SNP
PPIL2	23759	hgsc.bcm.edu	37	22	22049783	22049783	+	Silent	SNP	C	C	T	rs12484060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	95	168	0	0.458937	0	C|0.616;T|0.384	0.384	strong	.	PPIL2	38	.	NM_148176	exon20	c.C1563T	p.S521S	TAGCAGCAGGTTG	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90445889	90445889	+	Missense_Mutation	SNP	A	A	G	rs77469944	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	48	55	0	0.533333	0	A|0.957;G|0.043	0.043	strong	.	GPR98	605	.	NM_032119	exon88	c.A18475G	p.M6159V	AACCAAATGTGTT	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	70	148	0	0.466667	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_174913	exon6	c.C1237T	p.R413C	GCCTGTCGCAGAG	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22575777	22575777	+	Missense_Mutation	SNP	T	T	C	rs200167484	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	37	59	0	0.402174	0	C|0.005;G|0.039;T|0.955	0.005	strong	.	ZNF98	230	.	NM_001098626	exon4	c.A260G	p.Y87C	TAAGAATATACAA	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	110	0	1	0	C|0.730;N|0.000	.	strong	.	FBXO39	50	.	NM_153230	exon2	c.C28T	p.P10S	ATCCAGCCCCAAG	.	PASS	Atlas-SNP
IRGQ	126298	hgsc.bcm.edu	37	19	44096772	44096772	+	Silent	SNP	C	C	T	rs114508854	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	13	21	0	0.5	0	C|0.981;T|0.019	0.019	strong	.	IRGQ	40	.	NM_001007561	exon3	c.G1278A	p.E426E	CGGCGCCTCCTCC	.	PASS	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120378702	120378702	+	Silent	SNP	A	A	G	rs10158823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	105	152	0	0.517241	0	A|0.919;G|0.081	0.081	strong	.	NBPF7	46	.	NM_001047980	exon7	c.T1044C	p.V348V	CTGTTCAACTAGT	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197609	39197609	+	Missense_Mutation	SNP	C	C	A	rs138200823	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	46	234	0	0.25	0	C|0.950;A|0.050	0.050	strong	.	KRTAP1-1	23	.	NM_030967	exon1	c.G41T	p.C14F	GTGGAGCAGCTGG	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163124051	163124051	+	Missense_Mutation	SNP	C	C	T	rs1990760	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	139	0	0.47561	0	C|0.588;T|0.412	0.412	strong	.	IFIH1	102	.	NM_022168	exon15	c.G2836A	p.A946T	GCAGTGCTTTGTT	.	PASS	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220405230	220405230	+	Silent	SNP	G	G	A	rs6436154	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	123	83	0	0.991935	0	G|0.613;A|0.387	0.387	strong	.	CHPF	56	.	NM_024536	exon4	c.C1203T	p.H401H	GAAAGCGTGCTGC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378387	31378387	+	Silent	SNP	T	T	C	rs1063631	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	266	314	1	1	0.00318471	T|0.642;C|0.358	0.358	strong	MICA,bladder,carcinoma,0,1	MICA	21	1	NM_001177519	exon2	c.T138C	p.L46L	GTTTCTTGCTGAG	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324254	39324254	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	33	434	0	0.157143	0	.	.	none	.	KRTAP4-3	40	.	NM_033187	exon1	c.C171T	p.S57S	GCAGCTGGAGATA	.	PASS	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156539169	156539169	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	153	0	0.401869	0	.	.	none	.	IQGAP3	146	.	NM_178229	exon2	c.C124T	p.R42C	CTCACCGCTTGGC	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84752784	84752784	+	Silent	SNP	A	A	C	rs73945104	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	130	277	0	0.498084	0	A|0.989;C|0.011	0.011	strong	.	DNAH6	194	.	NM_001370	exon3	c.A321C	p.P107P	ACGTCCAGTAAGC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39874396	39874396	+	Missense_Mutation	SNP	T	T	G	rs41515347	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	76	0	0.43617	0	T|0.969;G|0.031	0.031	strong	.	THBS1	106	.	NM_003246	exon3	c.T70G	p.S24A	ACAGAGTCTGGCG	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111651620	111651620	+	Missense_Mutation	SNP	A	A	T	rs3204145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	65	117	0	0.656566	0	A|0.773;T|0.227	0.227	strong	.	IKBKAP	122	.	NM_003640	exon29	c.T3214A	p.C1072S	GGGCACACTCTTC	.	PASS	Atlas-SNP
LIPE	3991	hgsc.bcm.edu	37	19	42910416	42910416	+	Silent	SNP	C	C	T	rs28657829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	56	92	0	0.451613	0	C|0.978;T|0.022	0.022	strong	LIPE,rectum,carcinoma,-1,1	LIPE	83	1	NM_005357	exon7	c.G2262A	p.P754P	TGTGGCCGGGTAG	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167217960	167217960	+	Silent	SNP	C	C	T	rs13061106	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	34	78	0	0.515152	0	C|0.862;T|0.138	0.138	strong	.	WDR49	188	.	NM_178824	exon14	c.G1956A	p.E652E	CGGGGCCTCCAGA	.	PASS	Atlas-SNP
ODF2	4957	hgsc.bcm.edu	37	9	131260808	131260808	+	Missense_Mutation	SNP	C	C	G	rs16930426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	76	128	0	0.649573	0	C|0.971;G|0.029	0.029	strong	.	ODF2	227	.	NM_153435	exon19	c.C2321G	p.T774S	GTGGGACCCTGGC	.	PASS	Atlas-SNP
SPAG4	6676	hgsc.bcm.edu	37	20	34208869	34208869	+	Silent	SNP	G	G	A	rs34962502	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	66	92	0	0.568965	0	G|0.986;A|0.014	0.014	strong	SPAG4,colon,carcinoma,+1,1	SPAG4	36	1	NM_003116	exon12	c.G1239A	p.T413T	TTTCACGTGCTTG	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163965	73163965	+	Missense_Mutation	SNP	C	C	A	rs2973558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	79	133	0	0.526667	0	C|0.764;A|0.236	0.236	strong	.	.	.	.	NM_001080479	exon20	c.C2338A	p.H780N	AGTGACCATAACA	.	PASS	Atlas-SNP
TRIM6-TRIM34	445372	hgsc.bcm.edu	37	11	5629607	5629607	+	Silent	SNP	G	G	A	rs10769121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	93	170	0	0.472081	0	G|0.632;A|0.368	0.368	strong	TRIM6-TRIM34,NS,carcinoma,0,2	TRIM6-TRIM34	68	2	NM_001003819	exon5	c.G840A	p.V280V	GGATGTGAGTGAT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134748281	134748281	+	Missense_Mutation	SNP	G	G	A	rs74460040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	22	64	0	0.536585	0	G|0.972;A|0.028	0.028	strong	.	TTC40	100	.	NM_001200049	exon8	c.C841T	p.R281C	GAAAGCGCTGGTG	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32613020	32613020	+	Silent	SNP	A	A	G	rs1993050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	58	131	0	0.47541	0	A|0.420;G|0.580	0.580	strong	AVL9,NS,carcinoma,0,1	AVL9	66	1	NM_015060	exon12	c.A1560G	p.T520T	TGCCACACTGCAA	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123886648	123886648	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	939	202	1243	0	0.215122	0	.	.	none	OR10G4,right_lower_lobe,carcinoma,-2,1	OR10G4	77	1	NM_001004462	exon1	c.T367C	p.L123L	CGCTACTTGGCCA	.	scavenged	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50810405	50810405	+	Silent	SNP	C	C	T	rs201839634	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	17	66	0	0.425	0	C|0.999;T|0.001	0.001	strong	.	MYH14	261	.	NM_001145809	exon41	c.C5778T	p.L1926L	CCAGCTCCGGGAC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149509064	149509064	+	Missense_Mutation	SNP	T	T	C	rs73727632	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	39	69	0	0.433333	0	T|0.949;C|0.051	0.051	strong	.	.	.	.	NM_198455	exon68	c.T9610C	p.C3204R	GCCCGGTGCCATC	.	PASS	Atlas-SNP
SPON2	10417	hgsc.bcm.edu	37	4	1165748	1165748	+	Missense_Mutation	SNP	T	T	C	rs6836335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	62	176	0	0.424658	0	T|0.847;C|0.153	0.153	strong	.	SPON2	22	.	NM_012445	exon2	c.A112G	p.R38G	GGGCTCTGGCGGA	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501514	90501514	+	Missense_Mutation	SNP	C	C	G	rs4076794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	48	70	0	0.666667	0	C|0.751;G|0.249	0.249	strong	C9orf79,middle_lobe,carcinoma,+1,2	.	.	2	NM_178828	exon4	c.C2112G	p.D704E	CTCTGACAAGGGG	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43319180	43319180	+	Missense_Mutation	SNP	T	T	C	rs9981024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	50	77	0	0.434783	0	T|0.938;C|0.062	0.062	strong	.	C2CD2	47	.	NM_015500	exon13	c.A1852G	p.T618A	TGGCAGTGCCCGG	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219895548	219895548	+	Missense_Mutation	SNP	C	C	A	rs56411706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	50	109	0	0.515464	0	C|0.847;A|0.153	0.153	strong	.	CCDC108	208	.	NM_194302	exon9	c.G1024T	p.A342S	GCTGGGCGCACTT	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3148570	3148570	+	Missense_Mutation	SNP	G	G	A	rs35892913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	96	189	0	0.472906	0	G|0.955;A|0.045	0.045	strong	.	HTT	221	.	NM_002111	exon25	c.G3190A	p.V1064I	TGTACCGTTGGGA	.	PASS	Atlas-SNP
TMEM247	388946	hgsc.bcm.edu	37	2	46707812	46707812	+	Missense_Mutation	SNP	G	G	A	rs79819367	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	17	224	0	0.0790698	0	A|1.000;|0.000	1.000	weak	.	.	.	.	NM_001145051	exon2	c.G386A	p.R129Q	GGCAGCGGCAGCA	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011547	46011547	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	34	254	0	0.10303	0	.	.	none	.	KRTAP10-6	57	.	NM_198688	exon1	c.C819T	p.P273P	GCAGACGGGCACA	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16328115	16328115	+	Missense_Mutation	SNP	T	T	C	rs143125796	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	42	0	0.470588	0	T|0.999;C|0.001	0.001	strong	.	ATXN1	117	.	NM_001128164	exon7	c.A427G	p.I143V	ATGGGATGAAGCT	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879485	144879485	+	Missense_Mutation	SNP	G	G	C	rs113467089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	21	85	0	0.228261	0	G|0.665;C|0.335	0.335	strong	.	PDE4DIP	817	.	NM_014644	exon27	c.C3965G	p.T1322R	GCCAGTGTTGAGC	.	PASS	Atlas-SNP
GML	2765	hgsc.bcm.edu	37	8	143922620	143922620	+	Missense_Mutation	SNP	C	C	T	rs3764795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	91	181	0	0.466667	0	C|0.855;T|0.145	0.145	strong	.	GML	34	.	NM_002066	exon3	c.C160T	p.R54C	ATTAGGCGCTGTA	.	PASS	Atlas-SNP
CMTM2	146225	hgsc.bcm.edu	37	16	66613525	66613525	+	Silent	SNP	G	G	A	rs11553598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	24	31	0	0.533333	0	G|0.874;A|0.126	0.126	strong	CMTM2,NS,carcinoma,+1,2	CMTM2	33	2	NM_001199317	exon1	c.G15A	p.A5A	TAAGGCGGCAAAG	.	scavenged	Atlas-SNP
HPS4	89781	hgsc.bcm.edu	37	22	26860269	26860269	+	Missense_Mutation	SNP	G	G	C	rs2014410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	40	70	0	0.5	0	G|0.640;C|0.360	0.360	strong	.	HPS4	123	.	NM_022081	exon11	c.C1327G	p.L443V	CTTCGAGCTGCTC	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2667005	2667005	+	Silent	SNP	T	T	C	rs7239096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	54	97	0	0.55102	0	T|0.974;C|0.026	0.026	strong	.	SMCHD1	88	.	NM_015295	exon3	c.T399C	p.Y133Y	ATATTATGCCAGT	.	PASS	Atlas-SNP
TSPAN9	10867	hgsc.bcm.edu	37	12	3389559	3389559	+	Silent	SNP	C	C	T	rs877089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	13	38	0	0.342105	0	C|0.974;T|0.026	0.026	strong	.	TSPAN9	20	.	NM_006675	exon6	c.C342T	p.N114N	CGAGAACGCCAAG	.	PASS	Atlas-SNP
OR6C4	341418	hgsc.bcm.edu	37	12	55945856	55945856	+	Silent	SNP	A	A	G	rs57386660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	32	55	0	0.551724	0	A|0.902;G|0.098	0.098	strong	.	OR6C4	34	.	NM_001005494	exon1	c.A846G	p.L282L	TCCCTTACTGAAT	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377424	49377424	+	Missense_Mutation	SNP	G	G	A	rs11541192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	74	167	0	0.448485	0	G|0.811;A|0.189	0.189	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G934A	p.G312S	GAGGAGGGTGAGG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242036797	242036797	+	Missense_Mutation	SNP	A	A	G	rs2286323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	45	115	0	0.45	0	A|0.894;G|0.106	0.106	strong	.	MTERFD2	33	.	NM_182501	exon3	c.T566C	p.M189T	TGGCGCATGGTGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179613258	179613258	+	Silent	SNP	A	A	C	rs72648906	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	97	190	0	0.480198	0	A|0.977;C|0.023	0.023	strong	.	TTN	18412	.	NM_133379	exon46	c.T13869G	p.S4623S	TATATGAGAATAC	.	PASS	Atlas-SNP
C17orf77	146723	hgsc.bcm.edu	37	17	72588326	72588326	+	Missense_Mutation	SNP	A	A	C	rs493430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	136	1	0.992308	0.00735294	A|0.306;C|0.694	0.694	strong	CD300LD,NS,carcinoma,0,2	C17orf77	31	2	NM_152460	exon3	c.A141C	p.R47S	GCAGAGATGGGGA	.	PASS	Atlas-SNP
RORB	6096	hgsc.bcm.edu	37	9	77245265	77245265	+	Silent	SNP	C	C	T	rs41307459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	51	158	0	0.377778	0	C|0.996;T|0.004	0.004	strong	.	RORB	89	.	NM_006914	exon2	c.C75T	p.I25I	AGTCATCACATGT	.	PASS	Atlas-SNP
SRM	6723	hgsc.bcm.edu	37	1	11114940	11114940	+	Silent	SNP	G	G	T	rs13616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	96	202	0	0.516129	0	G|0.906;T|0.094	0.094	strong	SRM,NS,carcinoma,0,1	SRM	18	1	NM_003132	exon8	c.C891A	p.A297A	ATTCAGGGCCTGG	.	PASS	Atlas-SNP
WRN	7486	hgsc.bcm.edu	37	8	30954338	30954338	+	Silent	SNP	C	C	T	rs11574263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	12	28	0	0.413793	0	C|0.997;T|0.003	0.003	strong	.	WRN	116	.	NM_000553	exon17	c.C1953T	p.G651G	CATGGGCCTGCTC	.	PASS	Atlas-SNP
NPL	80896	hgsc.bcm.edu	37	1	182787951	182787951	+	Silent	SNP	C	C	T	rs10911142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	33	119	0	0.351064	0	C|0.918;T|0.082	0.082	strong	.	NPL	55	.	NM_001200052	exon10	c.C610T	p.L204L	TAGCAACTGTTGA	.	PASS	Atlas-SNP
EPB41L1	2036	hgsc.bcm.edu	37	20	34782156	34782156	+	Silent	SNP	G	G	A	rs111865221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	77	137	0	0.452941	0	G|0.991;A|0.009	0.009	strong	.	EPB41L1	111	.	NM_001258329	exon13	c.G1323A	p.S441S	AGCCTCGGTCAGC	.	PASS	Atlas-SNP
ATP8B2	57198	hgsc.bcm.edu	37	1	154320942	154320942	+	Silent	SNP	A	A	G	rs2297607	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	40	97	0	0.421053	0	G|0.226;N|0.000	0.226	strong	.	ATP8B2	158	.	NM_020452	exon27	c.A3321G	p.T1107T	CACCACAGTCGTC	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	168	349	0	0.488372	0	T|0.840;C|0.160	0.160	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon12	c.A1014G	p.V338V	AGTTGATACCTCA	.	PASS	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172835290	172835290	+	Missense_Mutation	SNP	C	C	T	rs1515441	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	339	168	278	1	0.495575	0.00359712	C|0.831;T|0.169	0.169	strong	SPATA16,NS,carcinoma,+2,1	SPATA16	111	1	NM_031955	exon2	c.G232A	p.E78K	CTTTCTCTAAATC	.	PASS	Atlas-SNP
RAD1	5810	hgsc.bcm.edu	37	5	34914829	34914829	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	3	170	0	0.0164835	0	.	.	none	RAD1,colon,carcinoma,+2,1	RAD1	17	1	NM_002853	exon2	c.A169G	p.K57E	CACACTTTGCATT	.	scavenged	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46932079	46932079	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	45	95	0	0.505618	0	.	.	none	.	CELSR1	242	.	NM_014246	exon1	c.C989T	p.T330M	GGCGGCGTACTGT	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376448	52376448	+	Silent	SNP	A	A	G	rs9807843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	34	78	0	0.373626	0	A|0.899;G|0.101	0.101	strong	.	ZNF577	63	.	NM_032679	exon7	c.T795C	p.T265T	CTCTCCAGTATGT	.	PASS	Atlas-SNP
KIAA1407	57577	hgsc.bcm.edu	37	3	113699599	113699599	+	Missense_Mutation	SNP	C	C	G	rs35546981	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	121	223	1	0.454887	0.00448431	C|0.997;G|0.003	0.003	strong	.	KIAA1407	80	.	NM_020817	exon14	c.G2205C	p.Q735H	TTCCAGCTGCTGG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721090	54721090	+	Missense_Mutation	SNP	A	A	G	rs141841040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	395	16	407	16	0.0405063	0.039312	A|0.988;G|0.012	0.012	strong	LILRB3,NS,carcinoma,0,4	LILRB3	67	4	NM_001081450	exon13	c.T1771C	p.S591P	CCTGGGAGGCTTC	.	scavenged	Atlas-SNP
NMI	9111	hgsc.bcm.edu	37	2	152138522	152138522	+	Silent	SNP	T	T	C	rs3771886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	63	132	0	0.59434	0	T|0.430;C|0.570	0.570	strong	.	NMI	21	.	NM_004688	exon3	c.A117G	p.Q39Q	CTTTAGTTGAATA	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115411598	115411598	+	Silent	SNP	C	C	A	rs4918861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	53	103	0	0.509615	0	C|0.712;A|0.288	0.288	strong	.	NRAP	208	.	NM_001261463	exon7	c.G639T	p.L213L	CCGTAGCAGCTCA	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112754	248112754	+	Missense_Mutation	SNP	T	T	C	rs201126494	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	46	178	0	0.133721	0	T|0.945;C|0.055	0.055	strong	.	OR2L8	92	.	NM_001001963	exon1	c.T595C	p.F199L	ACAGTGTTTTTGA	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170038674	170038674	+	Silent	SNP	T	T	C	rs115828649	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	137	0	1	0	T|0.959;C|0.041	0.041	strong	.	WDR27	129	.	NM_182552	exon18	c.A1830G	p.R610R	CCACATTCGCAGG	.	PASS	Atlas-SNP
TTYH2	94015	hgsc.bcm.edu	37	17	72248482	72248482	+	Missense_Mutation	SNP	C	C	A	rs9892705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	28	56	0	0.444444	0	C|0.959;A|0.041	0.041	strong	TTYH2,NS,carcinoma,-1,1	TTYH2	63	1	NM_032646	exon11	c.C1226A	p.A409E	TCTGTGCAGGGCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677409	100677409	+	Silent	SNP	G	G	A	rs150735476	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	34	106	0	0.213836	0	G|0.957;A|0.043	0.043	strong	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G2712A	p.S904S	CCGTTCGTCTCCT	.	PASS	Atlas-SNP
ST8SIA3	51046	hgsc.bcm.edu	37	18	55027334	55027334	+	Silent	SNP	G	G	T	rs1153626	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	82	209	0	0.448087	0	T|0.282;G|0.718;A|0.000	0.282	strong	.	ST8SIA3	73	.	NM_015879	exon4	c.G969T	p.P323P	TTGGCCGTTTGGA	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	31496426	31496426	+	Missense_Mutation	SNP	T	T	C	rs1800278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	95	229	0	0.452381	0	T|0.963;0|0.002	.	strong	.	DMD	2127	.	NM_004006	exon59	c.A8734G	p.N2912D	CAGTATTGACCTC	.	PASS	Atlas-SNP
OR10Z1	128368	hgsc.bcm.edu	37	1	158576472	158576472	+	Missense_Mutation	SNP	C	C	T	rs76424590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	93	211	0	0.442857	0	C|0.962;T|0.038	0.038	strong	OR10Z1,NS,carcinoma,-2,1	OR10Z1	99	1	NM_001004478	exon1	c.C244T	p.L82F	AGAATGCTCTCTG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	66	95	0	0.511628	0	G|0.920;T|0.080	0.080	strong	.	WDR65	76	.	NM_152498	exon2	c.G12T	p.V4V	AGCCGTGGTAGCT	.	PASS	Atlas-SNP
RALGDS	5900	hgsc.bcm.edu	37	9	135974054	135974054	+	Missense_Mutation	SNP	C	C	T	rs143209866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	65	132	0	0.343915	0	C|0.998;T|0.002	0.002	strong	.	RALGDS	75	.	NM_006266	exon18	c.G2665A	p.V889M	CCTTCACTCCCTT	.	PASS	Atlas-SNP
ATP6V0D2	245972	hgsc.bcm.edu	37	8	87162515	87162515	+	Missense_Mutation	SNP	G	G	A	rs10094744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	45	107	0	0.445545	0	G|0.970;A|0.030	0.030	strong	.	ATP6V0D2	61	.	NM_152565	exon6	c.G814A	p.G272R	CATTACGGAGTAT	.	PASS	Atlas-SNP
C11orf44	283171	hgsc.bcm.edu	37	11	130542882	130542882	+	Silent	SNP	C	C	T	rs7933829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	46	149	0	0.368	0	C|0.739;T|0.261	0.261	strong	.	C11orf44	6	.	NM_001271983	exon1	c.C9T	p.L3L	GGTCCTCCTCTGT	.	PASS	Atlas-SNP
ZP4	57829	hgsc.bcm.edu	37	1	238046056	238046056	+	Missense_Mutation	SNP	G	G	A	rs35187146	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	44	103	0	0.411215	0	G|0.985;A|0.015	0.015	strong	.	ZP4	161	.	NM_021186	exon11	c.C1481T	p.P494L	TCTGGAGGGTCCT	.	PASS	Atlas-SNP
CES5A	221223	hgsc.bcm.edu	37	16	55883667	55883667	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	31	58	0	0.574074	0	.	.	none	.	CES5A	206	.	NM_001190158	exon12	c.A1379G	p.Y460C	TAGAAGTAGACAG	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	37	6	168315978	168315978	+	Silent	SNP	G	G	C	rs3213590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	86	185	0	0.409524	0	G|0.880;C|0.120	0.120	strong	.	MLLT4	351	.	NM_001040000	exon18	c.G2409C	p.V803V	ATTGGTGACCGAC	.	PASS	Atlas-SNP
PRDM8	56978	hgsc.bcm.edu	37	4	81124299	81124299	+	Silent	SNP	C	C	T	rs150632206	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	2	0	1	0	C|0.982;T|0.018	0.018	strong	.	PRDM8	44	.	NM_001099403	exon4	c.C1683T	p.S561S	CGGGTCCCTGCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510266	195510266	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	18	79	2	0.26087	0.0253165	.	.	none	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.T8185G	p.S2729A	TGGATGATGAGGA	.	scavenged	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44119120	44119120	+	Nonsense_Mutation	SNP	C	C	T	rs74697345	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	81	0	0.417582	0	C|0.990;T|0.010	0.010	strong	PDE9A,colon,carcinoma,0,1	PDE9A	69	1	NM_001001570	exon5	c.C337T	p.R113X	ACTCTCCGGTAAG	.	PASS	Atlas-SNP
CCDC105	126402	hgsc.bcm.edu	37	19	15122104	15122104	+	Missense_Mutation	SNP	G	G	T	rs199904661	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	30	43	0	0.681818	0	G|0.993;T|0.007	0.007	strong	.	CCDC105	53	.	NM_173482	exon1	c.G467T	p.R156L	TGCTGCGCCAGCG	.	PASS	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	37	11	88027209	88027209	+	Missense_Mutation	SNP	T	T	C	rs3888798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	29	83	0	0.408451	0	T|0.939;C|0.061	0.061	strong	.	CTSC	46	.	NM_001814	exon7	c.A1357G	p.I453V	CTGCTATGCTCTC	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25149590	25149590	+	Silent	SNP	G	G	A	rs35475676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	51	96	0	0.459459	0	G|0.983;A|0.017	0.017	strong	.	DOCK5	167	.	NM_024940	exon6	c.G372A	p.L124L	CAGCCTGATCGAG	.	PASS	Atlas-SNP
DMGDH	29958	hgsc.bcm.edu	37	5	78328560	78328560	+	Silent	SNP	G	G	A	rs1805072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	41	94	0	0.42268	0	G|0.796;A|0.204	0.204	strong	.	DMGDH	88	.	NM_013391	exon9	c.C1467T	p.G489G	CTCCCAGCCAGCA	.	PASS	Atlas-SNP
CIAPIN1	57019	hgsc.bcm.edu	37	16	57474740	57474740	+	Missense_Mutation	SNP	G	G	T	rs11557672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	56	117	0	0.405797	0	G|0.975;T|0.025	0.025	strong	.	CIAPIN1	17	.	NM_020313	exon2	c.C101A	p.A34E	GTTAACGCTTGAA	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241826517	241826517	+	Silent	SNP	C	C	T	rs12616061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	37	70	0	0.513889	0	C|0.888;T|0.112	0.112	strong	.	C2orf54	14	.	NM_001085437	exon5	c.G1314A	p.K438K	CCTGGTCTTCTGG	.	PASS	Atlas-SNP
SRGN	5552	hgsc.bcm.edu	37	10	70863699	70863699	+	Silent	SNP	C	C	T	rs4892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	40	86	0	0.430108	0	C|0.925;T|0.075	0.075	strong	SRGN,mouth,carcinoma,+1,1	SRGN	15	1	NM_002727	exon3	c.C300T	p.S100S	CGGCTCCGGCTCC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74273299	74273299	+	Missense_Mutation	SNP	G	G	A	rs73350377	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	36	62	0	0.514286	0	G|0.879;A|0.121	0.121	strong	.	QRICH2	143	.	NM_032134	exon16	c.C4712T	p.P1571L	TGCTGCGGGCGGC	.	PASS	Atlas-SNP
C4orf29	80167	hgsc.bcm.edu	37	4	128949929	128949929	+	Missense_Mutation	SNP	C	C	A	rs60505265	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	63	178	0	0.431507	0	C|0.909;A|0.091	0.091	strong	.	C4orf29	58	.	NM_001039717	exon10	c.C999A	p.S333R	ACAAAGCAGAAAC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34827085	34827085	+	Missense_Mutation	SNP	A	A	T	rs9469913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	43	93	0	0.544304	0	A|0.822;T|0.178	0.178	strong	.	UHRF1BP1	102	.	NM_017754	exon14	c.A2952T	p.Q984H	AACCCAAGCCTCC	.	PASS	Atlas-SNP
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209933659	209933659	+	Missense_Mutation	SNP	G	G	A	rs78296889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	65	150	0	0.411392	0	G|0.984;A|0.016	0.016	strong	.	TRAF3IP3	68	.	NM_025228	exon3	c.G275A	p.R92Q	CCAGGCGGCCAGG	.	PASS	Atlas-SNP
CBX8	57332	hgsc.bcm.edu	37	17	77768654	77768654	+	Missense_Mutation	SNP	C	C	A	rs4889891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	29	54	0	0.617021	0	C|0.433;A|0.567	0.567	strong	CBX8,colon,carcinoma,-1,3	CBX8	42	3	NM_020649	exon5	c.G950T	p.G317V	CCCCCCCCAGAGC	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1119963	1119963	+	Silent	SNP	A	A	G	rs2074921	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	47	71	0	0.505376	0	A|0.566;C|0.000;G|0.433;T|0.000	0.433	strong	.	SBNO2	112	.	NM_014963	exon12	c.T1209C	p.A403A	TAGCACAGCCTTG	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17928811	17928811	+	Missense_Mutation	SNP	C	C	T	rs1071645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	45	0	0.42	0	T|0.339;G|0.122	0.339	strong	.	ASAH1	71	.	NM_001127505	exon4	c.G283A	p.V95M	ATACCACTGGTGC	.	PASS	Atlas-SNP
GABRR2	2570	hgsc.bcm.edu	37	6	89967498	89967498	+	Missense_Mutation	SNP	G	G	A	rs282129	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	118	272	0	0.462745	0	G|0.693;T|0.005	.	strong	.	GABRR2	41	.	NM_002043	exon9	c.C1289T	p.T430M	AAACCCGTCTGGC	.	PASS	Atlas-SNP
EPS8L3	79574	hgsc.bcm.edu	37	1	110299691	110299691	+	Missense_Mutation	SNP	G	G	A	rs11102001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	177	149	0	0.994382	0	G|0.831;A|0.169	0.169	strong	.	EPS8L3	73	.	NM_139053	exon12	c.C1069T	p.P357S	CAGGTGGGCTTAG	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52662388	52662388	+	Missense_Mutation	SNP	C	C	T	rs189981926	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	2	174	0	0.0103627	0	C|1.000;T|0.000	0.000	strong	MYO5A,NS,carcinoma,-1,1	MYO5A	145	1	NM_000259	exon22	c.G3044A	p.R1015Q	TTGTATCGATCTG	.	scavenged	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	34	32	0	0.68	0	T|0.723;C|0.277	0.277	strong	KIAA0649,NS,carcinoma,0,1	.	.	1	NM_014811	exon4	c.T293C	p.V98A	TGGCTGTCTGTGG	.	PASS	Atlas-SNP
LRRC38	126755	hgsc.bcm.edu	37	1	13802325	13802325	+	Missense_Mutation	SNP	T	T	C	rs3013105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	53	0	1	0	C|0.487;N|0.000	0.487	strong	LRRC38,NS,meningioma,0,1	LRRC38	12	1	NM_001010847	exon2	c.A874G	p.K292E	CATCCTTGTCCTC	.	PASS	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84270650	84270650	+	Missense_Mutation	SNP	C	C	T	rs61743417	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	59	126	0	0.415493	0	C|0.971;T|0.029	0.029	strong	KCNG4,NS,carcinoma,0,1	KCNG4	71	1	NM_172347	exon2	c.G442A	p.A148T	AGTAGGCCAGCTC	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55441971	55441971	+	Silent	SNP	G	G	A	rs61746780	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	105	0	0.567568	0	G|0.976;A|0.024	0.024	strong	.	NLRP7	411	.	NM_001127255	exon9	c.C2706T	p.A902A	GCTGCAGGCTTCT	.	PASS	Atlas-SNP
ACSL5	51703	hgsc.bcm.edu	37	10	114181773	114181773	+	Missense_Mutation	SNP	A	A	G	rs12254915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	22	88	0	0.314286	0	A|0.982;G|0.018	0.018	strong	.	ACSL5	51	.	NM_016234	exon16	c.A1624G	p.T542A	TACTTTACAGTGA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804612	804612	+	Silent	SNP	C	C	T	rs4986235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	23	30	0	0.522727	0	C|0.922;T|0.078	0.078	strong	.	PTBP1	43	.	NM_031990	exon6	c.C516T	p.D172D	CGTGGACGCAGGG	.	PASS	Atlas-SNP
KRT78	196374	hgsc.bcm.edu	37	12	53242389	53242389	+	Missense_Mutation	SNP	G	G	A	rs116117459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	89	142	0	0.475936	0	G|0.983;A|0.017	0.017	strong	.	KRT78	41	.	NM_173352	exon1	c.C326T	p.T109M	TCCTGCGTCCGCA	.	PASS	Atlas-SNP
WHAMM	123720	hgsc.bcm.edu	37	15	83499766	83499766	+	Missense_Mutation	SNP	G	G	A	rs3814281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	29	0	0.470588	0	G|0.866;A|0.134	0.134	strong	.	WHAMM	63	.	NM_001080435	exon9	c.G2057A	p.R686H	AGCCACGTCCTCT	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61719387	61719387	+	Silent	SNP	T	T	C	rs1800007	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	90	0	0.990654	0	T|0.448;C|0.552	0.552	strong	.	BEST1	85	.	NM_004183	exon2	c.T109C	p.L37L	GAGTTCTTAATCT	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	37	15	70960422	70960422	+	Silent	SNP	C	C	T	rs61742861	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	140	0	0.518519	0	C|0.985;T|0.015	0.015	strong	.	UACA	235	.	NM_018003	exon16	c.G2601A	p.E867E	TTTAACCTCTTCA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863438	144863438	+	Missense_Mutation	SNP	G	G	T	rs140993521	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	15	327	0	0.0522648	0	.	.	weak	PDE4DIP_ENST00000369356,NS,carcinoma,0,2	PDE4DIP	817	2	NM_014644	exon37	c.C5965A	p.Q1989K	TGTGCTGCAGTCT	.	scavenged	Atlas-SNP
PAPPA2	60676	hgsc.bcm.edu	37	1	176564092	176564092	+	Missense_Mutation	SNP	C	C	T	rs34698817	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	34	91	0	0.447368	0	C|0.997;T|0.003	0.003	strong	PAPPA2_ENST00000367661,NS,carcinoma,-1,1	PAPPA2	665	1	NM_021936	exon3	c.C1352T	p.A451V	AGGAAGCGACTGA	.	PASS	Atlas-SNP
AARS2	57505	hgsc.bcm.edu	37	6	44270189	44270189	+	Missense_Mutation	SNP	A	A	T	rs35967387	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	66	133	0	0.503817	0	A|0.977;T|0.023	0.023	strong	.	AARS2	77	.	NM_020745	exon18	c.T2426A	p.L809Q	CTCCCCAGACTCA	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs28529067	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	32	95	0	0.941176	0	A|0.870;G|0.130	0.130	strong	NCOA3,colon,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.A3792G	p.Q1264Q	GCAGCAACAGCAA	.	PASS	Atlas-SNP
FLI1	2313	hgsc.bcm.edu	37	11	128675292	128675292	+	Silent	SNP	T	T	A	rs7113191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	97	0	0.46	0	T|0.855;A|0.145	0.145	strong	.	FLI1	72	.	NM_002017	exon6	c.T687A	p.A229A	AGGAGCTTGGGGC	.	PASS	Atlas-SNP
IGSF5	150084	hgsc.bcm.edu	37	21	41137499	41137499	+	Silent	SNP	A	A	G	rs12626544	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	35	78	0	0.426829	0	A|0.661;G|0.339	0.339	strong	.	IGSF5	62	.	NM_001080444	exon3	c.A138G	p.Q46Q	CCCCCAAAATGCA	.	PASS	Atlas-SNP
GKN1	56287	hgsc.bcm.edu	37	2	69204671	69204671	+	Silent	SNP	A	A	T	rs9808077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	176	183	0	1	0	A|0.804;T|0.196	0.196	strong	.	GKN1	24	.	NM_019617	exon2	c.A99T	p.L33L	TGCCCTAGCTAAC	.	PASS	Atlas-SNP
NFKBID	84807	hgsc.bcm.edu	37	19	36387881	36387881	+	Missense_Mutation	SNP	A	A	G	rs8113704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	169	101	0	0.994118	0	A|0.840;G|0.160	0.160	strong	.	NFKBID	30	.	NM_139239	exon5	c.T86C	p.V29A	CGGGCCACCTCCA	.	PASS	Atlas-SNP
FBXL6	26233	hgsc.bcm.edu	37	8	145579962	145579962	+	Missense_Mutation	SNP	C	C	T	rs77494279	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	7	52	6	0.127273	0.115385	C|0.932;T|0.068	0.068	strong	FBXL6,colon,carcinoma,0,1	FBXL6	26	1	NM_012162	exon7	c.G1223A	p.R408Q	TGACCCCGACATG	.	scavenged	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15709252	15709252	+	Missense_Mutation	SNP	G	G	A	rs2302464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	72	191	2	0.436364	0.0104712	G|0.944;A|0.056	0.056	strong	BST1,NS,carcinoma,0,1	BST1	30	1	NM_004334	exon3	c.G434A	p.R145Q	GGTGTCGACAGAA	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110534512	110534512	+	Silent	SNP	G	G	A	rs1563578	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	115	1	0.517241	0.00869565	G|0.740;A|0.260	0.260	strong	PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	NM_177531	exon74	c.G12129A	p.S4043S	CATTTCGTCCATG	.	scavenged	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848125	54848125	+	Silent	SNP	C	C	T	rs138326444	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	42	230	0	0.154982	0	C|0.999;T|0.001	0.001	weak	.	LILRA4	91	.	NM_012276	exon6	c.G1242A	p.E414E	CACGAGCTCCAGG	.	PASS	Atlas-SNP
LRIT3	345193	hgsc.bcm.edu	37	4	110791453	110791453	+	Silent	SNP	T	T	C	rs9994891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	148	128	0	0.980132	0	T|0.866;C|0.134	0.134	strong	.	LRIT3	107	.	NM_198506	exon4	c.T1548C	p.T516T	AGTGACTGTGTTG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37226888	37226888	+	Silent	SNP	A	A	G	rs115435816	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	51	93	0	0.566667	0	A|0.984;G|0.016	0.016	strong	.	C5orf42	422	.	NM_023073	exon12	c.T1809C	p.T603T	AAAATGAGTGATA	.	PASS	Atlas-SNP
HMGB1	3146	hgsc.bcm.edu	37	13	31037445	31037445	+	Silent	SNP	T	T	C	rs983723	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	22	40	0	0.415094	0	T|0.941;C|0.059	0.059	strong	.	HMGB1	21	.	NM_002128	exon3	c.A195G	p.K65K	GTCCGCTTTTGCC	.	PASS	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46918529	46918529	+	Silent	SNP	C	C	T	rs879721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	86	0	0.460526	0	C|0.943;T|0.057	0.057	strong	.	LRP4	160	.	NM_002334	exon8	c.G813A	p.T271T	TTCTGCCGTACAC	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	37	1	57415310	57415310	+	Missense_Mutation	SNP	G	G	A	rs12085435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	56	136	0	0.4	0	G|0.944;A|0.056	0.056	strong	.	C8B	107	.	NM_000066	exon6	c.C782T	p.P261L	ATTCCAGGTATTT	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795993	29795993	+	Silent	SNP	G	G	A	rs1130355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	35	165	0	0.318182	0	G|0.500;A|0.500	0.500	strong	.	HLA-G	90	.	NM_002127	exon3	c.G243A	p.P81P	GGGGCCGGAGTAT	.	PASS	Atlas-SNP
GMNN	51053	hgsc.bcm.edu	37	6	24781719	24781719	+	Missense_Mutation	SNP	G	G	C	rs2307307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	44	131	0	0.423077	0	G|0.932;C|0.068	0.068	strong	.	GMNN	19	.	NM_001251991	exon4	c.G144C	p.L48F	AGGCTTGTCCAAA	.	PASS	Atlas-SNP
PRR3	80742	hgsc.bcm.edu	37	6	30529622	30529622	+	Missense_Mutation	SNP	G	G	A	rs3888778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	33	62	0	0.52381	0	G|0.963;A|0.037	0.037	strong	.	PRR3	5	.	NM_025263	exon3	c.G181A	p.G61S	CACAGAGGTCCTC	.	PASS	Atlas-SNP
SLC38A5	92745	hgsc.bcm.edu	37	X	48326270	48326270	+	Silent	SNP	C	C	T	rs34099520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	64	121	0	0.441379	0	C|0.997;T|0.003	0.003	strong	.	SLC38A5	98	.	NM_033518	exon3	c.G42A	p.S14S	AGCATCCGAAGGG	.	PASS	Atlas-SNP
RRP7A	27341	hgsc.bcm.edu	37	22	42908976	42908976	+	Silent	SNP	G	G	A	rs145348367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	26	197	0	0.114035	0	G|0.983;A|0.017	0.017	strong	RRP7A,NS,carcinoma,0,2	RRP7A	25	2	NM_015703	exon7	c.C783T	p.F261F	CTCCTCGAACTTC	.	PASS	Atlas-SNP
ORC5	5001	hgsc.bcm.edu	37	7	103844599	103844599	+	Missense_Mutation	SNP	T	T	A	rs2307413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	58	123	0	0.504348	0	T|0.985;A|0.015	0.015	strong	.	ORC5	48	.	NM_002553	exon2	c.A156T	p.K52N	TAAAGTTTTCAAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411091	105411091	+	Missense_Mutation	SNP	G	G	A	rs143814844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	254	241	2	0.988327	0.00829876	G|0.971;A|0.029	0.029	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C10697T	p.T3566M	TTGGGCGTCTTTA	.	PASS	Atlas-SNP
HIRA	7290	hgsc.bcm.edu	37	22	19340928	19340928	+	Silent	SNP	G	G	A	rs34000365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	50	96	0	0.46729	0	G|0.990;A|0.010	0.010	strong	.	HIRA	100	.	NM_003325	exon23	c.C2799T	p.H933H	GTACTCGTGGCTG	.	PASS	Atlas-SNP
RARS2	57038	hgsc.bcm.edu	37	6	88229953	88229953	+	Missense_Mutation	SNP	G	G	A	rs138460258	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	27	78	0	0.519231	0	G|1.000;A|0.000	0.000	strong	.	RARS2	61	.	NM_020320	exon13	c.C1057T	p.H353Y	GAAAATGCTTTTT	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84212928	84212928	+	Silent	SNP	G	G	A	rs3743642	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	56	106	0	0.509091	0	G|0.867;A|0.133	0.133	strong	.	TAF1C	60	.	NM_005679	exon14	c.C2229T	p.P743P	TCTCCCGGGCTCC	.	PASS	Atlas-SNP
TM2D1	83941	hgsc.bcm.edu	37	1	62190780	62190780	+	Missense_Mutation	SNP	A	A	G	rs200054903	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	34	63	0	0.596491	0	.	.	weak	TM2D1_ENST00000371177,right_upper_lobe,carcinoma,+1,3	TM2D1	37	3	NM_032027	exon1	c.T13C	p.W5R	ACGGCCAGGCGGC	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	37	X	117528142	117528142	+	Silent	SNP	C	C	T	rs6603401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	154	240	0	0.681416	0	C|0.475;T|0.525	0.525	strong	.	WDR44	188	.	NM_001184965	exon5	c.C951T	p.T317T	AGTTACCGCCCAG	.	PASS	Atlas-SNP
GET4	51608	hgsc.bcm.edu	37	7	931960	931960	+	Silent	SNP	G	G	A	rs11543218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	69	0	1	0	G|0.929;A|0.071	0.071	strong	.	GET4	17	.	NM_015949	exon6	c.G651A	p.T217T	CTTCACGACGTAC	.	PASS	Atlas-SNP
FBRSL1	57666	hgsc.bcm.edu	37	12	133084874	133084874	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	31	81	0	0.492063	0	.	.	none	.	FBRSL1	47	.	NM_001142641	exon2	c.G427A	p.G143R	AGCCCCGGGCAGG	.	PASS	Atlas-SNP
TAS2R8	50836	hgsc.bcm.edu	37	12	10959031	10959031	+	Silent	SNP	C	C	T	rs1548803	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	72	167	0	0.436364	0	C|0.498;T|0.502	0.502	strong	.	TAS2R8	42	.	NM_023918	exon1	c.G549A	p.L183L	GAGAGTCAAGGGT	.	PASS	Atlas-SNP
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893077	1893077	+	Silent	SNP	C	C	A	rs35854772	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	87	136	0	0.47541	0	C|0.873;A|0.127	0.127	strong	.	ADIPOR2	30	.	NM_024551	exon7	c.C870A	p.I290I	TGGAATCATTCCT	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39521248	39521248	+	Missense_Mutation	SNP	A	A	C	rs71373411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	164	131	0	1	0	A|0.853;C|0.147	0.147	strong	.	KRT33B	46	.	NM_002279	exon6	c.T880G	p.Y294D	GAGAGTATCGCTG	.	PASS	Atlas-SNP
LPIN3	64900	hgsc.bcm.edu	37	20	39977300	39977300	+	Missense_Mutation	SNP	G	G	C	rs150562240	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	17	44	0	0.386364	0	G|0.999;C|0.001	0.001	strong	.	LPIN3	69	.	NM_022896	exon4	c.G330C	p.W110C	CCCTTGGGGGGGT	.	PASS	Atlas-SNP
OSCAR	126014	hgsc.bcm.edu	37	19	54599119	54599119	+	Missense_Mutation	SNP	G	G	A	rs1110643	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	53	61	0	0.552083	0	G|0.993;A|0.007	0.007	strong	.	OSCAR	22	.	NM_206818	exon5	c.C685T	p.R229W	CGGGCCGGGCCTC	.	PASS	Atlas-SNP
CDK2	1017	hgsc.bcm.edu	37	12	56360876	56360876	+	Silent	SNP	G	G	A	rs2069398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	49	41	0	1	0	G|0.871;A|0.129	0.129	strong	.	CDK2	27	.	NM_052827	exon1	c.G84A	p.E28E	GGGAGAGGTGGTG	.	PASS	Atlas-SNP
STRN4	29888	hgsc.bcm.edu	37	19	47226434	47226434	+	Missense_Mutation	SNP	C	C	T	rs10409124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	61	189	0	0.38125	0	C|0.912;T|0.088	0.088	strong	.	STRN4	33	.	NM_001039877	exon13	c.G1723A	p.V575I	TGCGGACGGTGCC	.	PASS	Atlas-SNP
ZNF812	729648	hgsc.bcm.edu	37	19	9801668	9801668	+	Missense_Mutation	SNP	T	T	C	rs113307466	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	53	89	0	0.630952	0	T|0.946;C|0.054	0.054	strong	.	ZNF812	27	.	NM_001199814	exon6	c.A511G	p.R171G	CTTTTCTACATTC	.	PASS	Atlas-SNP
IL27RA	9466	hgsc.bcm.edu	37	19	14142705	14142705	+	Silent	SNP	C	C	T	rs113593439	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	41	0	0.5	0	C|0.891;T|0.109	0.109	strong	IL27RA,NS,haematopoietic_neoplasm,0,2	IL27RA	56	2	NM_004843	exon1	c.C21T	p.A7A	GGGCGCCCCTTTC	.	PASS	Atlas-SNP
ZNF331	55422	hgsc.bcm.edu	37	19	54080279	54080279	+	Silent	SNP	T	T	C	rs1351	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	49	116	1	0.449541	0.00862069	T|0.881;C|0.119	0.119	strong	ZNF331_ENST00000253144,NS,carcinoma,+2,1	ZNF331	66	1	NM_001253801	exon5	c.T465C	p.G155G	TACTGGTGAGAAA	.	scavenged	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74878259	74878259	+	Missense_Mutation	SNP	G	G	A	rs571264	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	81	115	0	0.532895	0	G|0.665;A|0.335	0.335	strong	MGAT5B,colon,carcinoma,0,1	MGAT5B	98	1	NM_198955	exon2	c.G241A	p.V81I	CGCGGCGTCCTGC	.	PASS	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23853547	23853547	+	Silent	SNP	C	C	T	rs35628352	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	59	117	0	0.541284	0	C|0.991;T|0.009	0.009	strong	.	SGCG	64	.	NM_000231	exon5	c.C435T	p.N145N	CTCCAACGACGGC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17081707	17081707	+	Missense_Mutation	SNP	G	G	T	rs9305083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	19	34	0	0.5	0	G|0.914;T|0.086	0.086	strong	.	CPAMD8	192	.	NM_015692	exon18	c.C2348A	p.P783H	CTGGGGGGGTGCC	.	PASS	Atlas-SNP
FAM69C	125704	hgsc.bcm.edu	37	18	72103782	72103782	+	Missense_Mutation	SNP	T	T	C	rs2278154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	30	42	0	0.461538	0	T|0.666;C|0.334	0.334	strong	.	FAM69C	45	.	NM_001044369	exon4	c.A1214G	p.Q405R	AGGAGTTGGCGAA	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108367020	108367020	+	Silent	SNP	C	C	T	rs7082289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	76	0	1	0	C|0.839;T|0.161	0.161	strong	.	SORCS1	534	.	NM_001206572	exon23	c.G3069A	p.A1023A	GAGCACCGCCACC	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123783934	123783934	+	Silent	SNP	T	T	C	rs10985126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	97	280	0	0.340351	0	T|0.764;C|0.236	0.236	strong	C5,NS,adenoma,0,1	C5	124	1	NM_001735	exon11	c.A1155G	p.G385G	TGGGACTCCTCCT	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	19	160	1	0.105556	0.00625	T|0.998;C|0.002	0.002	weak	KRTAP5-10,NS,neuroblastoma,0,1	KRTAP5-10	37	1	NM_001012710	exon1	c.T255C	p.G85G	CTGTGGTTCCTGT	.	scavenged	Atlas-SNP
CYP3A5	1577	hgsc.bcm.edu	37	7	99262835	99262835	+	Silent	SNP	C	C	T	rs10264272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	72	136	0	0.45	0	C|0.952;T|0.048	0.048	strong	.	CYP3A5	46	.	NM_000777	exon7	c.G624A	p.K208K	GAACTTCTTAGTG	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48234381	48234381	+	Missense_Mutation	SNP	G	G	A	rs41282045	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	24	50	0	0.5	0	G|0.996;A|0.004	0.004	strong	.	ABCC11	177	.	NM_033151	exon14	c.C1888T	p.R630W	GGCCCCGCTCTCC	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52985293	52985293	+	Silent	SNP	A	A	G	rs12824366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	121	282	0	0.467181	0	A|0.651;G|0.349	0.349	strong	.	KRT72	70	.	NM_001146225	exon5	c.T918C	p.I306I	TAGGGCAATCTCC	.	PASS	Atlas-SNP
CACNG6	59285	hgsc.bcm.edu	37	19	54501540	54501540	+	Missense_Mutation	SNP	C	C	T	rs78495589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	38	63	0	0.678571	0	C|0.986;T|0.014	0.014	strong	.	CACNG6	42	.	NM_145815	exon2	c.C379T	p.R127C	AATGCACGCATCT	.	PASS	Atlas-SNP
CEP85L	387119	hgsc.bcm.edu	37	6	118953755	118953755	+	Silent	SNP	T	T	C	rs9320659	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	31	83	0	0.54386	0	T|0.980;C|0.020	0.020	strong	.	CEP85L	26	.	NM_001178035	exon3	c.A102G	p.A34A	TAGCCATGCTGAT	.	PASS	Atlas-SNP
OR2T5	401993	hgsc.bcm.edu	37	1	248652011	248652011	+	Missense_Mutation	SNP	A	A	T	rs9439338	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	788	343	944	2	0.435279	0.00211864	A|0.250;T|0.750	0.750	weak	OR2T5,NS,other,0,1	OR2T5	17	1	NM_001004697	exon1	c.A122T	p.K41M	TCCTGAAGGCGTT	.	scavenged	Atlas-SNP
APCDD1L	164284	hgsc.bcm.edu	37	20	57042665	57042665	+	Missense_Mutation	SNP	A	A	G	rs7265854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	86	151	0	0.51497	0	A|0.920;G|0.080	0.080	strong	.	APCDD1L	48	.	NM_153360	exon3	c.T238C	p.Y80H	TGGGGTAGAAGGT	.	PASS	Atlas-SNP
SRGAP2D	100996712	hgsc.bcm.edu	37	1	121116732	121116732	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	11	288	0	0.0404412	0	.	.	none	.	.	.	.	NM_001271887	exon3	c.C289T	p.Q97X	AAAGCCCAGAATG	.	PASS	Atlas-SNP
CST4	1472	hgsc.bcm.edu	37	20	23669584	23669584	+	Missense_Mutation	SNP	A	A	T	rs73902131	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	48	102	0	0.393443	0	A|0.964;T|0.036	0.036	strong	.	CST4	37	.	NM_001899	exon1	c.T23A	p.L8Q	AGTAGCAGGGTAC	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452679	195452679	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	990	191	609	0	0.192929	0	.	.	none	.	MUC20	84	.	NM_152673	exon3	c.C692T	p.P231L	GGTCCCCGGGATC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919079	12919079	+	Missense_Mutation	SNP	C	C	G	rs9659529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	348	167	284	1	0.479885	0.00352113	C|0.887;G|0.113	0.113	strong	PRAMEF2,caecum,carcinoma,-1,2	PRAMEF2	85	2	NM_023014	exon2	c.C215G	p.T72R	TGAAGACGCTTCA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511944	4511944	+	Silent	SNP	A	A	G	rs143131726	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	134	321	0	0.437909	0	A|0.994;G|0.006	0.006	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T1986C	p.N662N	GGCCACATTCACA	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127622491	127622491	+	Missense_Mutation	SNP	T	T	C	rs32209	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	75	151	0	0.543478	0	T|0.831;C|0.169	0.169	strong	.	FBN2	858	.	NM_001999	exon55	c.A6931G	p.M2311V	TACACATCATGCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6579354	6579354	+	Silent	SNP	G	G	C	rs16915382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	65	103	0	0.503876	0	G|0.805;C|0.195	0.195	strong	.	DNHD1	198	.	NM_144666	exon25	c.G8829C	p.L2943L	GGCTCTGTTGGTA	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61945439	61945439	+	Missense_Mutation	SNP	G	G	C	rs147670144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	74	143	0	0.48366	0	G|0.946;C|0.054	0.054	strong	.	COL20A1	137	.	NM_020882	exon19	c.G2374C	p.A792P	CCAGGAGCCAGGA	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622380	121622380	+	Missense_Mutation	SNP	C	C	G	rs2230913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	65	0	0.5	0	C|0.955;G|0.045;T|0.000	0.045	strong	.	P2RX7	53	.	NM_002562	exon13	c.C1563G	p.H521Q	CAGACACGTCCTG	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360395	74360395	+	Silent	SNP	T	T	C	rs76670837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	55	88	0	0.604396	0	T|0.926;C|0.074	0.074	strong	.	TMEM2	112	.	NM_001135820	exon4	c.A573G	p.A191A	TTTTTCTGCTCCA	.	PASS	Atlas-SNP
EHBP1L1	254102	hgsc.bcm.edu	37	11	65347922	65347922	+	Silent	SNP	G	G	A	rs78852393	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	36	42	0	0.666667	0	G|0.990;A|0.010	0.010	strong	.	EHBP1L1	64	.	NM_001099409	exon6	c.G606A	p.P202P	AGCCCCGGAGGCC	.	PASS	Atlas-SNP
OR5H14	403273	hgsc.bcm.edu	37	3	97868523	97868523	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	508	7	506	0	0.0137795	0	.	.	none	OR5H14,NS,carcinoma,0,1	OR5H14	56	1	NM_001005514	exon1	c.G294A	p.K98K	ATGCAAGATACAG	.	scavenged	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616408	248616408	+	Missense_Mutation	SNP	C	C	T	rs73147579	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1137	257	1131	0	0.226033	0	C|0.875;T|0.125	0.125	strong	OR2T2,NS,carcinoma,-2,1	OR2T2	73	1	NM_001004136	exon1	c.C310T	p.L104F	ATCTTCCTCTACC	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	105261725	105261725	+	Silent	SNP	G	G	A	rs59975412		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	53	87	0	0.595506	0	.	.	weak	.	RIMS2	1357	.	NM_001100117	exon22	c.G3600A	p.Q1200Q	CATTCAGGTAGGA	.	PASS	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	37	17	28407876	28407876	+	Silent	SNP	T	T	G	rs7221743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	122	0	1	0	T|0.418;G|0.582	0.582	strong	.	EFCAB5	122	.	NM_198529	exon17	c.T3303G	p.G1101G	TAATGGTTCATTC	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657526	49657526	+	Silent	SNP	G	G	A	rs150557795		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	36	253	1	0.127208	0.00395257	G|0.999;A|0.001	0.001	weak	HRC,NS,carcinoma,0,1	HRC	85	1	NM_002152	exon1	c.C969T	p.D323D	TCTGTGGTCTTGG	.	scavenged	Atlas-SNP
HCN2	610	hgsc.bcm.edu	37	19	607984	607984	+	Silent	SNP	G	G	C	rs3752158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	65	0	0.473684	0	G|0.864;C|0.136;A|0.000	0.136	strong	.	HCN2	36	.	NM_001194	exon4	c.G1239C	p.L413L	TGAACTGTACTCC	.	PASS	Atlas-SNP
CHPF2	54480	hgsc.bcm.edu	37	7	150935367	150935367	+	Missense_Mutation	SNP	C	C	T	rs76509585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	10	36	0	0.263158	0	C|0.988;T|0.012	0.012	strong	.	CHPF2	52	.	NM_019015	exon4	c.C1919T	p.P640L	GGCCCCCGGGGGC	.	PASS	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158596032	158596032	+	Silent	SNP	G	G	A	rs61732785	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	167	334	1	0.473088	0.00299401	G|0.985;A|0.015	0.015	strong	RNF145,right_upper_lobe,carcinoma,+2,1	RNF145	110	1	NM_001199380	exon8	c.C1060T	p.L354L	CTGCCAGGATTAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195516980	195516980	+	Missense_Mutation	SNP	A	A	G	rs11923648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	78	165	0	0.45614	0	A|0.960;G|0.040	0.040	strong	.	MUC4	1505	.	NM_018406	exon2	c.T1471C	p.S491P	AGAATGAGGAAGG	.	PASS	Atlas-SNP
GYG1	2992	hgsc.bcm.edu	37	3	148714662	148714662	+	Missense_Mutation	SNP	A	A	T	rs35054019	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	85	154	0	0.47486	0	A|0.990;T|0.010	0.010	strong	.	GYG1	29	.	NM_004130	exon4	c.A452T	p.H151L	TGTTGCATCTTGC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331419	55331419	+	Missense_Mutation	SNP	C	C	T	rs2273731	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	104	92	0	0.509804	0	C|0.250;T|0.750	0.750	weak	KIR3DL1_ENST00000402254,NS,neuroblastoma,0,2	KIR3DL1	174	2	NM_013289	exon4	c.C607T	p.P203S	CACACCCCCTATC	.	PASS	Atlas-SNP
ZNF385C	201181	hgsc.bcm.edu	37	17	40180910	40180910	+	Silent	SNP	G	G	A	rs7208473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	39	75	0	0.464286	0	G|0.989;A|0.011	0.011	strong	.	ZNF385C	7	.	NM_001242704	exon5	c.C621T	p.A207A	TCCCACGGCAGCT	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31323360	31323360	+	Missense_Mutation	SNP	T	T	G	rs181499296	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	46	74	0	0.365079	0	T|0.999;G|0.001	0.001	strong	.	TRPM1	183	.	NM_001252020	exon22	c.A3004C	p.M1002L	CGATCATCTGAGT	.	PASS	Atlas-SNP
OR51F2	119694	hgsc.bcm.edu	37	11	4843119	4843119	+	Silent	SNP	C	C	T	rs142530902		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	83	134	0	0.58042	0	C|1.000;T|0.000	0.000	weak	.	OR51F2	72	.	NM_001004753	exon1	c.C504T	p.A168A	TGTTGCCGTCATG	.	PASS	Atlas-SNP
ATP1A2	477	hgsc.bcm.edu	37	1	160090993	160090993	+	Silent	SNP	G	G	A	rs61734527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	29	85	0	0.376623	0	G|0.991;A|0.009	0.009	strong	.	ATP1A2	167	.	NM_000702	exon3	c.G129A	p.K43K	CCACAAGCTGTCC	.	PASS	Atlas-SNP
ABLIM1	3983	hgsc.bcm.edu	37	10	116335246	116335246	+	Silent	SNP	G	G	A	rs985273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	149	0	1	0	G|0.719;A|0.281	0.281	strong	ABLIM1,NS,carcinoma,0,1	ABLIM1	131	1	NM_002313	exon3	c.C492T	p.F164F	CTCCACGAACTCC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	129	1	1	0.00775194	A|0.685;G|0.315	0.315	strong	.	KRT84	61	.	NM_033045	exon1	c.T423C	p.T141T	GTTCACAGTCACA	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	27	54	0	0.442623	0	C|0.400;N|0.000	.	strong	.	ESPL1	158	.	NM_012291	exon8	c.C1842A	p.S614R	GCTGAGCCCCGAG	.	PASS	Atlas-SNP
GLRA1	2741	hgsc.bcm.edu	37	5	151231140	151231140	+	Silent	SNP	C	C	G	rs76872663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	76	109	0	0.524138	0	C|0.994;G|0.006	0.006	strong	GLRA1,NS,carcinoma,-2,1	GLRA1	61	1	NM_000171	exon7	c.G723C	p.R241R	GTGGAACCGGGCC	.	PASS	Atlas-SNP
NFATC3	4775	hgsc.bcm.edu	37	16	68224786	68224786	+	Missense_Mutation	SNP	C	C	G	rs77352556	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	128	200	0	0.554113	0	C|0.991;G|0.009	0.009	strong	.	NFATC3	190	.	NM_173163	exon9	c.C2214G	p.D738E	ACATGACAGTGTA	.	PASS	Atlas-SNP
TEX10	54881	hgsc.bcm.edu	37	9	103064530	103064530	+	Silent	SNP	G	G	A	rs7472	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	93	0	1	0	G|0.502;A|0.498	0.498	strong	.	TEX10	99	.	NM_017746	exon15	c.C2733T	p.F911F	CACGTTGAAGCAG	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236760181	236760181	+	Silent	SNP	G	G	A	rs12135515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	46	76	0	0.403509	0	G|0.979;A|0.021	0.021	strong	.	HEATR1	197	.	NM_018072	exon6	c.C699T	p.D233D	TGATACGTCCTCT	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919983	12919983	+	Silent	SNP	G	G	A	rs77138000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	78	195	0	0.417112	0	G|0.863;A|0.137	0.137	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.G723A	p.R241R	CTCCAGGTGCCAT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79026539	79026539	+	Missense_Mutation	SNP	A	A	C	rs57544556	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	186	165	1	0.994652	0.00606061	A|0.757;C|0.243	0.243	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.A1951C	p.S651R	TCTGAGAGCTCTC	.	PASS	Atlas-SNP
H1FOO	132243	hgsc.bcm.edu	37	3	129267915	129267915	+	Silent	SNP	T	T	C	rs60616647	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	127	0	1	0	T|0.938;C|0.062	0.062	strong	.	H1FOO	20	.	NM_153833	exon3	c.T450C	p.G150G	AGCGGGTGAGGCC	.	PASS	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47575170	47575170	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	63	92	0	0.538462	0	.	.	none	.	ZC3H4	96	.	NM_015168	exon13	c.A2011G	p.M671V	GCATCATTGGAGG	.	PASS	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	37	19	57036012	57036012	+	Missense_Mutation	SNP	G	G	T	rs11667052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	30	49	0	0.545455	0	G|0.792;T|0.208	0.208	strong	.	ZNF471	99	.	NM_020813	exon5	c.G576T	p.M192I	TTCTATGGTAATA	.	PASS	Atlas-SNP
BPIFB3	359710	hgsc.bcm.edu	37	20	31661399	31661399	+	Silent	SNP	C	C	T	rs114341725	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	109	184	1	0.5	0.00543478	C|0.993;T|0.007	0.007	strong	C20orf185,caecum,carcinoma,+2,1	.	.	1	NM_182658	exon15	c.C1419T	p.T473T	GCTGACCGTGGCA	.	scavenged	Atlas-SNP
ZNF229	7772	hgsc.bcm.edu	37	19	44933706	44933706	+	Missense_Mutation	SNP	C	C	T	rs57014690	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	63	136	1	0.512195	0.00735294	C|0.848;T|0.152	0.152	strong	ZNF229,tonsil,carcinoma,0,1	ZNF229	123	1	NM_014518	exon6	c.G1250A	p.S417N	ACTGAGCTGTAAC	.	scavenged	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512933	4512933	+	Missense_Mutation	SNP	C	C	A	rs200149931	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	66	372	1	0.269388	0.00268817	C|0.989;A|0.011	0.011	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G997T	p.V333L	TGGCCACATTCAT	.	PASS	Atlas-SNP
PRPF4	9128	hgsc.bcm.edu	37	9	116053895	116053895	+	Silent	SNP	C	C	T	rs146201781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	78	102	0	0.639344	0	C|0.999;T|0.001	0.001	strong	.	PRPF4	56	.	NM_004697	exon14	c.C1524T	p.A508A	CATAGCCACTTGC	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011409	46011409	+	Silent	SNP	G	G	A	rs144363824	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	54	364	0	0.203774	0	G|0.975;A|0.025	0.025	strong	.	KRTAP10-6	57	.	NM_198688	exon1	c.C957T	p.P319P	GGGGACGGGCACG	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746414	143746414	+	Missense_Mutation	SNP	G	G	A	rs115218091	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	38	90	0	0.431818	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_003724	exon2	c.C1064T	p.A355V	TAGCGGGCATGGG	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	57	124	0	0.475	0	A|0.774;C|0.226	0.226	strong	.	SYNPO2	353	.	NM_001128934	exon3	c.A522C	p.Q174H	CTCCCAAAGAGGA	.	PASS	Atlas-SNP
SSTR5	6755	hgsc.bcm.edu	37	16	1128901	1128901	+	Silent	SNP	C	C	T	rs35128939	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	5	24	0	0.208333	0	C|0.997;T|0.003	0.003	strong	.	SSTR5	36	.	NM_001172560	exon2	c.C33T	p.S11S	GCCCAGCTGGAAC	.	PASS	Atlas-SNP
SLC3A2	6520	hgsc.bcm.edu	37	11	62648748	62648748	+	Silent	SNP	C	C	T	rs73487878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	57	0	0.493151	0	C|0.975;T|0.025	0.025	strong	.	SLC3A2	55	.	NM_001012662	exon4	c.C559T	p.L187L	GCACTGCTGCTGC	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167585652	167585652	+	Missense_Mutation	SNP	A	A	C	rs59203630	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	173	183	0	0.977401	0	A|0.966;C|0.034	0.034	strong	.	TCP10L2	41	.	NM_001145121	exon2	c.A20C	p.E7A	AGCTCGAGGCCAG	.	PASS	Atlas-SNP
GTPBP5	26164	hgsc.bcm.edu	37	20	60768497	60768497	+	Silent	SNP	C	C	T	rs2236527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	82	217	0	0.431579	0	C|0.827;T|0.173	0.173	strong	.	GTPBP5	43	.	NM_015666	exon2	c.C21T	p.F7F	GTGTTTCTCAGCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9048342	9048342	+	Missense_Mutation	SNP	C	C	T	rs10854118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	75	149	0	0.490196	0	C|0.570;T|0.430	0.430	strong	MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	NM_024690	exon5	c.G33289A	p.V11097M	TCACCACTCCTGA	.	PASS	Atlas-SNP
C3orf52	79669	hgsc.bcm.edu	37	3	111821747	111821747	+	Missense_Mutation	SNP	A	A	G	rs16859190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	88	184	0	0.475676	0	A|0.895;G|0.105	0.105	strong	.	C3orf52	28	.	NM_001171747	exon3	c.A331G	p.I111V	TTCTTCATCATGC	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80936082	80936082	+	Silent	SNP	C	C	T	rs11114503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	101	119	0	1	0	C|0.585;T|0.415	0.415	strong	.	PTPRQ	119	.	NM_001145026	exon19	c.C3144T	p.A1048A	TGCTGCCGCAAGA	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39873053	39873053	+	Missense_Mutation	SNP	G	G	A	rs72632016	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	57	112	0	0.475	0	G|0.929;A|0.071	0.071	strong	.	IDO2	78	.	NM_194294	exon11	c.G1195A	p.A399T	GGAACCGCAGTTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508524	195508524	+	Silent	SNP	G	G	A	rs141064104	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	57	197	0	0.478992	0	G|0.950;A|0.050	0.050	strong	MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	NM_018406	exon2	c.C9927T	p.H3309H	AGTGGCGTGACCT	.	PASS	Atlas-SNP
GRXCR1	389207	hgsc.bcm.edu	37	4	42895308	42895308	+	Missense_Mutation	SNP	G	G	A	rs78136490	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	122	0	0.401869	0	G|0.906;A|0.094	0.094	strong	.	GRXCR1	78	.	NM_001080476	exon1	c.G25A	p.E9K	AAGCCAGAAAGTG	.	PASS	Atlas-SNP
ADRB1	153	hgsc.bcm.edu	37	10	115804123	115804123	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	42	89	0	0.525	0	.	.	none	.	ADRB1	16	.	NM_000684	exon1	c.C232T	p.L78L	AATGTGCTGGTGA	.	PASS	Atlas-SNP
SLC14A2	8170	hgsc.bcm.edu	37	18	43246156	43246156	+	Missense_Mutation	SNP	G	G	A	rs9960464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	62	119	0	0.469697	0	G|0.615;A|0.385	0.385	strong	SLC14A2,NS,carcinoma,0,1	SLC14A2	121	1	NM_001242692	exon13	c.G1529A	p.R510Q	CCTATCGATACCG	.	PASS	Atlas-SNP
NUDT6	11162	hgsc.bcm.edu	37	4	123814170	123814170	+	Missense_Mutation	SNP	G	G	A	rs138619142	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	114	212	0	0.493506	0	G|0.998;A|0.002	0.002	strong	.	NUDT6	50	.	NM_007083	exon5	c.C764T	p.A255V	GTCTTCGCCAGGT	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147824864	147824864	+	Missense_Mutation	SNP	G	G	A	rs17610219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	115	1	1	0.00869565	G|0.507;A|0.493	0.493	strong	.	TTC29	63	.	NM_031956	exon6	c.C418T	p.H140Y	TATTATGTACATC	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	37	9	95766336	95766336	+	Silent	SNP	C	C	T	rs201073654	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	60	99	0	0.645161	0	C|1.000;T|0.000	0.000	strong	.	FGD3	116	.	NM_001083536	exon5	c.C597T	p.G199G	CATGGGCATATTC	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103519119	103519119	+	Silent	SNP	G	G	A	rs73573973	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	35	48	0	0.472973	0	G|0.994;A|0.006	0.006	strong	ERCC5,NS,carcinoma,+2,1	.	.	1	NM_001204425	exon19	c.G3819A	p.R1273R	AGCGCGGCATGTC	.	PASS	Atlas-SNP
PLEKHS1	79949	hgsc.bcm.edu	37	10	115531790	115531790	+	Missense_Mutation	SNP	C	C	T	rs143039412		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	56	141	0	0.444444	0	C|1.000;T|0.000	0.000	weak	.	PLEKHS1	19	.	NM_024889	exon8	c.C614T	p.A205V	CAGAAGCCACTCA	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82585803	82585803	+	Missense_Mutation	SNP	G	G	C	rs114445550	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	71	120	0	0.510791	0	G|0.997;C|0.003	0.003	strong	.	PCLO	1506	.	NM_014510	exon5	c.C4466G	p.S1489C	TTGCTGGAAGGAA	.	PASS	Atlas-SNP
TSC22D1	8848	hgsc.bcm.edu	37	13	45149662	45149662	+	Silent	SNP	G	G	A	rs9525984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	106	191	0	0.488479	0	G|0.924;A|0.076	0.076	strong	.	TSC22D1	88	.	NM_183422	exon1	c.C549T	p.A183A	TGTCTCGGCTTCC	.	PASS	Atlas-SNP
ASL	435	hgsc.bcm.edu	37	7	65551782	65551782	+	Silent	SNP	G	G	A	rs115468878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	35	90	0	0.472973	0	G|0.993;A|0.007	0.007	strong	.	ASL	39	.	NM_000048	exon8	c.G576A	p.K192K	GCGGAAGCGGATC	.	PASS	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	74	173	1	0.432749	0.00578035	C|0.826;T|0.174	0.174	strong	IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	NM_001563	exon15	c.G2132A	p.R711H	TTGCAGCGACACT	.	scavenged	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376040	52376040	+	Silent	SNP	G	G	A	rs10407707	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	48	128	0	0.424779	0	G|0.892;A|0.108	0.108	strong	.	ZNF577	63	.	NM_032679	exon7	c.C1203T	p.S401S	GAGTTCGCTCATG	.	PASS	Atlas-SNP
JAG2	3714	hgsc.bcm.edu	37	14	105622157	105622157	+	Silent	SNP	G	G	A	rs61750261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	68	161	0	0.444444	0	G|0.974;A|0.026	0.026	strong	.	JAG2	69	.	NM_145159	exon4	c.C645T	p.N215N	AAAGTCGTTGCGG	.	PASS	Atlas-SNP
PCDHA9	9752	hgsc.bcm.edu	37	5	140229925	140229925	+	Silent	SNP	G	G	C	rs58792000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	111	220	0	0.526066	0	G|0.937;C|0.063	0.063	strong	.	PCDHA9	373	.	NM_031857	exon1	c.G1845C	p.T615T	AGAAACGGCCAGC	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31756954	31756954	+	Missense_Mutation	SNP	G	G	A	rs17124277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	47	141	0	0.405172	0	G|0.963;A|0.037	0.037	strong	.	.	.	.	NM_080574	exon2	c.G3A	p.M1I	AAAGATGCTTCAG	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694569	139694569	+	Missense_Mutation	SNP	A	A	C	rs7859194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	18	15	0	1	0	A|0.754;C|0.246	0.246	strong	.	KIAA1984	39	.	NM_001039374	exon4	c.A386C	p.D129A	AGCTGGACAGCCT	.	PASS	Atlas-SNP
MVP	9961	hgsc.bcm.edu	37	16	29841950	29841950	+	Missense_Mutation	SNP	G	G	A	rs142997389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	52	132	0	0.422764	0	G|0.991;A|0.009	0.009	strong	.	MVP	80	.	NM_017458	exon2	c.G80A	p.R27H	TGTCCCGTGTGGA	.	PASS	Atlas-SNP
ITGA5	3678	hgsc.bcm.edu	37	12	54795410	54795410	+	Silent	SNP	A	A	G	rs73322228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	72	194	0	0.421053	0	A|0.960;G|0.040	0.040	strong	.	ITGA5	99	.	NM_002205	exon23	c.T2346C	p.F782F	GAGCCGAAAGGAA	.	PASS	Atlas-SNP
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803167	43803167	+	Missense_Mutation	SNP	T	T	C	rs2839500	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	48	80	0	0.585366	0	A|0.006;C|0.194	0.194	strong	.	TMPRSS3	40	.	NM_001256317	exon8	c.A757G	p.I253V	CAGTGATGATCCA	.	PASS	Atlas-SNP
CASP8	841	hgsc.bcm.edu	37	2	202149696	202149696	+	Silent	SNP	G	G	A	rs1045487	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	60	122	0	0.46875	0	G|0.862;A|0.138	0.138	strong	.	CASP8	272	.	NM_001080125	exon8	c.G1137A	p.K379K	AGACAAGGGCATC	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	179983153	179983153	+	Missense_Mutation	SNP	A	A	G	rs111349041	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	46	75	0	0.613333	0	A|0.986;G|0.014	0.014	strong	.	CEP350	418	.	NM_014810	exon10	c.A1565G	p.D522G	ATAAGGACTTTTT	.	PASS	Atlas-SNP
KLHDC7B	113730	hgsc.bcm.edu	37	22	50987843	50987843	+	Silent	SNP	C	C	T	rs61746062	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	43	75	0	0.494253	0	C|0.896;T|0.104	0.104	strong	.	KLHDC7B	39	.	NM_138433	exon1	c.C1248T	p.Y416Y	CCTGTACAGCATG	.	PASS	Atlas-SNP
NCF4	4689	hgsc.bcm.edu	37	22	37260123	37260123	+	Silent	SNP	G	G	A	rs10854695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	72	150	0	0.517986	0	G|0.930;A|0.070	0.070	strong	NCF4_ENST00000397147,NS,carcinoma,+1,2	NCF4	66	2	NM_000631	exon2	c.G69A	p.S23S	CATCTCGGCCAAC	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443739	5443739	+	Silent	SNP	T	T	C	rs2736587	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	197	185	1	1	0.00540541	T|0.601;C|0.399	0.399	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.T309C	p.F103F	TCAGTTTTTCTTC	.	PASS	Atlas-SNP
QRFP	347148	hgsc.bcm.edu	37	9	133768987	133768987	+	Missense_Mutation	SNP	T	T	C	rs111763002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	95	134	0	0.655172	0	T|0.983;C|0.017	0.017	strong	.	QRFP	14	.	NM_198180	exon1	c.A239G	p.E80G	GCATGCTCTCTGC	.	PASS	Atlas-SNP
STAU2	27067	hgsc.bcm.edu	37	8	74526081	74526081	+	Silent	SNP	G	G	A	rs28728027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	26	79	0	0.464286	0	G|0.995;A|0.005	0.005	strong	STAU2_ENST00000524300,NS,carcinoma,-1,3	STAU2	148	3	NM_001164380	exon9	c.C789T	p.R263R	CGCAGCGCGCTTC	.	PASS	Atlas-SNP
ZNF70	7621	hgsc.bcm.edu	37	22	24087319	24087319	+	Silent	SNP	A	A	C	rs2070451	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	64	101	0	0.533333	0	A|0.865;C|0.135	0.135	strong	.	ZNF70	49	.	NM_021916	exon2	c.T9G	p.V3V	TGGGGGAACCTCC	.	PASS	Atlas-SNP
IFT52	51098	hgsc.bcm.edu	37	20	42252587	42252587	+	Silent	SNP	G	G	A	rs73274323	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	56	129	0	0.440945	0	G|0.980;A|0.020	0.020	strong	.	IFT52	40	.	NM_016004	exon10	c.G825A	p.E275E	TCGAGAGTGTCTC	.	PASS	Atlas-SNP
ROR1	4919	hgsc.bcm.edu	37	1	64643650	64643650	+	Silent	SNP	C	C	T	rs35586842	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	76	121	0	0.603175	0	C|0.972;T|0.028	0.028	strong	.	ROR1	113	.	NM_005012	exon9	c.C1926T	p.S642S	TTACTCCGCTGAT	.	PASS	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	37	2	71044076	71044076	+	Missense_Mutation	SNP	T	T	C	rs61754946	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	112	199	0	0.440945	0	T|0.979;C|0.021	0.021	strong	.	CLEC4F	95	.	NM_173535	exon4	c.A437G	p.N146S	TCAGCATTGGTGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149489443	149489443	+	Silent	SNP	C	C	A	rs893603	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	37	81	0	0.330357	0	C|0.975;A|0.025	0.025	strong	.	.	.	.	NM_198455	exon37	c.C5596A	p.R1866R	TGGCCCCGGCAGT	.	PASS	Atlas-SNP
ZNF76	7629	hgsc.bcm.edu	37	6	35263009	35263009	+	Missense_Mutation	SNP	C	C	T	rs73745177	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	18	52	0	0.45	0	C|0.994;T|0.006	0.006	strong	.	ZNF76	37	.	NM_003427	exon14	c.C1697T	p.S566L	CAGTGTCGGAGAG	.	PASS	Atlas-SNP
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570892	186570892	+	Silent	SNP	T	T	G	rs2241766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	144	314	0	0.472131	0	T|0.885;G|0.115	0.115	strong	ADIPOQ,colon,carcinoma,+2,2	ADIPOQ	35	2	NM_001177800	exon3	c.T45G	p.G15G	GCCCGGTCATGAC	.	PASS	Atlas-SNP
NPNT	255743	hgsc.bcm.edu	37	4	106819089	106819089	+	Silent	SNP	C	C	T	rs147630398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	113	191	0	0.55122	0	C|0.999;T|0.001	0.001	strong	.	NPNT	69	.	NM_001184692	exon2	c.C103T	p.L35L	ATTGGCCTATGTC	.	PASS	Atlas-SNP
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788264	140788264	+	Silent	SNP	C	C	T	rs58047392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	80	0	0.419753	0	C|0.824;T|0.176	0.176	strong	.	PCDHGB6	120	.	NM_032100	exon1	c.C495T	p.N165N	CATAAACTCAATT	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76109877	76109877	+	Silent	SNP	G	G	A	rs149301449	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	135	214	0	0.567227	0	G|0.997;A|0.003	0.003	strong	.	DTX2	64	.	NM_001102596	exon1	c.G51A	p.A17A	CCCCGCGGCTGTG	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117130838	117130838	+	Missense_Mutation	SNP	C	C	T	rs138188658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	66	104	0	0.55	0	C|0.996;T|0.004	0.004	strong	.	AKNA	119	.	NM_030767	exon5	c.G1454A	p.S485N	TGGATGCTGTGGT	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632820	32632820	+	Missense_Mutation	SNP	C	C	G	rs1130375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	24	40	0	0.96	0	G|0.228;C|0.772	0.228	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G134C	p.G45A	CACATGCCCTTAA	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118511726	118511726	+	Missense_Mutation	SNP	C	C	T	rs9668527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	84	0	0.448718	0	C|0.937;T|0.063	0.063	strong	.	VSIG10	41	.	NM_019086	exon5	c.G997A	p.V333M	CAGACACCTGGCA	.	PASS	Atlas-SNP
C9orf114	51490	hgsc.bcm.edu	37	9	131588888	131588888	+	Missense_Mutation	SNP	G	G	C	rs6478854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	12	61	0	0.244898	0	G|0.583;C|0.417	0.417	strong	.	C9orf114	28	.	NM_016390	exon5	c.C389G	p.T130R	ACTCCTGTGAATT	.	PASS	Atlas-SNP
CCDC37	348807	hgsc.bcm.edu	37	3	126137456	126137456	+	Silent	SNP	T	T	C	rs76764772	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	67	0	0.439394	0	T|0.941;C|0.059	0.059	strong	.	CCDC37	69	.	NM_182628	exon7	c.T489C	p.Y163Y	CCAGTATGCCCTG	.	PASS	Atlas-SNP
POTEG	404785	hgsc.bcm.edu	37	14	19553677	19553677	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1110	83	704	1	0.0747748	0.00142045	.	.	none	POTEG,NS,carcinoma,0,2	POTEG	118	2	NM_001005356	exon1	c.C261T	p.D87D	CCACGACGACTCT	.	scavenged	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234394487	234394487	+	Missense_Mutation	SNP	G	G	A	rs1048603	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	238	207	0	1	0	G|0.604;T|0.006	.	strong	.	USP40	174	.	NM_018218	exon28	c.C3367T	p.R1123C	GAAGACGATAGAA	.	PASS	Atlas-SNP
UHMK1	127933	hgsc.bcm.edu	37	1	162467927	162467927	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	115	0	0.467213	0	.	.	none	UHMK1_ENST00000489294,NS,carcinoma,0,2	UHMK1	65	2	NM_175866	exon1	c.C137G	p.P46R	GCAACCCTGGCTC	.	PASS	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	37	2	71046536	71046536	+	Silent	SNP	G	G	A	rs17006361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	85	180	0	0.508982	0	G|0.948;A|0.052	0.052	strong	CLEC4F,NS,carcinoma,0,3	CLEC4F	95	3	NM_173535	exon3	c.C219T	p.A73A	AATTACGGCTTGC	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102514227	102514227	+	Silent	SNP	T	T	C	rs13749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	60	1	1	0.0166667	T|0.681;C|0.319	0.319	strong	DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	NM_001376	exon73	c.T13080C	p.T4360T	AGAGACTGAGAAG	.	scavenged	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	30143259	30143259	+	Silent	SNP	G	G	T	rs192127241	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	9	15	0	0.45	0	G|0.998;T|0.002	0.002	strong	.	ALK	533	.	NM_004304	exon1	c.C267A	p.G89G	TAGCGAGCCGCGG	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721798	49721798	+	Silent	SNP	C	C	A	rs13085791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	367	189	372	1	0.514986	0.00268817	C|0.725;A|0.275	0.275	strong	.	MST1	84	.	NM_020998	exon17	c.G1965T	p.R655R	ACTCTCCCGCACA	.	PASS	Atlas-SNP
OR8B12	219858	hgsc.bcm.edu	37	11	124413491	124413491	+	Silent	SNP	C	C	T	rs61746453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	27	60	0	0.529412	0	C|0.974;T|0.026	0.026	strong	OR8B12,bladder,carcinoma,-1,1	OR8B12	66	1	NM_001005195	exon1	c.G60A	p.P20P	CAGTCCCGGCTGG	.	PASS	Atlas-SNP
PCNP	57092	hgsc.bcm.edu	37	3	101293097	101293097	+	Missense_Mutation	SNP	A	A	G	rs116752753	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	114	161	0	0.542857	0	A|0.993;G|0.007	0.007	strong	.	PCNP	8	.	NM_020357	exon1	c.A38G	p.K13R	CTGAAAAGTCGCA	.	PASS	Atlas-SNP
NCL	4691	hgsc.bcm.edu	37	2	232320281	232320281	+	Silent	SNP	G	G	A	rs78372304	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	109	259	0	0.519048	0	G|0.994;A|0.006	0.006	strong	.	NCL	80	.	NM_005381	exon13	c.C1887T	p.A629A	TTCCATGGCCTCC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376126	52376126	+	Missense_Mutation	SNP	C	C	T	rs10407547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	47	107	0	0.38843	0	C|0.892;T|0.108	0.108	strong	ZNF577,NS,carcinoma,+2,1	ZNF577	63	1	NM_032679	exon7	c.G1117A	p.E373K	TTTTCTCATGTTT	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23861811	23861811	+	Missense_Mutation	SNP	A	A	G	rs365990	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	83	167	0	0.468927	0	A|0.576;G|0.424	0.424	strong	.	MYH6	274	.	NM_002471	exon25	c.T3302C	p.V1101A	GCCAGCACCTGCT	.	PASS	Atlas-SNP
LGI3	203190	hgsc.bcm.edu	37	8	22005939	22005939	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	21	48	0	0.456522	0	.	.	none	.	LGI3	44	.	NM_139278	exon8	c.G1381A	p.A461T	GCAGGGCCTGCAC	.	PASS	Atlas-SNP
PRODH2	58510	hgsc.bcm.edu	37	19	36304143	36304143	+	Missense_Mutation	SNP	G	G	A	rs138605929	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	28	50	0	0.651163	0	G|0.992;A|0.008	0.008	strong	.	PRODH2	68	.	NM_021232	exon1	c.C41T	p.S14F	CTTTGGGAGGCCA	.	PASS	Atlas-SNP
NLN	57486	hgsc.bcm.edu	37	5	65084101	65084101	+	Missense_Mutation	SNP	A	A	G	rs6863012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	88	175	0	0.517647	0	A|0.936;G|0.064	0.064	strong	.	NLN	51	.	NM_020726	exon8	c.A1115G	p.K372R	AACTCAAGTATTC	.	PASS	Atlas-SNP
C4BPA	722	hgsc.bcm.edu	37	1	207305069	207305069	+	Silent	SNP	A	A	C	rs6663608	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	52	87	0	0.444444	0	A|0.930;C|0.070	0.070	strong	.	C4BPA	70	.	NM_000715	exon8	c.A1068C	p.P356P	GACCCCATACCAA	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130188009	130188009	+	Silent	SNP	C	C	T	rs59160673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	49	103	0	0.453704	0	C|0.989;T|0.011	0.011	strong	.	COL6A5	205	.	NM_153264	exon38	c.C7161T	p.G2387G	TATTGGCCATGCC	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66391232	66391232	+	Silent	SNP	A	A	G	rs7342975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	104	220	1	0.472727	0.00454545	A|0.894;G|0.106	0.106	strong	.	ARSG	55	.	NM_001267727	exon10	c.A1110G	p.P370P	TTTTCCAACTGTG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	82	0	1	0	A|0.689;G|0.311	0.311	strong	.	TNS1	251	.	NM_022648	exon24	c.T3972C	p.G1324G	ATAGCCACCATAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509170	195509170	+	Missense_Mutation	SNP	A	A	G	rs202189117	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	35	252	1	0.119454	0.00396825	A|0.994;G|0.006	0.006	strong	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.T9281C	p.L3094P	GAGGAAAGGCTGG	.	scavenged	Atlas-SNP
OBFC1	79991	hgsc.bcm.edu	37	10	105657363	105657363	+	Silent	SNP	C	C	G	rs11191853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	115	87	0	0.982906	0	C|0.780;G|0.220	0.220	strong	.	OBFC1	33	.	NM_024928	exon7	c.G696C	p.V232V	AGACTCCACCATT	.	PASS	Atlas-SNP
ANKRD20A1	84210	hgsc.bcm.edu	37	9	67938633	67938633	+	Missense_Mutation	SNP	G	G	T	rs200989194	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	570	10	851	5	0.0175439	0.00587544	G|0.990;T|0.010	0.010	strong	ANKRD20A1,bladder,carcinoma,0,3	ANKRD20A1	16	3	NM_032250	exon6	c.G768T	p.K256N	TAAAAAGAAGATA	.	scavenged	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	89982132	89982132	+	Silent	SNP	T	T	C	rs6972561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	28	37	0	0.595745	0	T|0.731;C|0.269	0.269	strong	.	GTPBP10	31	.	NM_001042717	exon2	c.T36C	p.Y12Y	TAAGTATGGAAAT	.	PASS	Atlas-SNP
LRP5L	91355	hgsc.bcm.edu	37	22	25753321	25753321	+	Silent	SNP	G	G	A	rs9624807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	102	169	0	0.488038	0	G|0.895;A|0.105	0.105	strong	.	LRP5L	23	.	NM_001135772	exon4	c.C339T	p.R113R	CAGCACGCGCAGC	.	PASS	Atlas-SNP
APBA2	321	hgsc.bcm.edu	37	15	29347019	29347019	+	Missense_Mutation	SNP	T	T	C	rs8040932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	22	7	0	1	0	T|0.681;C|0.319	0.319	strong	.	APBA2	132	.	NM_005503	exon3	c.T932C	p.L311P	AGAGGCTGAAGTG	.	PASS	Atlas-SNP
APPL1	26060	hgsc.bcm.edu	37	3	57303684	57303684	+	Missense_Mutation	SNP	A	A	G	rs11544593	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	59	117	0	0.472	0	A|0.892;G|0.108	0.108	strong	.	APPL1	59	.	NM_012096	exon22	c.A2099G	p.E700G	TGGGAGAAGGAGG	.	PASS	Atlas-SNP
LRRC8C	84230	hgsc.bcm.edu	37	1	90179470	90179470	+	Silent	SNP	A	A	G	rs34576461	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	81	0	0.514706	0	A|0.979;G|0.021	0.021	strong	.	LRRC8C	73	.	NM_032270	exon3	c.A1341G	p.Q447Q	GTTGCAATCTCTA	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128364787	128364787	+	Missense_Mutation	SNP	G	G	C	rs201386852	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	93	192	0	0.516667	0	.	.	weak	.	MYO7B	359	.	NM_001080527	exon21	c.G2431C	p.V811L	ATCCTCGTGGGCT	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1109577	1109577	+	Silent	SNP	C	C	T	rs200767766	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	50	88	0	0.480769	0	C|0.986;T|0.014	0.014	strong	.	SBNO2	112	.	NM_014963	exon28	c.G3144A	p.L1048L	CCACTTCAGGCCG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412138	105412138	+	Missense_Mutation	SNP	A	A	G	rs200384326	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	335	30	336	0	0.0895522	0	.	.	weak	AHNAK2_ENST00000333244,NS,neuroblastoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.T9650C	p.L3217P	CCCTCGAGAACGT	.	PASS	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17216556	17216556	+	Silent	SNP	C	C	T	rs2273734	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	27	85	0	0.435484	0	C|0.581;T|0.419	0.419	strong	.	TRDMT1	46	.	NM_004412	exon2	c.G168A	p.T56T	TTCAATCGTCTTG	.	PASS	Atlas-SNP
OR10A4	283297	hgsc.bcm.edu	37	11	6898663	6898663	+	Missense_Mutation	SNP	G	G	A	rs10839635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	28	74	0	0.383562	0	G|0.724;A|0.276	0.276	strong	OR10A4,NS,carcinoma,-1,1	OR10A4	65	1	NM_207186	exon1	c.G785A	p.R262Q	ATTTCCGACCCCA	.	PASS	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42448659	42448659	+	Missense_Mutation	SNP	C	C	A	rs636604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	70	136	0	0.518519	0	C|0.939;A|0.061	0.061	strong	.	PLA2G4F	75	.	NM_213600	exon1	c.G89T	p.G30V	AGAGGGCCCCTCT	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24207399	24207399	+	Silent	SNP	G	G	C	rs7829944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	62	147	0	0.442857	0	G|0.947;C|0.053	0.053	strong	.	ADAM28	100	.	NM_014265	exon19	c.G2013C	p.V671V	TGGGGTGCTGTTC	.	PASS	Atlas-SNP
PIH1D1	55011	hgsc.bcm.edu	37	19	49950298	49950298	+	Missense_Mutation	SNP	C	C	T	rs13394	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	101	0	1	0	C|0.264;N|0.000	.	strong	PIH1D1,bladder,carcinoma,+1,1	PIH1D1	23	1	NM_017916	exon7	c.G670A	p.V224I	GGTCAACTTCGGC	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176540	8176540	+	Silent	SNP	C	C	T	rs116402506	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	26	32	0	0.565217	0	C|0.970;T|0.030	0.030	strong	.	.	.	.	NM_001080826	exon5	c.G3345A	p.A1115A	CTCGTACGCCTCG	.	PASS	Atlas-SNP
ZP1	22917	hgsc.bcm.edu	37	11	60642633	60642633	+	Silent	SNP	C	C	T	rs112864814	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	60	99	0	0.47619	0	C|0.980;T|0.020	0.020	strong	.	ZP1	69	.	NM_207341	exon11	c.C1686T	p.D562D	TAATGACACTGCC	.	PASS	Atlas-SNP
LIPM	340654	hgsc.bcm.edu	37	10	90580012	90580012	+	Silent	SNP	C	C	T	rs12255753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	9	41	0	0.290323	0	C|0.969;T|0.031	0.031	strong	.	LIPM	17	.	NM_001128215	exon9	c.C1026T	p.V342V	CAGAGTCAGAGAT	.	PASS	Atlas-SNP
KCNK2	3776	hgsc.bcm.edu	37	1	215342573	215342573	+	Silent	SNP	C	C	T	rs17024342	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	95	232	0	0.437788	0	C|0.859;T|0.141	0.141	strong	.	KCNK2	135	.	NM_001017425	exon4	c.C507T	p.G169G	AGAAGGCGGCAAA	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89874756	89874756	+	Missense_Mutation	SNP	G	G	A	rs17232246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	87	172	0	0.448454	0	G|0.950;A|0.050	0.050	strong	.	FANCA	99	.	NM_000135	exon6	c.C542T	p.A181V	CACACCGCTTCAA	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905222	1905222	+	Silent	SNP	A	A	G	rs146227529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	38	67	0	0.527778	0	A|0.996;G|0.004	0.004	strong	.	ARHGEF10	255	.	NM_014629	exon29	c.A3828G	p.S1276S	CAGATCAGAGGAC	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47455923	47455923	+	Silent	SNP	C	C	T	rs2298628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	26	43	0	0.590909	0	C|0.563;T|0.437	0.437	strong	.	MYO5B	178	.	NM_001080467	exon17	c.G2049A	p.V683V	CTCCAACACCCCG	.	PASS	Atlas-SNP
CHRNA1	1134	hgsc.bcm.edu	37	2	175613477	175613477	+	Missense_Mutation	SNP	T	T	A	rs6739001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	59	175	0	0.440298	0	T|0.971;A|0.029	0.029	strong	.	CHRNA1	92	.	NM_001039523	exon9	c.A1148T	p.D383V	TTTTTGTCTTGCT	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226032896	226032896	+	Silent	SNP	T	T	C	rs2234700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	78	143	0	0.530612	0	T|0.980;C|0.020	0.020	strong	.	EPHX1	57	.	NM_001136018	exon9	c.T1216C	p.L406L	GAGCTATTGCACA	.	PASS	Atlas-SNP
DCDC1	341019	hgsc.bcm.edu	37	11	31327316	31327316	+	Silent	SNP	C	C	T	rs2616815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	133	111	0	0.985185	0	C|0.298;T|0.702	0.702	strong	.	DCDC1	74	.	NM_181807	exon6	c.G600A	p.E200E	GCACTCCTCCAGC	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744310	31744310	+	Missense_Mutation	SNP	G	G	C	rs3804010	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	96	180	1	0.55814	0.00555556	G|0.841;C|0.159	0.159	strong	KRTAP13-2,NS,carcinoma,-1,1	KRTAP13-2	29	1	NM_181621	exon1	c.C222G	p.S74R	GCAGGGGCTGGAC	.	PASS	Atlas-SNP
SSR1	6745	hgsc.bcm.edu	37	6	7310259	7310259	+	Missense_Mutation	SNP	A	A	G	rs10004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	63	96	0	0.543103	0	T|0.123;G|0.260	0.260	strong	SSR1,NS,carcinoma,0,1	SSR1	21	1	NM_003144	exon2	c.T83C	p.L28S	GCTAACAAGCCTA	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223178226	223178226	+	Missense_Mutation	SNP	A	A	G	rs61743732	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	12	27	0	0.428571	0	A|0.971;G|0.029	0.029	strong	.	DISP1	145	.	NM_032890	exon10	c.A3487G	p.S1163G	AGTCCCAGTGACA	.	PASS	Atlas-SNP
TBC1D9B	23061	hgsc.bcm.edu	37	5	179300131	179300131	+	Silent	SNP	T	T	C	rs269469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	60	144	0	0.431655	0	T|0.899;C|0.101	0.101	strong	.	TBC1D9B	157	.	NM_198868	exon13	c.A2304G	p.K768K	GGACACTTTCAGG	.	PASS	Atlas-SNP
ARHGEF37	389337	hgsc.bcm.edu	37	5	149006640	149006640	+	Missense_Mutation	SNP	C	C	T	rs9324624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	62	127	0	0.469697	0	C|0.590;T|0.410	0.410	strong	.	ARHGEF37	45	.	NM_001001669	exon11	c.C1466T	p.P489L	CCCAGCCGCTCCT	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Silent	SNP	C	C	T	rs10258429	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	79	161	0	0.537415	0	C|0.889;T|0.111	0.111	strong	.	EGFR	20426	.	NM_201284	exon16	c.C1968T	p.H656H	GTCCCACCAGAGC	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558384	140558384	+	Missense_Mutation	SNP	C	C	T	rs116452537	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	140	469	1	0.491228	0.0021322	C|0.994;T|0.006	0.006	strong	.	PCDHB8	199	.	NM_019120	exon1	c.C769T	p.P257S	GACAGTCCAATAA	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149509508	149509508	+	Missense_Mutation	SNP	G	G	A	rs74943037	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	58	100	1	0.43609	0.01	G|0.972;A|0.028	0.028	strong	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	NM_002609	exon10	c.C1391T	p.T464M	AGCAGCGTGGGCG	.	scavenged	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	85	0	1	0	T|0.759;C|0.241	0.241	strong	.	KIAA1984	39	.	NM_001039374	exon2	c.T113C	p.M38T	AGAATATGGACCA	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651412	1651412	+	Silent	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	7	109	1	0.0551181	0.00917431	.	.	none	KRTAP5-5,NS,carcinoma,+1,2	KRTAP5-5	86	2	NM_001001480	exon1	c.G342C	p.G114G	TGGGGGGTCCAAG	.	scavenged	Atlas-SNP
SLC22A7	10864	hgsc.bcm.edu	37	6	43270151	43270151	+	Silent	SNP	C	C	T	rs2270860	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	20	0	1	0	C|0.562;T|0.436	0.436	strong	.	SLC22A7	69	.	NM_153320	exon7	c.C1275T	p.S425S	GTCCTCCGGTGAG	.	PASS	Atlas-SNP
TMEM241	85019	hgsc.bcm.edu	37	18	20953720	20953720	+	Missense_Mutation	SNP	G	G	A	rs8099409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	31	48	0	0.516667	0	G|0.541;A|0.459	0.459	strong	.	.	.	.	NM_032933	exon7	c.C391T	p.L131F	GGAGGAGGAGGGC	.	PASS	Atlas-SNP
UPF3A	65110	hgsc.bcm.edu	37	13	115047305	115047305	+	Missense_Mutation	SNP	G	G	A	rs3752105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	80	0	0.419753	0	G|0.728;A|0.272	0.272	strong	UPF3A,NS,carcinoma,0,1	UPF3A	47	1	NM_080687	exon1	c.G191A	p.R64K	AGAAGAGGACGGC	.	PASS	Atlas-SNP
IFRD2	7866	hgsc.bcm.edu	37	3	50326883	50326883	+	Silent	SNP	A	A	G	rs78165652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	70	117	0	0.440252	0	A|0.992;G|0.008	0.008	strong	.	IFRD2	34	.	NM_006764	exon7	c.T966C	p.L322L	CCTGTCAAGGATG	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25009288	25009288	+	Missense_Mutation	SNP	C	C	T	rs1050114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	81	151	0	0.512658	0	C|0.940;T|0.060	0.060	strong	.	PARP4	142	.	NM_006437	exon31	c.G3991A	p.A1331T	CGCGGGCAGTCGG	.	PASS	Atlas-SNP
RCC2	55920	hgsc.bcm.edu	37	1	17739586	17739586	+	Silent	SNP	G	G	A	rs942457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	110	196	0	0.466102	0	G|0.657;A|0.343	0.343	strong	.	RCC2	46	.	NM_001136204	exon9	c.C1296T	p.I432I	GCTCCGGATTCTC	.	PASS	Atlas-SNP
IGFALS	3483	hgsc.bcm.edu	37	16	1841033	1841033	+	Silent	SNP	G	G	A	rs17559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	6	7	0	0.75	0	G|0.790;A|0.210	0.210	strong	IGFALS,NS,carcinoma,0,1	IGFALS	29	1	NM_001146006	exon2	c.C1500T	p.Y500Y	CAGCAGGTACTCC	.	scavenged	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77690563	77690563	+	Silent	SNP	T	T	C	rs16939357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	59	96	0	0.491667	0	T|0.674;C|0.326	0.326	strong	.	ZFHX4	878	.	NM_024721	exon4	c.T3213C	p.H1071H	GAAGCATCAGCAG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13902220	13902220	+	Missense_Mutation	SNP	T	T	C	rs1530498	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	65	0	1	0	T|0.601;C|0.399	0.399	strong	.	DNAH5	868	.	NM_001369	exon13	c.A1672G	p.T558A	CAAATGTAACATC	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178283474	178283474	+	Missense_Mutation	SNP	A	A	G	rs35418725	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	55	146	0	0.443548	0	A|0.996;G|0.004	0.004	strong	.	NEIL3	89	.	NM_018248	exon10	c.A1667G	p.H556R	GCAACCATGGCAA	.	PASS	Atlas-SNP
GLT1D1	144423	hgsc.bcm.edu	37	12	129360518	129360518	+	Missense_Mutation	SNP	G	G	A	rs73438369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	72	140	0	0.476821	0	G|0.981;A|0.019	0.019	strong	.	GLT1D1	48	.	NM_144669	exon2	c.G128A	p.S43N	TTGAAAGCCGATC	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61511498	61511498	+	Missense_Mutation	SNP	C	C	T	rs3741252	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	12	12	0	0.705882	0	C|0.840;T|0.160	0.160	strong	.	DAGLA	109	.	NM_006133	exon20	c.C2666T	p.P889L	GCGGGCCGGCCTC	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17370190	17370190	+	Silent	SNP	T	T	G	rs11880383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	120	0	0.52	0	T|0.737;G|0.263	0.263	strong	USHBP1,NS,carcinoma,-2,1	USHBP1	85	1	NM_031941	exon7	c.A954C	p.L318L	TCCCTGTAGCACA	.	PASS	Atlas-SNP
PCDHGC4	56098	hgsc.bcm.edu	37	5	140867347	140867347	+	Silent	SNP	C	C	T	rs1423149	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	39	0	0.5	0	C|0.866;T|0.134	0.134	strong	.	PCDHGC4	91	.	NM_032406	exon1	c.C2607T	p.F869F	CTGTTTCGTGAAT	.	PASS	Atlas-SNP
NPNT	255743	hgsc.bcm.edu	37	4	106859549	106859549	+	Missense_Mutation	SNP	G	G	C	rs35132891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	51	43	0	1	0	G|0.658;C|0.342	0.342	strong	.	NPNT	69	.	NM_001184691	exon6	c.G567C	p.Q189H	CCTGCAGCTGGCT	.	PASS	Atlas-SNP
UBE3D	90025	hgsc.bcm.edu	37	6	83667045	83667045	+	Missense_Mutation	SNP	C	C	T	rs7739323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	62	101	0	0.449275	0	C|0.843;T|0.157	0.157	strong	.	.	.	.	NM_198920	exon9	c.G1135A	p.V379M	AATTCACACGGCG	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119445139	119445139	+	Silent	SNP	A	A	G	rs9835381	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	62	153	0	0.473282	0	A|0.983;G|0.017	0.017	strong	.	.	.	.	NM_033364	exon7	c.A804G	p.K268K	GAGGAAAATGATG	.	PASS	Atlas-SNP
FBXL14	144699	hgsc.bcm.edu	37	12	1702561	1702561	+	Silent	SNP	G	G	A	rs35524129	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	74	0	0.486486	0	G|0.964;A|0.036	0.036	strong	.	FBXL14	19	.	NM_152441	exon1	c.C672T	p.S224S	CCCTCGGGAGATG	.	PASS	Atlas-SNP
ACVRL1	94	hgsc.bcm.edu	37	12	52308344	52308344	+	Silent	SNP	G	G	A	rs1058563	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	113	190	0	0.511312	0	G|0.957;A|0.043	0.043	strong	.	ACVRL1	60	.	NM_000020	exon6	c.G747A	p.V249V	CACAGTGTTGCTC	.	PASS	Atlas-SNP
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	58	160	0	0.411348	0	0|0.004;G|0.504	0.504	strong	.	AIFM1	75	.	NM_001130847	exon3	c.T273C	p.D91D	TTTTTCATCCTCT	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10976876	10976876	+	Silent	SNP	A	A	G	rs2245532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	90	147	0	0.48913	0	A|0.595;G|0.405	0.405	strong	.	SLC6A11	87	.	NM_014229	exon13	c.A1737G	p.T579T	GGGGACACTGCCC	.	PASS	Atlas-SNP
DDX49	54555	hgsc.bcm.edu	37	19	19035080	19035080	+	Missense_Mutation	SNP	G	G	C	rs143159618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	99	214	0	0.428571	0	G|1.000;C|0.000	0.000	weak	.	DDX49	37	.	NM_019070	exon7	c.G815C	p.S272T	AATTCAGCTTCCC	.	PASS	Atlas-SNP
OR1E1	8387	hgsc.bcm.edu	37	17	3301246	3301246	+	Silent	SNP	G	G	A	rs11078447	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	121	200	0	0.497942	0	G|0.983;A|0.017	0.017	strong	.	OR1E1	37	.	NM_003553	exon1	c.C459T	p.T153T	ATGGAAGGTGGTC	.	PASS	Atlas-SNP
GADL1	339896	hgsc.bcm.edu	37	3	30842517	30842517	+	Missense_Mutation	SNP	C	C	A	rs61738477	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	46	99	0	0.377049	0	C|0.996;A|0.004	0.004	strong	.	GADL1	91	.	NM_207359	exon12	c.G1114T	p.D372Y	TCACATCATAGAA	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3556398	3556398	+	Missense_Mutation	SNP	G	G	T	rs34115694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	63	98	0	0.623762	0	G|0.974;T|0.026	0.026	strong	.	CLUAP1	32	.	NM_015041	exon3	c.G202T	p.A68S	ATTAAGGCAATTG	.	PASS	Atlas-SNP
RGL4	266747	hgsc.bcm.edu	37	22	24034288	24034288	+	Missense_Mutation	SNP	A	A	G	rs738786	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	118	0	1	0	A|0.483;G|0.517	0.517	strong	.	RGL4	29	.	NM_153615	exon1	c.A71G	p.Q24R	TGCTCCAGGGCCT	.	PASS	Atlas-SNP
GAB2	9846	hgsc.bcm.edu	37	11	77937800	77937800	+	Silent	SNP	G	G	A	rs2248407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	104	159	0	0.571429	0	G|0.738;A|0.262	0.262	strong	.	GAB2	63	.	NM_080491	exon4	c.C918T	p.F306F	GTCCCCGAACTCC	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52351876	52351876	+	Silent	SNP	A	A	G	rs3212523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	55	100	0	0.5	0	A|0.897;G|0.103	0.103	strong	.	ITGA2	211	.	NM_002203	exon9	c.A993G	p.A331A	AAAAGCAATCGCT	.	PASS	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	37	16	20471487	20471487	+	Missense_Mutation	SNP	G	G	C	rs74483128		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	68	124	0	0.566667	0	.	.	weak	.	ACSM2A	120	.	NM_001010845	exon3	c.G51C	p.Q17H	TACTCAGATGTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511788	195511788	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	37	394	0	0.183168	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C6663T	p.H2221H	GATGGCGTGACCT	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	37	19	12805431	12805431	+	Missense_Mutation	SNP	T	T	C	rs10424623	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	81	0	0.444444	0	T|0.921;C|0.079	0.079	strong	.	FBXW9	30	.	NM_032301	exon3	c.A655G	p.T219A	GCTTAGTGCCTAA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158632531	158632531	+	Missense_Mutation	SNP	T	T	C	rs7547313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	104	179	0	0.507317	0	T|0.946;C|0.054	0.054	strong	SPTA1,NS,carcinoma,+2,1	SPTA1	720	1	NM_003126	exon17	c.A2425G	p.I809V	CTTGGATCCAGGC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15791066	15791066	+	Missense_Mutation	SNP	C	C	T	rs61731193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	355	89	254	0	0.250704	0	C|0.988;T|0.012	0.012	strong	.	CYP4F12	89	.	NM_023944	exon4	c.C356T	p.P119L	TTGCACCCAAGGA	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127231763	127231763	+	Missense_Mutation	SNP	G	G	A	rs114565703	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	137	131	1	0.958042	0.00763359	G|0.975;A|0.025	0.025	strong	.	GPR144	33	.	NM_001161808	exon16	c.G2495A	p.R832H	GTGCCCGCCGCCG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	86	172	0	0.508876	0	G|0.721;C|0.279	0.279	strong	OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	NM_001271223	exon38	c.G10200C	p.R3400R	CCTGCGGCTCACC	.	PASS	Atlas-SNP
PLEKHN1	84069	hgsc.bcm.edu	37	1	909238	909238	+	Missense_Mutation	SNP	G	G	C	rs3829740	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	130	146	0	0.992366	0	G|0.322;C|0.678	0.678	strong	.	PLEKHN1	49	.	NM_032129	exon14	c.G1460C	p.R487P	GTGCACGTGGACC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152346979	152346979	+	Missense_Mutation	SNP	T	T	C	rs1061305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	96	0	1	0	T|0.628;C|0.370	0.370	strong	.	NEB	1697	.	NM_001271208	exon181	c.A25309G	p.I8437V	CACTGATGCTTAG	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136574968	136574968	+	Silent	SNP	G	G	C	rs35093754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	44	102	0	0.473118	0	G|0.950;C|0.050	0.050	strong	.	LCT	309	.	NM_002299	exon6	c.C1650G	p.G550G	GCCATAGCCTGCG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8150393	8150393	+	Missense_Mutation	SNP	C	C	T	rs17160151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	34	0	0.530612	0	C|0.903;T|0.097	0.097	strong	.	FBN3	300	.	NM_032447	exon55	c.G6941A	p.S2314N	CTGCTGCTGGACA	.	PASS	Atlas-SNP
NR5A1	2516	hgsc.bcm.edu	37	9	127245070	127245070	+	Silent	SNP	C	C	T	rs79833327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	42	113	0	0.365217	0	C|0.983;T|0.017	0.017	strong	.	NR5A1	32	.	NM_004959	exon7	c.G1353A	p.L451L	GATGAGCAGGTTG	.	PASS	Atlas-SNP
ECH1	1891	hgsc.bcm.edu	37	19	39308190	39308190	+	Silent	SNP	C	C	T	rs15570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	83	0	0.505882	0	C|0.851;T|0.149	0.149	strong	.	ECH1	14	.	NM_001398	exon4	c.G375A	p.S125S	GATGTCCGAAGCC	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	62	97	0	0.574074	0	G|0.879;T|0.121	0.121	strong	.	ZC3H3	75	.	NM_015117	exon11	c.C2639A	p.S880X	GGGGATGAGGAGG	.	PASS	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33648144	33648144	+	Silent	SNP	C	C	T	rs11967839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	30	53	0	0.6	0	C|0.890;T|0.110	0.110	strong	.	ITPR3	409	.	NM_002224	exon32	c.C4263T	p.Y1421Y	CTGCTACGTGGAC	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Silent	SNP	A	A	G	rs56041036	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	76	125	0	0.452381	0	A|0.879;G|0.121	0.121	strong	ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	NM_153813	exon8	c.A948G	p.G316G	TCCAGGAGAGCGG	.	PASS	Atlas-SNP
DENND5A	23258	hgsc.bcm.edu	37	11	9286515	9286515	+	Silent	SNP	C	C	T	rs75717840	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	25	15	0	0.595238	0	C|0.980;T|0.020	0.020	strong	.	DENND5A	84	.	NM_015213	exon1	c.G102A	p.E34E	CGACAGCTCGTCC	.	PASS	Atlas-SNP
AMOTL1	154810	hgsc.bcm.edu	37	11	94602457	94602457	+	Silent	SNP	G	G	A	rs181764487	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	69	120	0	0.496403	0	G|0.995;A|0.005	0.005	strong	AMOTL1,NS,carcinoma,+1,2	AMOTL1	95	2	NM_130847	exon12	c.G2583A	p.T861T	CACTACGGCAGCC	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28378450	28378450	+	Missense_Mutation	SNP	T	T	C	rs61744744	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	44	97	0	0.419048	0	T|0.988;C|0.012	0.012	strong	.	TTC28	84	.	NM_001145418	exon23	c.A7205G	p.N2402S	TTCTTATTGTGCC	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107354	55107354	+	Silent	SNP	C	C	G	rs61739190	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	70	265	0	0.44586	0	C|0.920;G|0.080	0.080	strong	.	LILRA1	105	.	NM_006863	exon6	c.C912G	p.S304S	CCTCTCCTCCGAG	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201286771	201286771	+	Silent	SNP	C	C	T	rs1722779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	104	224	0	0.509804	0	T|0.178;C|0.822;A|0.000	0.178	strong	.	PKP1	127	.	NM_001005337	exon5	c.C918T	p.A306A	GCAGGCCGCGGCA	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88965992	88965992	+	Missense_Mutation	SNP	T	T	G	rs115968745	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	93	169	0	0.481865	0	T|0.996;G|0.004	0.004	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T3696G	p.I1232M	CCCTATTGCTCAT	.	PASS	Atlas-SNP
C3orf70	285382	hgsc.bcm.edu	37	3	184801099	184801099	+	Missense_Mutation	SNP	G	G	A	rs61747892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	92	193	1	0.476684	0.00518135	G|0.972;A|0.028	0.028	strong	C3orf70,colon,carcinoma,+1,1	C3orf70	29	1	NM_001025266	exon2	c.C449T	p.P150L	GGTGCCGGCTGCT	.	scavenged	Atlas-SNP
TTBK1	84630	hgsc.bcm.edu	37	6	43251608	43251608	+	Missense_Mutation	SNP	C	C	T	rs146633224	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	44	99	0	0.444444	0	C|0.997;T|0.003	0.003	strong	.	TTBK1	124	.	NM_032538	exon14	c.C3130T	p.R1044C	CCCAGACGCCATG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678483	100678483	+	Silent	SNP	C	C	T	rs73168390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	26	125	0	0.18705	0	C|0.975;T|0.025	0.025	strong	.	MUC17	804	.	NM_001040105	exon3	c.C3786T	p.T1262T	TACAACCGCTGAA	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49310831	49310831	+	Missense_Mutation	SNP	A	A	G	rs140228766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	68	143	0	0.388571	0	A|0.999;G|0.001	0.001	strong	.	CCDC65	41	.	NM_033124	exon4	c.A549G	p.I183M	CTATATAGATTCT	.	PASS	Atlas-SNP
RECQL	5965	hgsc.bcm.edu	37	12	21643223	21643223	+	Missense_Mutation	SNP	C	C	T	rs1065751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	60	128	0	0.521739	0	T|0.045;G|0.039	0.045	strong	.	RECQL	45	.	NM_032941	exon5	c.G304A	p.V102I	TTGTTACGTTAAT	.	PASS	Atlas-SNP
ESRRG	2104	hgsc.bcm.edu	37	1	216692741	216692741	+	Silent	SNP	C	C	T	rs10863247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	10	37	0	0.294118	0	C|0.910;T|0.090	0.090	strong	.	ESRRG	111	.	NM_001243518	exon7	c.G921A	p.A307A	CTGGTCCGCCAGG	.	PASS	Atlas-SNP
POMT1	10585	hgsc.bcm.edu	37	9	134393834	134393834	+	Silent	SNP	A	A	G	rs62620174	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	68	110	0	0.591304	0	A|0.976;G|0.024	0.024	strong	.	POMT1	59	.	NM_007171	exon14	c.A1341G	p.E447E	GCAGGAAATTGTG	.	PASS	Atlas-SNP
OR5R1	219479	hgsc.bcm.edu	37	11	56185689	56185689	+	Missense_Mutation	SNP	A	A	G	rs7931261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	21	23	0	0.567568	0	A|0.675;G|0.325	0.325	strong	OR5R1,NS,carcinoma,0,1	OR5R1	83	1	NM_001004744	exon1	c.T20C	p.I7T	ACATAAATGATAT	.	PASS	Atlas-SNP
RAPGEF5	9771	hgsc.bcm.edu	37	7	22202117	22202117	+	Silent	SNP	G	G	A	rs12592	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	54	68	0	0.5	0	G|0.404;A|0.596	0.596	strong	.	RAPGEF5	96	.	NM_012294	exon13	c.C867T	p.D289D	CGGAACGTCTGAG	.	PASS	Atlas-SNP
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566903	45566903	+	Silent	SNP	T	T	C	rs114461217	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	376	168	365	1	0.446809	0.00273973	T|0.990;C|0.010	0.010	strong	.	ZBTB7C	73	.	NM_001039360	exon2	c.A576G	p.T192T	ATGGTCTGTCTTG	.	PASS	Atlas-SNP
TFCP2L1	29842	hgsc.bcm.edu	37	2	121981950	121981950	+	Silent	SNP	A	A	G	rs11890430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	88	0	0.517241	0	A|0.666;G|0.334	0.334	strong	TFCP2L1,NS,carcinoma,0,1	TFCP2L1	54	1	NM_014553	exon15	c.T1407C	p.D469D	GTAGCCATCATTG	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276657	71276657	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	39	358	58	0.127036	0.162011	.	.	none	KRTAP5-10,NS,carcinoma,0,2	KRTAP5-10	37	2	NM_001012710	exon1	c.A24G	p.G8G	CTCCGGAGGCTGT	.	scavenged	Atlas-SNP
KRT31	3881	hgsc.bcm.edu	37	17	39553676	39553676	+	Missense_Mutation	SNP	G	G	C	rs6503628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	90	215	0	0.439024	0	G|0.997;C|0.003	0.003	strong	.	KRT31	158	.	NM_002277	exon1	c.C116G	p.A39G	ACATTGGCGGGGA	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114454735	114454735	+	Silent	SNP	T	T	C	rs73656294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	9	57	0	0.225	0	T|0.988;C|0.012	0.012	strong	.	C9orf84	207	.	NM_173521	exon25	c.A3330G	p.S1110S	TTGCGGTGATTTT	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235971802	235971802	+	Silent	SNP	G	G	A	rs16832868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	90	189	0	0.520231	0	G|0.934;A|0.066	0.066	strong	.	LYST	370	.	NM_000081	exon5	c.C2316T	p.D772D	AAGCACGTCCTGA	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16492163	16492163	+	Silent	SNP	T	T	C	rs16997775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	40	0	0.42	0	T|0.978;C|0.022	0.022	strong	.	KIF16B	305	.	NM_001199865	exon6	c.A456G	p.E152E	ATAAATTTCTAAG	.	PASS	Atlas-SNP
GNB2L1	10399	hgsc.bcm.edu	37	5	180665123	180665123	+	Silent	SNP	G	G	A	rs11540200	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	75	158	0	0.446429	0	G|0.977;A|0.023	0.023	strong	.	GNB2L1	22	.	NM_006098	exon6	c.C753T	p.A251A	GCCTGTGGCAGCA	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942961	12942961	+	Missense_Mutation	SNP	A	A	C	rs4625290	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	512	239	434	0	0.466797	0	A|0.894;C|0.106	0.106	strong	.	PRAMEF4	62	.	NM_001009611	exon2	c.T255G	p.D85E	CAGCCCATCGAGC	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125476252	125476252	+	Silent	SNP	C	C	G	rs34964592	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	80	178	0	0.40201	0	C|0.891;G|0.109	0.109	strong	.	STT3A	52	.	NM_152713	exon8	c.C672G	p.L224L	CGTCCTCGTGCTG	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39091546	39091546	+	Missense_Mutation	SNP	G	G	A	rs114068623	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	46	90	0	0.560976	0	G|0.990;A|0.010	0.010	strong	.	ADAM32	70	.	NM_145004	exon16	c.G1763A	p.R588Q	TGCCTCGAACAGT	.	PASS	Atlas-SNP
ATP1A1	476	hgsc.bcm.edu	37	1	116932921	116932921	+	Silent	SNP	G	G	A	rs11540956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	67	107	0	0.452703	0	G|0.903;A|0.097	0.097	strong	.	ATP1A1	87	.	NM_001160233	exon9	c.G1110A	p.T370T	GTCCACGTCCACC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062132	64062132	+	Silent	SNP	G	G	A	rs11175111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	32	78	0	0.426667	0	G|0.957;A|0.043	0.043	strong	.	DPY19L2	97	.	NM_173812	exon1	c.C42T	p.S14S	GCGGCCGGAAGAT	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214814571	214814571	+	Silent	SNP	C	C	T	rs3795521	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	30	96	0	0.37037	0	C|0.681;T|0.319	0.319	strong	CENPF,NS,carcinoma,0,2	CENPF	321	2	NM_016343	exon12	c.C2890T	p.L964L	ATTTCTCTAAATA	.	PASS	Atlas-SNP
IPO7	10527	hgsc.bcm.edu	37	11	9456506	9456506	+	Silent	SNP	T	T	C	rs148344816	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	55	102	0	0.617977	0	T|0.998;C|0.002	0.002	strong	.	IPO7	72	.	NM_006391	exon19	c.T2100C	p.Y700Y	TAATTATGTAACA	.	PASS	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	37	1	79392756	79392756	+	Missense_Mutation	SNP	C	C	A	rs12754818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	75	0	1	0	C|0.374;A|0.625	0.625	strong	.	ELTD1	143	.	NM_022159	exon8	c.G898T	p.V300L	AATATACAAATGC	.	PASS	Atlas-SNP
TREX2	11219	hgsc.bcm.edu	37	X	152710238	152710238	+	Silent	SNP	A	A	G	rs916046	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	35	121	0	0.248227	0	A|0.851;0|0.006	.	strong	.	TREX2	36	.	NM_080701	exon2	c.T651C	p.R217R	CCACCCACGGGCC	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299467	125299467	+	Missense_Mutation	SNP	G	G	T	rs10126452	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	271	251	1	0.996324	0.00398406	G|0.479;T|0.521	0.521	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.C441A	p.H147Q	GCCCTGGTGGGCC	.	PASS	Atlas-SNP
DDX31	64794	hgsc.bcm.edu	37	9	135493792	135493792	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	48	129	0	0.4	0	.	.	none	.	DDX31	76	.	NM_022779	exon18	c.C2065T	p.R689X	TGGCTCGCTCTCG	.	PASS	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219561778	219561778	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	2	96	0	0.0188679	0	.	.	none	STK36,right_upper_lobe,carcinoma,-1,1	STK36	111	1	NM_015690	exon23	c.T2603C	p.L868P	CTAGCCTAATCAG	.	scavenged	Atlas-SNP
SERPINB4	6318	hgsc.bcm.edu	37	18	61310738	61310738	+	Missense_Mutation	SNP	T	T	C	rs79086230	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	547	254	550	0	0.464351	0	.	.	weak	.	SERPINB4	89	.	NM_002974	exon2	c.A74G	p.N25S	ATGTTGTTCTCTT	.	PASS	Atlas-SNP
C17orf74	201243	hgsc.bcm.edu	37	17	7330437	7330437	+	Missense_Mutation	SNP	A	A	G	rs3892554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	30	68	0	0.447761	0	A|0.955;G|0.045	0.045	strong	.	C17orf74	56	.	NM_175734	exon3	c.A1127G	p.Q376R	GCTCCCAGGACCC	.	PASS	Atlas-SNP
RCBTB1	55213	hgsc.bcm.edu	37	13	50141345	50141345	+	Missense_Mutation	SNP	G	G	A	rs4942848	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	113	125	0	1	0	G|0.431;A|0.568	0.568	strong	.	RCBTB1	34	.	NM_018191	exon3	c.C71T	p.A24V	ACACACGCCTTCC	.	PASS	Atlas-SNP
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	97	0	0.46988	0	C|0.795;A|0.205	0.205	strong	.	AGXT2	89	.	NM_031900	exon14	c.G1492T	p.V498L	CTTCTACTGCAAA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100695138	100695138	+	Missense_Mutation	SNP	G	G	A	rs73168398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	56	107	0	0.523364	0	G|0.898;A|0.102	0.102	strong	.	MUC17	804	.	NM_001040105	exon9	c.G12998A	p.R4333Q	AGTACCGGGACCA	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13563767	13563767	+	Silent	SNP	G	G	A	rs1800039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	98	198	0	0.453704	0	G|0.992;A|0.008	0.008	strong	.	CACNA1A	715	.	NM_001127221	exon3	c.C462T	p.A154A	CCCAAGGGCAATG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134626383	134626383	+	Silent	SNP	C	C	T	rs7090011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	8	17	0	0.380952	0	C|0.966;T|0.034	0.034	strong	.	TTC40	100	.	NM_001200049	exon55	c.G7407A	p.Q2469Q	CAGGGCCTGCTCC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1236	124	957	0	0.100324	0	.	.	weak	.	MUC6	408	.	NM_005961	exon31	c.A5279C	p.E1760A	GTGACTTCAGGAT	.	PASS	Atlas-SNP
IL1RAPL2	26280	hgsc.bcm.edu	37	X	104992963	104992963	+	Silent	SNP	T	T	C	rs3764765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	100	281	0	0.334448	0	T|0.833;C|0.167	0.167	strong	.	IL1RAPL2	105	.	NM_017416	exon9	c.T1059C	p.Y353Y	AATCTATAAAATT	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123886466	123886466	+	Missense_Mutation	SNP	C	C	T	rs75423810		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	696	318	658	0	0.456897	0	T|1.000;|0.000	1.000	weak	OR10G4,NS,carcinoma,0,1	OR10G4	77	1	NM_001004462	exon1	c.C185T	p.T62I	TCCTCACCAACCT	.	scavenged	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7385774	7385774	+	Silent	SNP	C	C	T	rs201649944	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	120	235	1	0.510638	0.00425532	C|0.999;T|0.001	0.001	weak	.	.	.	.	NM_001102614	exon2	c.C471T	p.Y157Y	TGGCTACGACTGG	.	PASS	Atlas-SNP
LIFR	3977	hgsc.bcm.edu	37	5	38523529	38523529	+	Missense_Mutation	SNP	C	C	T	rs140538535	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	115	280	0	0.430712	0	C|0.999;T|0.001	0.001	strong	LIFR_ENST00000263409,NS,carcinoma,0,2	LIFR	348	2	NM_002310	exon5	c.G553A	p.V185I	ATTTTACGAGCTC	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123419733	123419733	+	Missense_Mutation	SNP	A	A	G	rs3732486	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	24	52	0	0.489796	0	A|0.858;G|0.142	0.142	strong	.	MYLK	224	.	NM_053025	exon18	c.T2582C	p.L861P	TCCTCTAGCCAAC	.	PASS	Atlas-SNP
MORN2	729967	hgsc.bcm.edu	37	2	39108693	39108693	+	Silent	SNP	G	G	A	rs6756998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	60	100	0	0.521739	0	G|0.983;A|0.017	0.017	strong	.	MORN2	3	.	NM_001145450	exon4	c.G111A	p.K37K	GGCAAAGTATACT	.	PASS	Atlas-SNP
ASXL1	171023	hgsc.bcm.edu	37	20	31024488	31024488	+	Missense_Mutation	SNP	C	C	T	rs6057581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	31	79	0	0.449275	0	C|0.971;T|0.029	0.029	strong	.	ASXL1	1114	.	NM_015338	exon12	c.C3973T	p.L1325F	ATGCCTCTTCCTG	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	25	46	0	0.5	0	A|0.892;T|0.108	0.108	strong	.	FAM71F2	19	.	NM_001012454	exon2	c.A341T	p.D114V	CTGGTGACGCCCC	.	PASS	Atlas-SNP
KCNJ6	3763	hgsc.bcm.edu	37	21	39087236	39087236	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	3	254	0	0.0106383	0	.	.	none	KCNJ6,NS,carcinoma,-1,1	KCNJ6	58	1	NM_002240	exon3	c.G224A	p.R75H	AGGTAGCGATAGG	.	scavenged	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100856380	100856380	+	Silent	SNP	A	A	C	rs28361212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	32	59	0	0.470588	0	A|0.885;C|0.115	0.115	strong	.	CDC14A	65	.	NM_033313	exon4	c.A309C	p.A103A	CTATGCAGTAAGT	.	PASS	Atlas-SNP
PRKG1	5592	hgsc.bcm.edu	37	10	53921655	53921655	+	Silent	SNP	T	T	C	rs56047641	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	37	104	0	0.445783	0	T|0.947;C|0.053	0.053	strong	.	PRKG1	167	.	NM_006258	exon9	c.T1008C	p.F336F	CTCTTTTAAACAT	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179621253	179621253	+	Missense_Mutation	SNP	G	G	T	rs147309264	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	107	164	0	0.497674	0	G|0.997;T|0.003	0.003	strong	.	TDRD5	149	.	NM_173533	exon13	c.G2081T	p.G694V	AACTGGGTTATCC	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95604664	95604664	+	Silent	SNP	A	A	G	rs4762289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	78	178	0	0.484472	0	A|0.949;G|0.051	0.051	strong	.	FGD6	127	.	NM_018351	exon2	c.T396C	p.V132V	CTCTAAAACAAGC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	Silent	SNP	G	G	A	rs28575980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	48	91	0	0.516129	0	G|0.777;A|0.223	0.223	strong	KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	NM_001080484	exon18	c.C2061T	p.A687A	GGTGGCGGCTTTG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	347	59	332	0	0.170029	0	.	.	weak	DSPP,NS,carcinoma,-1,2	DSPP	174	2	NM_014208	exon5	c.A2054G	p.N685S	GCAGCAACAGCAG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129903592	129903592	+	Missense_Mutation	SNP	G	G	A	rs45549235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	466	227	507	2	0.487124	0.00394477	G|0.973;A|0.027	0.027	strong	.	MKI67	363	.	NM_002417	exon13	c.C6512T	p.A2171V	CTTGCTGCTGGGT	.	PASS	Atlas-SNP
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876181	74876181	+	Silent	SNP	T	T	G	rs12590672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	34	78	0	0.485714	0	T|0.508;G|0.492	0.492	strong	.	SYNDIG1L	24	.	NM_001105579	exon2	c.A267C	p.T89T	GAAGCTTGTCTCA	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1637998	1637998	+	Missense_Mutation	SNP	G	G	A	rs8058674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	50	103	0	0.531915	0	G|0.978;A|0.022	0.022	strong	.	IFT140	128	.	NM_014714	exon8	c.C838T	p.R280W	CTGCCCGGCGGCC	.	PASS	Atlas-SNP
KLK14	43847	hgsc.bcm.edu	37	19	51582090	51582090	+	Silent	SNP	G	G	A	rs79507858	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	61	0	1	0	G|0.981;A|0.019	0.019	strong	.	KLK14	49	.	NM_022046	exon6	c.C633T	p.G211G	CTTCCCGCCCTGG	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1522325	1522325	+	Missense_Mutation	SNP	C	C	T	rs11553055	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	100	151	0	0.520833	0	C|0.977;T|0.023	0.023	strong	.	ASMTL	56	.	NM_004192	exon13	c.G1703A	p.R568H	AGGGCGCGCTGCG	.	PASS	Atlas-SNP
NDFIP2	54602	hgsc.bcm.edu	37	13	80094993	80094993	+	Missense_Mutation	SNP	C	C	T	rs55887763	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	57	110	0	0.487179	0	C|0.952;T|0.048	0.048	strong	.	NDFIP2	23	.	NM_019080	exon2	c.C370T	p.P124S	CAGCCACCTACTT	.	PASS	Atlas-SNP
ZNF189	7743	hgsc.bcm.edu	37	9	104170580	104170580	+	Missense_Mutation	SNP	A	A	G	rs148414030	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	102	157	0	0.64557	0	A|0.998;G|0.002	0.002	strong	.	ZNF189	79	.	NM_003452	exon3	c.A530G	p.Q177R	CTTTTCAGTGCAA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152286002	152286002	+	Missense_Mutation	SNP	T	T	C	rs2011331	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	457	457	434	0	1	0	T|0.667;C|0.333	0.333	strong	.	FLG	900	.	NM_002016	exon3	c.A1360G	p.T454A	CACGTGTGGACTC	.	PASS	Atlas-SNP
CCNH	902	hgsc.bcm.edu	37	5	86695228	86695228	+	Silent	SNP	A	A	T	rs150856919	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	33	86	0	0.44	0	A|1.000;T|0.000	0.000	strong	.	CCNH	40	.	NM_001239	exon7	c.T855A	p.L285L	AAGTGCAAGCTCA	.	PASS	Atlas-SNP
SLC8A3	6547	hgsc.bcm.edu	37	14	70634546	70634546	+	Silent	SNP	C	C	T	rs7161524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	65	123	0	0.460993	0	C|0.830;T|0.170	0.170	strong	.	SLC8A3	234	.	NM_183002	exon2	c.G594A	p.K198K	TAGATGCTTGATC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2147500	2147500	+	Missense_Mutation	SNP	C	C	G	rs61747420	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	14	31	0	0.5	0	C|0.948;G|0.052	0.052	strong	.	PKD1	184	.	NM_001009944	exon33	c.G10225C	p.V3409L	AGCACACCAGACT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195481111	195481111	+	Missense_Mutation	SNP	G	G	T	rs73079395	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	155	232	0	0.504886	0	G|0.924;T|0.076	0.076	strong	.	MUC4	1505	.	NM_018406	exon19	c.C15301A	p.L5101M	CAGTCAGGTTTGG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47925485	47925485	+	Missense_Mutation	SNP	T	T	G	rs113527998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	81	185	0	0.409091	0	T|0.950;G|0.050	0.050	strong	.	PKD1L1	328	.	NM_138295	exon18	c.A3004C	p.T1002P	CTGAAGTGGCAGG	.	PASS	Atlas-SNP
DDX25	29118	hgsc.bcm.edu	37	11	125778305	125778305	+	Silent	SNP	C	C	T	rs34007659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	83	153	0	0.568493	0	C|0.985;T|0.015	0.015	strong	.	DDX25	65	.	NM_013264	exon6	c.C414T	p.N138N	CCAGAACCTCATA	.	PASS	Atlas-SNP
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940066	70940066	+	Silent	SNP	C	C	T	rs12251842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	27	59	0	0.435484	0	C|0.962;T|0.038	0.038	strong	.	SUPV3L1	61	.	NM_003171	exon1	c.C19T	p.L7L	CGTGCCCTATTGT	.	PASS	Atlas-SNP
HIPK4	147746	hgsc.bcm.edu	37	19	40895493	40895493	+	Missense_Mutation	SNP	G	G	A	rs79236726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	53	96	1	0.509615	0.0104167	G|0.992;A|0.008	0.008	strong	HIPK4_ENST00000291823,colon,carcinoma,+1,2	HIPK4	100	2	NM_144685	exon1	c.C317T	p.A106V	AGGGGCGCGAAGT	.	scavenged	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	37	19	50412516	50412516	+	Silent	SNP	C	C	T	rs1984656	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	120	190	0	0.533333	0	C|0.978;T|0.022	0.022	strong	.	NUP62	50	.	NM_153719	exon3	c.G549A	p.T183T	AGGTGCCGTGGGC	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	48	76	0	0.510638	0	A|0.630;G|0.370	0.370	strong	.	PHC1	67	.	NM_004426	exon10	c.A2077G	p.T693A	GCTAATACTCCAA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149498903	149498903	+	Missense_Mutation	SNP	T	T	C	rs2074689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	116	0	1	0	T|0.858;C|0.142	0.142	strong	.	.	.	.	NM_198455	exon50	c.T7355C	p.M2452T	CTACCATGGCCCT	.	PASS	Atlas-SNP
LRFN3	79414	hgsc.bcm.edu	37	19	36430465	36430465	+	Silent	SNP	A	A	C	rs2242590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	26	40	0	1	0	A|0.876;C|0.124	0.124	strong	.	LRFN3	43	.	NM_024509	exon2	c.A138C	p.P46P	GTGCCCAGGGGCA	.	PASS	Atlas-SNP
GJB5	2709	hgsc.bcm.edu	37	1	35223345	35223345	+	Silent	SNP	G	G	A	rs3738345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	40	103	0	0.430108	0	G|0.718;A|0.282	0.282	strong	GJB5,NS,carcinoma,0,1	GJB5	35	1	NM_005268	exon2	c.G414A	p.K138K	GTTCAAGGCGAGC	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17305781	17305781	+	Missense_Mutation	SNP	T	T	G	rs45541337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	32	81	0	0.385542	0	T|0.934;G|0.066	0.066	strong	.	MYO9B	264	.	NM_001130065	exon22	c.T3545G	p.V1182G	GAAGGGTCACCCA	.	PASS	Atlas-SNP
GIMAP1-GIMAP5	0	hgsc.bcm.edu	37	7	150439554	150439554	+	Silent	SNP	G	G	A	rs61751040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	52	95	1	0.477064	0.0105263	G|0.953;A|0.047	0.047	strong	GIMAP5,NS,carcinoma,+1,1	.	.	1	NM_001199577	exon6	c.G939A	p.P313P	TGCCCCGGGGCCC	.	scavenged	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42772717	42772717	+	Silent	SNP	G	G	T	rs9533031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	99	0	0.567568	0	G|0.519;T|0.481	0.481	strong	.	DGKH	106	.	NM_001204504	exon19	c.G2271T	p.P757P	TGACCCGGATCTA	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909524	123909524	+	Missense_Mutation	SNP	G	G	A	rs75423810		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	468	56	624	0	0.119658	0	A|1.000;|0.000	1.000	weak	OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	NM_001004463	exon1	c.C185T	p.T62I	AGGTTGGTGAGGA	.	scavenged	Atlas-SNP
TRPC6	7225	hgsc.bcm.edu	37	11	101347093	101347093	+	Silent	SNP	A	A	G	rs12366144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	118	0	0.443182	0	A|0.699;G|0.301	0.301	strong	.	TRPC6	132	.	NM_004621	exon6	c.T1683C	p.N561N	AGTATCATTTGCG	.	PASS	Atlas-SNP
ARL5C	390790	hgsc.bcm.edu	37	17	37317566	37317566	+	Silent	SNP	C	C	A	rs11653423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	35	63	0	0.583333	0	C|0.933;A|0.067	0.067	strong	.	ARL5C	3	.	NM_001143968	exon4	c.G294T	p.R98R	CAGCAGCCGATCC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8196645	8196645	+	Missense_Mutation	SNP	G	G	A	rs61729592	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	96	156	0	0.530387	0	G|0.996;A|0.004	0.004	strong	.	FBN3	300	.	NM_032447	exon14	c.C1783T	p.R595C	GGCAGCGGAAGGA	.	PASS	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	719592	719592	+	Missense_Mutation	SNP	G	G	A	rs11557858	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	27	47	0	0.5	0	G|0.760;A|0.240	0.240	strong	.	RHOT2	35	.	NM_138769	exon5	c.G262A	p.A88T	GAGGAGGCCACCA	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	37	6	42932080	42932080	+	Missense_Mutation	SNP	G	G	A	rs115180949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	45	107	0	0.459184	0	G|0.993;A|0.007	0.007	strong	.	PEX6	44	.	NM_000287	exon17	c.C2936T	p.A979V	TAGCAGGCAGCAA	.	PASS	Atlas-SNP
GLDC	2731	hgsc.bcm.edu	37	9	6587176	6587176	+	Silent	SNP	G	G	A	rs74461075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	64	125	0	0.474074	0	G|0.987;A|0.013	0.013	strong	.	GLDC	118	.	NM_000170	exon15	c.C1815T	p.L605L	ACCTGTGAGTTCA	.	PASS	Atlas-SNP
FAM187B	148109	hgsc.bcm.edu	37	19	35719577	35719577	+	Missense_Mutation	SNP	G	G	A	rs34873156	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	15	30	0	0.348837	0	G|0.721;A|0.279	0.279	strong	.	FAM187B	28	.	NM_152481	exon1	c.C7T	p.P3S	GCATGGGTGGCAT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74300497	74300497	+	Missense_Mutation	SNP	G	G	A	rs73996306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	27	62	0	0.54	0	G|0.919;A|0.081	0.081	strong	.	QRICH2	143	.	NM_032134	exon3	c.C206T	p.A69V	TTCACCGCTTGTG	.	PASS	Atlas-SNP
LCE1C	353133	hgsc.bcm.edu	37	1	152777874	152777874	+	Silent	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	403	21	282	0	0.0521092	0	.	.	none	.	LCE1C	40	.	NM_178351	exon2	c.A81T	p.P27P	ACACTTTGGGGTG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721337	54721337	+	Missense_Mutation	SNP	G	G	A	rs75437884	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	384	90	534	0	0.234375	0	G|0.996;A|0.004	0.004	strong	LILRB3,NS,lymphoid_neoplasm,+2,1	LILRB3	67	1	NM_001081450	exon12	c.C1603T	p.H535Y	CATCGTGTGGGCT	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20435262	20435262	+	Silent	SNP	T	T	G	rs12103211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	176	166	0	1	0	T|0.853;G|0.147	0.147	strong	.	ACSM5	101	.	NM_017888	exon6	c.T792G	p.S264S	CGAATCTGACATC	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52282873	52282873	+	Missense_Mutation	SNP	A	A	T	rs697636	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	45	138	0	0.436893	0	A|0.714;N|0.001	.	strong	.	ANKRD33	33	.	NM_182608	exon3	c.A419T	p.Y140F	CATGCTACCACGG	.	PASS	Atlas-SNP
OR10A2	341276	hgsc.bcm.edu	37	11	6891704	6891704	+	Missense_Mutation	SNP	T	T	C	rs10839632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	96	164	0	0.545455	0	T|0.723;C|0.277	0.277	strong	.	OR10A2	55	.	NM_001004460	exon1	c.T719C	p.I240T	TCTATATATCATT	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	358	148	305	0	0.413408	0	G|0.873;C|0.127	0.127	strong	PLEKHM1,caecum,carcinoma,-1,1	PLEKHM1	69	1	NM_014798	exon4	c.C672G	p.S224S	AGAATGGGAAATG	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180219842	180219842	+	Missense_Mutation	SNP	C	C	T	rs34344788	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	36	76	0	0.413793	0	C|0.993;T|0.007	0.007	strong	.	MGAT1	48	.	NM_001114617	exon3	c.G130A	p.D44N	CGCCATCGAGAGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228437772	228437772	+	Silent	SNP	G	G	A	rs12080655	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	376	182	354	1	0.484043	0.00282486	G|0.955;A|0.045	0.045	strong	.	OBSCN	2142	.	NM_001271223	exon15	c.G4416A	p.E1472E	GACAGAGGTGACG	.	PASS	Atlas-SNP
JPH2	57158	hgsc.bcm.edu	37	20	42743454	42743454	+	Silent	SNP	A	A	G	rs6093935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	125	1	1	0.008	A|0.685;G|0.315	0.315	strong	.	JPH2	86	.	NM_020433	exon5	c.T2073C	p.F691F	GTGAACAAAGAGG	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89474818	89474818	+	Missense_Mutation	SNP	A	A	G	rs17433780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	207	212	0	0.990431	0	A|0.714;G|0.286	0.286	strong	.	GBP3	53	.	NM_018284	exon10	c.T1471C	p.C491R	TTACACATTCCAC	.	PASS	Atlas-SNP
ARL5C	390790	hgsc.bcm.edu	37	17	37319029	37319029	+	Missense_Mutation	SNP	T	T	G	rs544198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	131	0	0.508065	0	T|0.752;G|0.248	0.248	strong	.	ARL5C	3	.	NM_001143968	exon3	c.A190C	p.M64L	CCCACATGAAGAA	.	PASS	Atlas-SNP
MIA	8190	hgsc.bcm.edu	37	19	41281700	41281700	+	Silent	SNP	C	C	T	rs2233156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	64	128	0	0.463768	0	C|0.913;A|0.000	.	strong	.	MIA	16	.	NM_001202553	exon3	c.C171T	p.P57P	GGCCCCCGACTGC	.	PASS	Atlas-SNP
ZNF326	284695	hgsc.bcm.edu	37	1	90493026	90493026	+	Silent	SNP	G	G	A	rs10922744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	101	206	0	0.528796	0	A|0.588;G|0.412	0.588	strong	.	ZNF326	60	.	NM_182976	exon12	c.G1515A	p.E505E	AGATGAGGAAGAA	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	10	14	0	0.47619	0	C|0.883;T|0.117	0.117	strong	.	USP6	213	.	NM_004505	exon9	c.C579T	p.T193T	CATCACCGCCTTG	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782401	54782401	+	Missense_Mutation	SNP	G	G	C	rs7247055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	67	194	0	0.387283	0	G|0.964;C|0.036	0.036	strong	.	LILRB2	94	.	NM_005874	exon7	c.C971G	p.T324R	AAGGGTGTGCCAC	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	37	9	138662273	138662273	+	Silent	SNP	G	G	A	rs17038714	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	51	81	0	0.566667	0	G|0.695;A|0.305	0.305	strong	.	KCNT1	139	.	NM_020822	exon17	c.G1749A	p.A583A	CTACGCGGCCTTC	.	PASS	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31963860	31963860	+	Missense_Mutation	SNP	C	C	G	rs2734319	bycluster;by2hit2allele;byhapmap;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	527	256	750	0	0.485768	0	.	.	alt	.	C4A	15	.	NM_007293	exon26	c.T3359G	p.L1120R	AGGACCCCTGTCC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66042231	66042231	+	Missense_Mutation	SNP	T	T	G	rs12207746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	31	48	0	0.430556	0	T|0.889;G|0.111	0.111	strong	.	EYS	527	.	NM_001142801	exon12	c.A1846C	p.I616L	TTACGATAAATCC	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120608031	120608031	+	Silent	SNP	A	A	G	rs2286050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	69	133	0	0.475862	0	A|0.709;G|0.291	0.291	strong	.	GCN1L1	207	.	NM_006836	exon15	c.T1461C	p.T487T	CCCTTCAGTGATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512219	195512219	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	75	439	1	0.340909	0.0022779	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.G6232A	p.A2078T	GGGTGGCGTGACC	.	PASS	Atlas-SNP
OR2A25	392138	hgsc.bcm.edu	37	7	143771408	143771408	+	Silent	SNP	G	G	C	rs59319753	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	148	261	0	0.472843	0	G|0.684;C|0.316	0.316	strong	.	OR2A25	66	.	NM_001004488	exon1	c.G96C	p.L32L	CTCCCTGTTCTAC	.	PASS	Atlas-SNP
BIRC8	112401	hgsc.bcm.edu	37	19	53793162	53793162	+	Missense_Mutation	SNP	C	C	T	rs35880972	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	101	199	0	0.457014	0	C|0.937;T|0.063	0.063	strong	.	BIRC8	54	.	NM_033341	exon1	c.G466A	p.A156T	TCTGAGCGCTCAC	.	PASS	Atlas-SNP
UBA7	7318	hgsc.bcm.edu	37	3	49845526	49845526	+	Missense_Mutation	SNP	T	T	C	rs2230149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	90	0	0.452381	0	T|0.973;C|0.027	0.027	strong	.	UBA7	64	.	NM_003335	exon20	c.A2450G	p.H817R	TCCACATGGAAGT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23905481	23905481	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	59	103	0	0.561905	0	.	.	none	.	SACS	871	.	NM_014363	exon10	c.G12534A	p.P4178P	TTCTCCCGGGTAA	.	PASS	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	37	6	111695304	111695304	+	Silent	SNP	A	A	G	rs3218589	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	76	122	0	0.517007	0	A|0.999;G|0.001	0.001	strong	.	REV3L	386	.	NM_002912	exon13	c.T4254C	p.N1418N	CAAAAAATTAGGG	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52368472	52368472	+	Silent	SNP	C	C	T	rs3212583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	44	73	0	0.60274	0	C|0.875;T|0.125	0.125	strong	.	ITGA2	211	.	NM_002203	exon19	c.C2376T	p.D792D	TGAGGACGGACTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228565325	228565325	+	Silent	SNP	C	C	T	rs61743077	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	94	142	0	0.552941	0	C|0.992;T|0.008	0.008	strong	.	OBSCN	2142	.	NM_001271223	exon113	c.C26286T	p.L8762L	CCTGCTCAAGGTC	.	PASS	Atlas-SNP
C1orf94	84970	hgsc.bcm.edu	37	1	34663180	34663180	+	Silent	SNP	G	G	A	rs3795412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	31	97	0	0.348315	0	G|0.833;A|0.167	0.167	strong	.	C1orf94	156	.	NM_001134734	exon2	c.G675A	p.R225R	GGACAGGGGCCGC	.	PASS	Atlas-SNP
SF3B3	23450	hgsc.bcm.edu	37	16	70569215	70569215	+	Silent	SNP	A	A	T	rs33910368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	179	189	0	1	0	A|0.596;T|0.404	0.404	strong	.	SF3B3	99	.	NM_012426	exon6	c.A717T	p.P239P	AGTTCCAGGAGGG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	37	127	1	0.393617	0.00787402	G|0.760;A|0.240	0.240	strong	RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	NM_001256071	exon6	c.G990A	p.K330K	CGGTAAGAATGAA	.	scavenged	Atlas-SNP
RANBP3L	202151	hgsc.bcm.edu	37	5	36257134	36257134	+	Missense_Mutation	SNP	G	G	A	rs16902872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	75	172	0	0.551471	0	G|0.906;A|0.094	0.094	strong	.	RANBP3L	41	.	NM_001161429	exon11	c.C887T	p.A296V	GCAGCAGCTGATT	.	PASS	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75938236	75938236	+	Silent	SNP	A	A	G	rs1062293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	163	2	1	0.0122699	A|0.598;G|0.402	0.402	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.A645G	p.V215V	GCCAGTACCCCAG	.	scavenged	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60884473	60884473	+	Silent	SNP	C	C	T	rs115306720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	21	28	0	0.65625	0	C|0.976;T|0.024	0.024	strong	.	LAMA5	268	.	NM_005560	exon80	c.G11007A	p.A3669A	GTTCACCGCCAGC	.	PASS	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	37	1	196887411	196887411	+	Missense_Mutation	SNP	T	T	C	rs200907976	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	393	216	354	1	0.549618	0.00282486	.	.	weak	.	CFHR4	141	.	NM_001201550	exon10	c.T1612C	p.Y538H	ATAAAATATTATG	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	89	97	0	0.978022	0	C|0.515;T|0.485	0.485	strong	RPS6KB2_ENST00000312629,NS,carcinoma,0,2	RPS6KB2	92	2	NM_003952	exon14	c.C1259T	p.A420V	CCCGGGCCCCCGT	.	PASS	Atlas-SNP
ALDH8A1	64577	hgsc.bcm.edu	37	6	135254034	135254034	+	Silent	SNP	G	G	A	rs114000920	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	43	92	0	0.544304	0	G|0.987;A|0.013	0.013	strong	.	ALDH8A1	68	.	NM_022568	exon5	c.C729T	p.S243S	GGGAGCGCTCAGC	.	PASS	Atlas-SNP
BPIFB3	359710	hgsc.bcm.edu	37	20	31644436	31644436	+	Silent	SNP	A	A	C	rs35539872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	64	97	0	0.496124	0	A|0.957;C|0.043	0.043	strong	.	.	.	.	NM_182658	exon2	c.A213C	p.G71G	CTCAGGAGGGCTG	.	PASS	Atlas-SNP
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159406	18159406	+	Silent	SNP	C	C	G	rs28628238	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	123	0	0.992754	0	C|0.948;G|0.052	0.052	strong	.	MRGPRX3	59	.	NM_054031	exon3	c.C657G	p.L219L	CATCCTCCTCACA	.	PASS	Atlas-SNP
B4GALT3	8703	hgsc.bcm.edu	37	1	161141862	161141862	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	43	73	0	0.483146	0	.	.	none	.	B4GALT3	39	.	NM_003779	exon8	c.G926A	p.R309H	TGGGTACGGACCA	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15841534	15841534	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	55	110	0	0.572917	0	.	.	none	.	MYH11	520	.	NM_001040114	exon20	c.C2325A	p.I775I	GAAGAAGATTTTG	.	PASS	Atlas-SNP
ZNF689	115509	hgsc.bcm.edu	37	16	30616317	30616317	+	Silent	SNP	A	A	G	rs34007971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	47	62	0	0.522222	0	A|0.917;G|0.083	0.083	strong	.	ZNF689	48	.	NM_138447	exon3	c.T771C	p.G257G	TTTTTCACCTGTG	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204198209	204198209	+	Silent	SNP	A	A	G	rs3795571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	110	0	1	0	A|0.469;G|0.531	0.531	strong	.	PLEKHA6	115	.	NM_014935	exon19	c.T2607C	p.H869H	TACCTCATGGATG	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152497088	152497088	+	Silent	SNP	G	G	A	rs61730771	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	190	374	0	0.588235	0	G|0.977;A|0.023	0.023	strong	.	NEB	1697	.	NM_004543	exon61	c.C8466T	p.H2822H	GGCCACGTGCATG	.	PASS	Atlas-SNP
KIAA1211L	343990	hgsc.bcm.edu	37	2	99412654	99412654	+	Missense_Mutation	SNP	C	C	T	rs73962467	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	54	119	0	0.482143	0	C|0.991;T|0.009	0.009	strong	.	.	.	.	NM_207362	exon9	c.G2678A	p.R893Q	TGCTTCCGGTCCA	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469734	98469734	+	Missense_Mutation	SNP	G	G	A	rs73334383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	40	94	0	0.43956	0	G|0.987;A|0.013	0.013	strong	.	PIK3AP1	111	.	NM_152309	exon2	c.C20T	p.P7L	CCTCTGGGCACCC	.	PASS	Atlas-SNP
AIFM3	150209	hgsc.bcm.edu	37	22	21333605	21333605	+	Missense_Mutation	SNP	G	G	C	rs61356271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	98	133	0	0.535519	0	G|0.946;C|0.054	0.054	strong	.	AIFM3	49	.	NM_001146288	exon17	c.G1541C	p.S514T	AGATGAGCACTGT	.	PASS	Atlas-SNP
EFR3B	22979	hgsc.bcm.edu	37	2	25359422	25359422	+	Silent	SNP	G	G	A	rs3731631	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	29	65	0	0.367089	0	G|0.665;A|0.335	0.335	strong	.	EFR3B	29	.	NM_014971	exon14	c.G1515A	p.L505L	GAAGCTGAAAGTG	.	PASS	Atlas-SNP
PAMR1	25891	hgsc.bcm.edu	37	11	35492351	35492351	+	Silent	SNP	G	G	A	rs16927500	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	71	97	0	0.577236	0	G|0.906;A|0.094	0.094	strong	.	PAMR1	85	.	NM_001001991	exon5	c.C510T	p.S170S	CTCCAGGCTCAAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515550	195515550	+	Silent	SNP	G	G	C	rs59408218	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	300	265	0	0.996678	0	G|0.897;C|0.103	0.103	strong	.	MUC4	1505	.	NM_018406	exon2	c.C2901G	p.T967T	GGCCGTGGTGAAG	.	PASS	Atlas-SNP
BFSP2	8419	hgsc.bcm.edu	37	3	133191385	133191385	+	Missense_Mutation	SNP	C	C	A	rs79087781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	76	138	0	0.562963	0	C|0.964;A|0.036	0.036	strong	.	BFSP2	48	.	NM_003571	exon6	c.C1220A	p.A407D	ACCACGCCCTGCT	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28610988	28610988	+	Missense_Mutation	SNP	C	C	T	rs276938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	122	150	0	0.99187	0	T|0.384;G|0.001	0.384	strong	.	DSC3	225	.	NM_024423	exon3	c.G305A	p.R102K	TGTTTCCTTTTGT	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	65	149	1	0.454545	0.00671141	G|0.628;N|0.001	.	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon11	c.G1042A	p.A348T	CAGGCCGCTGTGT	.	scavenged	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107457532	107457532	+	Missense_Mutation	SNP	C	C	T	rs10761073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	77	233	0	0.366667	0	C|0.321;T|0.679	0.679	strong	OR13D1,colon,carcinoma,+1,1	OR13D1	42	1	NM_001004484	exon1	c.C830T	p.S277L	CGCACTCGATTGT	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	112	207	1	0.513761	0.00483092	T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong	.	MED24	89	.	NM_014815	exon13	c.G1161A	p.A387A	TCGGTCCGCTTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510158	195510158	+	Missense_Mutation	SNP	G	G	C	rs200688112		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	61	186	7	0.268722	0.0376344	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,+2,4	MUC4	1505	4	NM_018406	exon2	c.C8293G	p.H2765D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
VENTX	27287	hgsc.bcm.edu	37	10	135051543	135051543	+	Missense_Mutation	SNP	T	T	C	rs2240892	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	19	59	0	0.263889	0	T|0.766;C|0.234	0.234	strong	VENTX,caecum,carcinoma,0,1	VENTX	24	1	NM_014468	exon1	c.T125C	p.L42P	TCTCCCTGGGGAG	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104376693	104376693	+	Missense_Mutation	SNP	G	G	A	rs4135113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	144	300	0	0.428571	0	G|0.911;A|0.089	0.089	strong	.	TDG	43	.	NM_003211	exon5	c.G595A	p.G199S	ACGCCCGGCAGCA	.	PASS	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3688030	3688030	+	Silent	SNP	C	C	G	rs3737592	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	22	48	0	0.468085	0	C|0.876;G|0.124	0.124	strong	CCDC27,caecum,carcinoma,+2,1	CCDC27	79	1	NM_152492	exon12	c.C1914G	p.P638P	GCCCCCCCTGCAA	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	35	82	0	0.479452	0	A|0.862;G|0.138	0.138	strong	.	OR10S1	78	.	NM_001004474	exon1	c.T926C	p.V309A	TGCTTCACCTCCT	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	43	70	0	0.52439	0	G|0.756;C|0.244	0.244	strong	.	PDIA2	51	.	NM_006849	exon2	c.G393C	p.P131P	GCACCCGGAGGAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414559	105414559	+	Missense_Mutation	SNP	T	T	C	rs11845746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	236	208	0	0.983333	0	T|0.967;C|0.033	0.033	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A7229G	p.K2410R	GGCATCTTGAAAC	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	65	171	0	0.40625	0	.	.	weak	LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	NM_001270974	exon29	c.C4475A	p.P1492H	ATTTGGGGAAAGA	.	PASS	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581440	99581440	+	Missense_Mutation	SNP	T	T	C	rs35403084	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	57	81	0	0.619565	0	T|0.971;C|0.029	0.029	strong	.	ZNF782	64	.	NM_001001662	exon6	c.A865G	p.T289A	CTCCTGTGAGAGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679136	100679136	+	Missense_Mutation	SNP	T	T	C	rs7780935	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	60	139	0	0.495868	0	T|0.875;C|0.125	0.125	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4439C	p.V1480A	CTCCTGTTGACTC	.	PASS	Atlas-SNP
DMRT2	10655	hgsc.bcm.edu	37	9	1056517	1056517	+	Silent	SNP	C	C	G	rs16928356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	160	0	0.992754	0	C|0.951;G|0.049	0.049	strong	.	DMRT2	70	.	NM_181872	exon4	c.C930G	p.T310T	TTTAACCATGCAG	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114146832	114146832	+	Silent	SNP	C	C	T	rs16916040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	82	145	0	0.607407	0	C|0.908;T|0.092	0.092	strong	KIAA0368,NS,carcinoma,0,2	KIAA0368	144	2	NM_001080398	exon35	c.G4185A	p.A1395A	TTCTGCCGCTTTT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13701422	13701422	+	Missense_Mutation	SNP	G	G	T	rs113425437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	41	80	0	0.561644	0	G|0.961;T|0.039	0.039	strong	.	DNAH5	868	.	NM_001369	exon77	c.C13462A	p.P4488T	CCTGGGGGTTAAA	.	PASS	Atlas-SNP
MZT2A	653784	hgsc.bcm.edu	37	2	132241731	132241731	+	Missense_Mutation	SNP	T	T	C	rs75021268	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	137	251	1	0.505535	0.00398406	T|0.872;C|0.128	0.128	strong	.	MZT2A	6	.	NM_001085365	exon3	c.A380G	p.H127R	CCCTCGTGGTTGC	.	PASS	Atlas-SNP
MOB3C	148932	hgsc.bcm.edu	37	1	47080741	47080741	+	Missense_Mutation	SNP	C	C	T	rs12029680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	62	158	0	0.416107	0	C|0.666;T|0.334	0.334	strong	.	MOB3C	1	.	NM_145279	exon1	c.G8A	p.R3H	TTTCTGCGCTTCA	.	PASS	Atlas-SNP
OR8K1	390157	hgsc.bcm.edu	37	11	56113923	56113923	+	Silent	SNP	C	C	T	rs61745885	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	71	152	0	0.47973	0	C|0.993;T|0.007	0.007	strong	OR8K1,shoulder,malignant_melanoma,0,1	OR8K1	93	1	NM_001002907	exon1	c.C409T	p.L137L	CCTCTTCTGTACG	.	PASS	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7064457	7064457	+	Silent	SNP	T	T	C	rs76429148	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	65	172	0	0.442177	0	T|0.938;C|0.062	0.062	strong	.	NLRP14	187	.	NM_176822	exon4	c.T1200C	p.F400F	TCTGTTTACCTGC	.	PASS	Atlas-SNP
MCM2	4171	hgsc.bcm.edu	37	3	127340583	127340583	+	Silent	SNP	C	C	T	rs6794323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	41	81	0	0.455556	0	C|0.930;T|0.070	0.070	strong	.	MCM2	79	.	NM_004526	exon16	c.C2682T	p.D894D	CCACGACCTGAAA	.	PASS	Atlas-SNP
LNP1	348801	hgsc.bcm.edu	37	3	100170634	100170634	+	Silent	SNP	T	T	C	rs9848109	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	18	127	1	0.152542	0.00787402	T|0.500;C|0.500	0.500	strong	LNP1,caecum,carcinoma,0,2	LNP1	26	2	NM_001085451	exon3	c.T228C	p.F76F	AGAATTTCGATGC	.	scavenged	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24250809	24250809	+	Missense_Mutation	SNP	T	T	C	rs77012108	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	68	124	0	0.535433	0	T|0.973;C|0.027	0.027	strong	ADAMDEC1,arm,malignant_melanoma,-1,1	ADAMDEC1	69	1	NM_014479	exon3	c.T242C	p.I81T	AGATGATCTTAAA	.	PASS	Atlas-SNP
TPPP3	51673	hgsc.bcm.edu	37	16	67424122	67424122	+	Silent	SNP	G	G	A	rs11552319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	57	123	0	0.428571	0	G|0.897;A|0.103	0.103	strong	.	TPPP3	13	.	NM_016140	exon5	c.C486T	p.S162S	GTAGGCGCTCACG	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6103281	6103281	+	Silent	SNP	A	A	T	rs11537642	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	36	71	0	0.409091	0	A|0.955;T|0.045	0.045	strong	.	VWF	338	.	NM_000552	exon37	c.T6345A	p.T2115T	CTGCACAGTCCAT	.	PASS	Atlas-SNP
MRI1	84245	hgsc.bcm.edu	37	19	13875453	13875453	+	Silent	SNP	C	C	T	rs141796284	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	48	107	0	0.390244	0	C|0.993;T|0.007	0.007	strong	.	MRI1	35	.	NM_001031727	exon1	c.C51T	p.D17D	CCTAGACCAGCTG	.	PASS	Atlas-SNP
EEF2	1938	hgsc.bcm.edu	37	19	3980852	3980852	+	Silent	SNP	G	G	A	rs140573073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	27	32	0	0.509434	0	G|0.997;A|0.003	0.003	strong	.	EEF2	57	.	NM_001961	exon8	c.C1137T	p.D379D	AGCCTCGTCGTCC	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	161	166	0	0.975758	0	C|0.466;T|0.534	0.534	strong	PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	NM_014935	exon18	c.G2510A	p.R837K	TTCTCCCTCATGG	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	86	170	0	0.508876	0	A|0.902;G|0.098	0.098	strong	ENGASE,NS,carcinoma,+1,1	ENGASE	55	1	NM_001042573	exon9	c.A1155G	p.R385R	GGGCCGACTGGAG	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127873114	127873114	+	Silent	SNP	G	G	C	rs73348287	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	77	0	0.485437	0	G|0.894;C|0.106	0.106	strong	.	FBN2	858	.	NM_001999	exon1	c.C183G	p.P61P	ATACTCGGGCGCT	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	37	19	42853782	42853782	+	Silent	SNP	T	T	C	rs28621009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	31	55	0	0.54386	0	T|0.835;C|0.165	0.165	strong	.	MEGF8	358	.	NM_001271938	exon14	c.T2430C	p.N810N	GCTCAATGGCTCG	.	PASS	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12089903	12089903	+	Silent	SNP	G	G	A	rs112017572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	26	24	0	0.65	0	G|0.941;A|0.059	0.059	strong	ZNF763,caecum,carcinoma,+2,3	ZNF763	31	3	NM_001012753	exon4	c.G1173A	p.A391A	GAATGCGCTCTGG	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	37	20	47849904	47849904	+	Missense_Mutation	SNP	C	C	T	rs145681733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	34	85	0	0.409639	0	C|1.000;T|0.000	0.000	weak	.	DDX27	74	.	NM_017895	exon10	c.C1186T	p.R396C	CACCACCGCCAGA	.	PASS	Atlas-SNP
C7orf71	285941	hgsc.bcm.edu	37	7	26678881	26678881	+	Missense_Mutation	SNP	G	G	A	rs78525926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	28	36	0	1	0	G|0.964;A|0.036	0.036	strong	.	C7orf71	6	.	NM_001145531	exon2	c.G118A	p.G40S	CAAGGCGGCTACC	.	PASS	Atlas-SNP
ATP6AP2	10159	hgsc.bcm.edu	37	X	40464822	40464822	+	Missense_Mutation	SNP	G	G	C	rs35798522	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	19	25	0	0.558824	0	G|0.977;C|0.023	0.023	strong	.	ATP6AP2	45	.	NM_005765	exon9	c.G868C	p.A290P	AACCCAGCAAGTC	.	PASS	Atlas-SNP
ORM2	5005	hgsc.bcm.edu	37	9	117094200	117094200	+	Silent	SNP	C	C	T	rs1826232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	49	136	0	0.30625	0	C|0.873;T|0.127	0.127	strong	ORM2,face,carcinoma,-2,1	ORM2	13	1	NM_000608	exon5	c.C531T	p.D177D	CACCGACTGGAAA	.	PASS	Atlas-SNP
CSRP2BP	57325	hgsc.bcm.edu	37	20	18142564	18142564	+	Silent	SNP	A	A	G	rs3828013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	59	93	0	0.578431	0	A|0.896;G|0.104	0.104	strong	CSRP2BP,NS,carcinoma,0,2	CSRP2BP	80	2	NM_020536	exon5	c.A783G	p.K261K	AGAGAAAAGGTCT	.	PASS	Atlas-SNP
MRS2	57380	hgsc.bcm.edu	37	6	24412530	24412530	+	Silent	SNP	G	G	T	rs61733147	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	211	196	0	1	0	G|0.964;T|0.036	0.036	strong	.	MRS2	31	.	NM_020662	exon5	c.G495T	p.R165R	GTTCCGGGAACTC	.	PASS	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186168	39186168	+	Missense_Mutation	SNP	A	A	C	rs8074887	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	62	113	0	0.508197	0	A|0.588;C|0.412	0.412	strong	.	KRTAP1-4	4	.	NM_001257305	exon1	c.T163G	p.S55A	TCACAGATCCACC	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24199218	24199218	+	Missense_Mutation	SNP	C	C	A	rs36041430	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	95	183	0	0.579268	0	C|0.922;A|0.078	0.078	strong	.	ADAM28	100	.	NM_014265	exon16	c.C1778A	p.T593K	AAGACACAAGTCA	.	PASS	Atlas-SNP
COG2	22796	hgsc.bcm.edu	37	1	230796533	230796533	+	Silent	SNP	T	T	G	rs16852160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	105	232	0	0.428571	0	T|0.962;G|0.038	0.038	strong	.	COG2	61	.	NM_007357	exon3	c.T264G	p.L88L	CCAGCTTTCTGTG	.	PASS	Atlas-SNP
INHA	3623	hgsc.bcm.edu	37	2	220439826	220439826	+	Missense_Mutation	SNP	G	G	A	rs12720061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	75	121	0	0.539568	0	G|0.973;A|0.027	0.027	strong	.	INHA	30	.	NM_002191	exon2	c.G679A	p.G227R	AGTGGAGGGGAGA	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46826319	46826319	+	Silent	SNP	C	C	G	rs150389766		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	61	141	0	0.438849	0	C|1.000;G|0.000	0.000	weak	.	GPR116	133	.	NM_015234	exon17	c.G3321C	p.L1107L	GAGGCCCAGTGTC	.	PASS	Atlas-SNP
CCDC155	147872	hgsc.bcm.edu	37	19	49920719	49920719	+	Silent	SNP	C	C	T	rs79452032	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	41	62	0	0.493976	0	C|0.987;T|0.013	0.013	strong	.	CCDC155	46	.	NM_144688	exon20	c.C1641T	p.P547P	ACCTCCCACCTGG	.	PASS	Atlas-SNP
ASAH2	56624	hgsc.bcm.edu	37	10	52005153	52005153	+	Silent	SNP	A	A	G	rs7097319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	69	244	1	0.35567	0.00409836	A|0.738;G|0.262	0.262	strong	ASAH2_ENST00000395526,NS,carcinoma,-1,2	ASAH2	69	2	NM_019893	exon2	c.T189C	p.A63A	TTGGGCAGCTGTG	.	scavenged	Atlas-SNP
METTL21A	151194	hgsc.bcm.edu	37	2	208478055	208478055	+	Silent	SNP	A	A	G	rs17520056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	94	0	0.5	0	A|0.705;G|0.295	0.295	strong	METTL21A,NS,carcinoma,0,1	METTL21A	24	1	NM_145280	exon4	c.T372C	p.T124T	TCCCCAAGTCAGC	.	PASS	Atlas-SNP
MIER2	54531	hgsc.bcm.edu	37	19	327182	327182	+	Silent	SNP	C	C	T	rs7256086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	61	114	1	0.554545	0.00877193	C|0.849;T|0.151	0.151	strong	MIER2,lower_third,carcinoma,-1,1	MIER2	51	1	NM_017550	exon5	c.G444A	p.P148P	CACGGACGGGGTG	.	scavenged	Atlas-SNP
CEACAM1	634	hgsc.bcm.edu	37	19	43031369	43031369	+	Missense_Mutation	SNP	G	G	A	rs8110904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	456	238	449	1	0.52193	0.00222717	G|0.900;A|0.100	0.100	strong	.	CEACAM1	43	.	NM_001184816	exon2	c.C248T	p.A83V	CCTATTGCATATC	.	PASS	Atlas-SNP
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	30	67	0	0.461538	0	A|0.439;G|0.561	0.561	strong	TPH2,colon,carcinoma,+1,1	TPH2	81	1	NM_173353	exon7	c.A936G	p.P312P	CACCCCAGAACCG	.	PASS	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	37	19	44732658	44732658	+	Silent	SNP	C	C	G	rs922063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	271	262	0	0.992674	0	C|0.816;G|0.184	0.184	strong	.	ZNF227	62	.	NM_182490	exon4	c.C120G	p.L40L	ACTGCTCGATCTT	.	PASS	Atlas-SNP
GPANK1	7918	hgsc.bcm.edu	37	6	31631907	31631907	+	Silent	SNP	G	G	A	rs928814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	85	155	0	0.480226	0	G|0.935;A|0.065	0.065	strong	.	GPANK1	19	.	NM_001199238	exon3	c.C349T	p.L117L	CTGGCAGGTCCCC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45124708	45124708	+	Silent	SNP	C	C	T	rs13438759	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	43	75	0	0.43	0	C|0.918;T|0.082	0.082	strong	.	NACAD	44	.	NM_001146334	exon2	c.G1071A	p.T357T	GGCAGACGTGCTG	.	PASS	Atlas-SNP
KCNN1	3780	hgsc.bcm.edu	37	19	18084724	18084724	+	Silent	SNP	C	C	T	rs77030907	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	7	2	0	0.583333	0	C|0.990;T|0.010	0.010	strong	.	KCNN1	74	.	NM_002248	exon3	c.C27T	p.S9S	TGGCAGCGTGGGG	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5743512	5743512	+	Missense_Mutation	SNP	T	T	C	rs6414624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	105	0	0.470588	0	T|0.274;C|0.726	0.726	strong	.	EVC	90	.	NM_153717	exon6	c.T772C	p.Y258H	GAACTATACCAGA	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117099574	117099574	+	Silent	SNP	A	A	G	rs148856699	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	99	136	0	0.673469	0	A|0.995;G|0.005	0.005	strong	.	AKNA	119	.	NM_030767	exon22	c.T4080C	p.P1360P	TCCTGCAGGCGCA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537198	88537198	+	Missense_Mutation	SNP	C	C	A	rs200796238		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	40	78	17	0.4	0.217949	.	.	weak	DSPP,NS,lymphoid_neoplasm,+1,1	DSPP	174	1	NM_014208	exon5	c.C3384A	p.D1128E	CAGTGACAGCAGC	.	scavenged	Atlas-SNP
SPAG8	26206	hgsc.bcm.edu	37	9	35811215	35811215	+	Silent	SNP	C	C	T	rs73444820	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	71	89	1	0.71	0.011236	C|0.978;T|0.022	0.022	strong	SPAG8_ENST00000396638,caecum,carcinoma,0,2	SPAG8	67	2	NM_001039592	exon2	c.G828A	p.P276P	GCCCCGCGGCAAA	.	scavenged	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713625	32713625	+	Missense_Mutation	SNP	C	C	T	rs116163401	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	488	91	468	0	0.186475	0	C|0.998;T|0.002	0.002	weak	.	HLA-DQA2	27	.	NM_020056	exon3	c.C389T	p.T130I	CCAACACCCTCAT	.	PASS	Atlas-SNP
SERPINE3	647174	hgsc.bcm.edu	37	13	51936079	51936079	+	Silent	SNP	T	T	C	rs74084815	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	95	222	1	0.470297	0.0045045	T|0.992;C|0.008	0.008	strong	.	SERPINE3	37	.	NM_001101320	exon7	c.T1221C	p.S407S	TCTCTCTAGCAAC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45122464	45122464	+	Missense_Mutation	SNP	A	A	C	rs10243185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	19	40	0	0.44186	0	A|0.565;C|0.435	0.435	strong	.	NACAD	44	.	NM_001146334	exon2	c.T3315G	p.D1105E	AGGCGCATCGGGG	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81582868	81582868	+	Silent	SNP	G	G	A	rs8031107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	162	178	0	0.981818	0	G|0.455;A|0.545	0.545	strong	IL16_ENST00000302987,right_upper_lobe,carcinoma,+1,2	IL16	254	2	NM_001172128	exon11	c.G1407A	p.Q469Q	GCATCAGTGGAGT	.	PASS	Atlas-SNP
ROBO4	54538	hgsc.bcm.edu	37	11	124765511	124765511	+	Missense_Mutation	SNP	T	T	G	rs60888551	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	31	93	0	0.333333	0	T|0.952;G|0.048	0.048	strong	.	ROBO4	130	.	NM_019055	exon6	c.A878C	p.Q293P	GCTCCCTGGCCTC	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465389	39465389	+	Silent	SNP	T	T	A	rs12451604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	62	117	0	0.452555	0	T|0.764;A|0.236	0.236	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.A117T	p.T39T	CTGCCATGTCTGG	.	PASS	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	37	19	56303806	56303806	+	Missense_Mutation	SNP	A	A	C	rs80143194	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	122	0	0.5	0	A|0.976;C|0.024	0.024	strong	.	NLRP11	139	.	NM_145007	exon9	c.T2374G	p.C792G	CGCTGCAGCAATT	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157106968	157106968	+	Silent	SNP	C	C	T	rs6892478	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	66	152	0	0.5	0	C|0.837;G|0.000;T|0.162	0.162	strong	.	C5orf52	17	.	NM_001145132	exon3	c.C441T	p.S147S	GAACAGCAACCGG	.	PASS	Atlas-SNP
C10orf62	414157	hgsc.bcm.edu	37	10	99350017	99350017	+	Missense_Mutation	SNP	G	G	C	rs7093840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	13	43	0	0.382353	0	G|0.706;C|0.294	0.294	strong	.	C10orf62	14	.	NM_001009997	exon1	c.G363C	p.E121D	TGATGAGGCCACG	.	PASS	Atlas-SNP
LCE5A	254910	hgsc.bcm.edu	37	1	152484129	152484129	+	Missense_Mutation	SNP	G	G	A	rs2105117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	91	170	0	0.494565	0	G|0.469;A|0.531	0.531	strong	.	LCE5A	15	.	NM_178438	exon2	c.G119A	p.C40Y	CCCAGTGTTCAGC	.	PASS	Atlas-SNP
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	24	53	0	0.358209	0	A|0.686;G|0.314	0.314	strong	SDC4,NS,carcinoma,0,1	SDC4	16	1	NM_002999	exon1	c.T34C	p.F12L	CGAAGAACAGCAG	.	PASS	Atlas-SNP
ERBB3	2065	hgsc.bcm.edu	37	12	56487201	56487201	+	Silent	SNP	T	T	C	rs2229046	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	97	177	0	0.570588	0	T|0.932;C|0.068	0.068	strong	.	ERBB3	350	.	NM_001982	exon12	c.T1347C	p.I449I	GGAAATTAGTGCT	.	PASS	Atlas-SNP
ST3GAL5	8869	hgsc.bcm.edu	37	2	86088311	86088311	+	Missense_Mutation	SNP	T	T	C	rs1138484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	94	0	0.453333	0	T|0.829;C|0.171	0.171	strong	.	ST3GAL5	51	.	NM_003896	exon3	c.A311G	p.H104R	TTTACATGGTCAG	.	PASS	Atlas-SNP
OR52H1	390067	hgsc.bcm.edu	37	11	5565906	5565906	+	Missense_Mutation	SNP	A	A	G	rs7934354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	147	336	1	0.512195	0.00297619	A|0.887;G|0.113	0.113	strong	.	OR52H1	46	.	NM_001005289	exon1	c.T848C	p.M283T	GCAAACATGATGT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123843946	123843946	+	Missense_Mutation	SNP	C	C	T	rs60531929	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	16	32	0	0.516129	0	C|0.965;T|0.035	0.035	strong	.	TACC2	271	.	NM_206862	exon4	c.C1931T	p.T644M	GGCACACGGACGG	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523636	42523636	+	Missense_Mutation	SNP	C	C	A	rs3915951	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	14	127	1	0.089172	0.00787402	C|0.500;A|0.500	0.500	weak	CYP2D6_ENST00000360608,NS,carcinoma,0,11	CYP2D6	104	11	NM_000106	exon7	c.G986T	p.R329L	ACACGGCCTGGAC	.	scavenged	Atlas-SNP
ROS1	6098	hgsc.bcm.edu	37	6	117725578	117725578	+	Silent	SNP	T	T	A	rs2243378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	90	0	1	0	T|0.406;A|0.594	0.594	strong	.	ROS1	728	.	NM_002944	exon5	c.A303T	p.L101L	AGTTGGTAGGTCT	.	PASS	Atlas-SNP
GRIK3	2899	hgsc.bcm.edu	37	1	37325477	37325477	+	Missense_Mutation	SNP	A	A	C	rs6691840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	61	137	0	0.435714	0	A|0.660;C|0.340	0.340	strong	.	GRIK3	195	.	NM_000831	exon6	c.T928G	p.S310A	ACTCGGACCGGGG	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	37	6	46976812	46976812	+	Missense_Mutation	SNP	T	T	C	rs1226475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	63	189	0	0.431507	0	T|0.836;C|0.164	0.164	strong	.	GPR110	102	.	NM_153840	exon11	c.A2359G	p.I787V	CGCGGATGATGGT	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	879943	879943	+	Silent	SNP	G	G	A	rs76403059	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	48	105	0	0.396694	0	.	.	weak	MED16,colon,carcinoma,0,1	MED16	61	1	NM_005481	exon8	c.C1347T	p.H449H	CTTCCCGTGGCTG	.	PASS	Atlas-SNP
JAKMIP3	282973	hgsc.bcm.edu	37	10	133918372	133918372	+	Silent	SNP	G	G	A	rs10870252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	87	165	0	0.508772	0	G|0.741;A|0.259	0.259	strong	.	JAKMIP3	69	.	NM_001105521	exon1	c.G60A	p.A20A	CGCGGCGCTGCAG	.	PASS	Atlas-SNP
FBP2	8789	hgsc.bcm.edu	37	9	97325726	97325726	+	Silent	SNP	A	A	G	rs41281154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	24	75	0	0.303797	0	A|0.912;G|0.088	0.088	strong	.	FBP2	26	.	NM_003837	exon6	c.T723C	p.Y241Y	GGCCCCATAGGGA	.	PASS	Atlas-SNP
LCN8	138307	hgsc.bcm.edu	37	9	139649701	139649701	+	Missense_Mutation	SNP	C	C	T	rs144857499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	55	78	0	0.6875	0	C|0.997;T|0.003	0.003	strong	.	LCN8	14	.	NM_178469	exon5	c.G416A	p.R139Q	CCAGGCCGGGCCG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	45	51	0	1	0	T|0.691;C|0.309	0.309	strong	.	NUP133	111	.	NM_018230	exon10	c.A1217G	p.Q406R	GTCAACTGACACA	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112554	248112554	+	Missense_Mutation	SNP	T	T	C	rs202165563		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	41	253	0	0.121302	0	.	.	weak	OR2L8,trunk,malignant_melanoma,0,1	OR2L8	92	1	NM_001001963	exon1	c.T395C	p.L132P	ACTATCTCATCCG	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1271582	1271582	+	Missense_Mutation	SNP	C	C	T	rs4963055	by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	596	279	827	2	0.468121	0.00241838	.	.	weak	.	MUC5B	473	.	NM_002458	exon31	c.C13472T	p.T4491I	CAGTCACCAGCTC	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45741416	45741416	+	Missense_Mutation	SNP	T	T	A	rs61737925	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	78	125	0	0.527027	0	T|0.960;A|0.040	0.040	strong	.	SMC1B	215	.	NM_148674	exon24	c.A3530T	p.Q1177L	TGAAACTGGTCTT	.	PASS	Atlas-SNP
WBSCR27	155368	hgsc.bcm.edu	37	7	73249092	73249092	+	Missense_Mutation	SNP	C	C	T	rs73369956	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	111	0	1	0	C|0.962;T|0.038	0.038	strong	.	WBSCR27	21	.	NM_152559	exon6	c.G719A	p.R240Q	CTGGGTCGCCTTC	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	37	X	63410110	63410110	+	Silent	SNP	T	T	C	rs61730681	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	157	149	0	1	0	T|0.758;C|0.242	0.242	strong	.	.	.	.	NM_152424	exon2	c.A3057G	p.Q1019Q	AGCTAGTTGAGGC	.	PASS	Atlas-SNP
UBE2M	9040	hgsc.bcm.edu	37	19	59067585	59067585	+	Silent	SNP	G	G	A	rs8105097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	54	140	0	0.412214	0	G|0.907;A|0.093	0.093	strong	.	UBE2M	14	.	NM_003969	exon6	c.C423T	p.P141P	GTCCTCGGGGTTG	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	47	137	0	0.385246	0	T|0.563;C|0.437	0.437	strong	.	ABCC1	156	.	NM_004996	exon8	c.T825C	p.V275V	GAAGGTTGTGTAC	.	PASS	Atlas-SNP
SMC3	9126	hgsc.bcm.edu	37	10	112349422	112349422	+	Silent	SNP	T	T	C	rs75323904	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	95	166	0	0.502645	0	T|0.942;C|0.058	0.058	strong	.	SMC3	103	.	NM_005445	exon14	c.T1365C	p.Y455Y	AAAATATTACGAA	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62198686	62198686	+	Silent	SNP	G	G	A	rs3827025	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	13	16	0	0.464286	0	G|0.823;A|0.177	0.177	strong	.	.	.	.	NM_001037335	exon7	c.C2025T	p.C675C	GGCCTCGCACTCC	.	PASS	Atlas-SNP
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259709	71259709	+	Silent	SNP	C	C	T	rs180808688	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	521	234	453	1	0.449136	0.00220751	C|0.999;T|0.001	0.001	strong	.	KRTAP5-9	19	.	NM_005553	exon1	c.C6T	p.G2G	CATGGGCTGCTGT	.	PASS	Atlas-SNP
CRTAC1	55118	hgsc.bcm.edu	37	10	99696031	99696031	+	Missense_Mutation	SNP	G	G	A	rs80014629	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	52	132	0	0.464286	0	G|0.999;A|0.001	0.001	strong	CRTAC1,NS,carcinoma,0,2	CRTAC1	86	2	NM_001206528	exon3	c.C317T	p.A106V	CGCAGCGCGTAGT	.	PASS	Atlas-SNP
PCNXL2	80003	hgsc.bcm.edu	37	1	233225848	233225848	+	Silent	SNP	T	T	C	rs12059884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	67	152	0	0.51145	0	T|0.854;C|0.146	0.146	strong	.	PCNXL2	204	.	NM_014801	exon23	c.A4035G	p.T1345T	ATATGATGTGATG	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	37	6	46977458	46977458	+	Missense_Mutation	SNP	T	T	C	rs937057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	43	97	0	0.40566	0	T|0.832;C|0.168	0.168	strong	.	GPR110	102	.	NM_153840	exon11	c.A1713G	p.I571M	CATCAATATGGAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417766	105417766	+	Missense_Mutation	SNP	G	G	A	rs2396457	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	263	386	1	1	0.00259067	G|0.824;A|0.176	0.176	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4022T	p.S1341F	GGGGCAGACACCC	.	PASS	Atlas-SNP
EAPP	55837	hgsc.bcm.edu	37	14	34985645	34985645	+	Silent	SNP	G	G	A	rs7797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	145	298	1	0.557692	0.0033557	G|0.697;A|0.303	0.303	strong	.	EAPP	28	.	NM_018453	exon6	c.C729T	p.A243A	CTTCTCGGCAGCA	.	PASS	Atlas-SNP
PIGR	5284	hgsc.bcm.edu	37	1	207106478	207106478	+	Missense_Mutation	SNP	G	G	A	rs291102	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	80	0	0.542857	0	G|0.748;T|0.004	.	strong	PIGR,rectum,carcinoma,-1,3	PIGR	98	3	NM_002644	exon7	c.C1739T	p.A580V	GGAGCAGCGTCTG	.	PASS	Atlas-SNP
GPR39	2863	hgsc.bcm.edu	37	2	133175152	133175152	+	Silent	SNP	C	C	T	rs34714906	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	36	93	0	0.375	0	C|0.926;T|0.074	0.074	strong	.	GPR39	60	.	NM_001508	exon1	c.C537T	p.P179P	GTACCCCCTGGTG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134698626	134698626	+	Missense_Mutation	SNP	T	T	C	rs73393250	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	71	0	0.470588	0	T|0.913;C|0.087	0.087	strong	.	TTC40	100	.	NM_001200049	exon27	c.A3608G	p.N1203S	ATGGCGTTGTTGT	.	PASS	Atlas-SNP
ASGR2	433	hgsc.bcm.edu	37	17	7011225	7011225	+	Silent	SNP	T	T	G	rs61731746	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	136	0	0.518519	0	T|0.891;G|0.109	0.109	strong	ASGR2,NS,carcinoma,0,1	ASGR2	38	1	NM_080912	exon5	c.A354C	p.G118G	GCTGCCTCCTGGA	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42631976	42631976	+	Silent	SNP	G	G	A	rs35039186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	119	102	0	0.983471	0	G|0.910;A|0.090	0.090	strong	GANC,brain,glioma,0,1	GANC	57	1	NM_198141	exon17	c.G1953A	p.K651K	CACCAAGCGACGA	.	PASS	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22067070	22067070	+	Silent	SNP	C	C	T	rs4076619	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	168	147	0	0.994083	0	A|0.000;C|0.871;G|0.000;T|0.129	0.129	strong	.	BMP1	131	.	NM_006129	exon19	c.C2688T	p.A896A	TGTGGCCGAGGAA	.	PASS	Atlas-SNP
APBA1	320	hgsc.bcm.edu	37	9	72131577	72131577	+	Missense_Mutation	SNP	A	A	C	rs34788368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	29	61	0	0.537037	0	A|0.828;C|0.172	0.172	strong	.	APBA1	96	.	NM_001163	exon2	c.T550G	p.S184A	GCTCGGAGTAGGG	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2048831	2048831	+	Missense_Mutation	SNP	A	A	G	rs968381	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	140	0	1	0	A|0.561;G|0.439	0.439	strong	MYOM2,NS,carcinoma,0,1	MYOM2	251	1	NM_003970	exon20	c.A2606G	p.N869S	CAGCCAACCGTTA	.	PASS	Atlas-SNP
ARL10	285598	hgsc.bcm.edu	37	5	175793532	175793532	+	Silent	SNP	C	C	T	rs2303666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	43	78	0	0.467391	0	C|0.894;T|0.106	0.106	strong	.	ARL10	19	.	NM_173664	exon2	c.C333T	p.G111G	CTGGGGCTTCAAC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20845521	20845521	+	Silent	SNP	A	A	C	rs2229101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	47	71	0	0.51087	0	A|0.936;C|0.064	0.064	strong	.	TEP1	224	.	NM_007110	exon41	c.T6006G	p.L2002L	GGACTGAAGGGAG	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206665052	206665052	+	Missense_Mutation	SNP	C	C	T	rs12059562	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	56	113	0	0.509091	0	C|0.864;T|0.136	0.136	strong	.	IKBKE	77	.	NM_001193322	exon18	c.C1805T	p.A602V	ATCAAGCGTCCTT	.	PASS	Atlas-SNP
PMVK	10654	hgsc.bcm.edu	37	1	154904840	154904840	+	Silent	SNP	T	T	C	rs1891805	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	72	154	0	0.461538	0	T|0.769;C|0.231	0.231	strong	.	PMVK	17	.	NM_006556	exon2	c.A147G	p.E49E	ATACTGTTCCTTG	.	PASS	Atlas-SNP
DUOXA1	90527	hgsc.bcm.edu	37	15	45409732	45409732	+	Missense_Mutation	SNP	C	C	G	rs61751061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	76	209	0	0.393782	0	C|0.819;G|0.181	0.181	strong	.	DUOXA1	32	.	NM_144565	exon11	c.G1433C	p.R478P	GTGTGGCGGGAGG	.	PASS	Atlas-SNP
GPANK1	7918	hgsc.bcm.edu	37	6	31630241	31630241	+	Silent	SNP	C	C	T	rs7992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	100	190	0	0.414938	0	C|0.620;T|0.380	0.380	strong	.	GPANK1	19	.	NM_001199238	exon4	c.G873A	p.R291R	CTGGTCCCTCTTG	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154525446	154525446	+	Silent	SNP	A	A	C	rs17030219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	75	135	0	0.559702	0	A|0.987;C|0.013	0.013	strong	.	KIAA0922	214	.	NM_001131007	exon25	c.A3282C	p.S1094S	AACTTCAGAGAAC	.	PASS	Atlas-SNP
AVPI1	60370	hgsc.bcm.edu	37	10	99439541	99439541	+	Missense_Mutation	SNP	G	G	C	rs2275047	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	78	176	0	0.503226	0	G|0.524;C|0.476	0.476	strong	AVPI1,NS,carcinoma,0,2	AVPI1	16	2	NM_021732	exon2	c.C122G	p.A41G	AACAGGGCTTGGA	.	PASS	Atlas-SNP
PDE5A	8654	hgsc.bcm.edu	37	4	120440278	120440278	+	Missense_Mutation	SNP	A	A	G	rs116396619	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	129	241	1	0.494253	0.00414938	A|0.996;G|0.004	0.004	strong	.	PDE5A	83	.	NM_001083	exon14	c.T1922C	p.L641P	ATCTCCAGGTCAG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8196499	8196499	+	Silent	SNP	G	G	A	rs3813774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	102	167	0	0.463636	0	G|0.878;A|0.122	0.122	strong	.	FBN3	300	.	NM_032447	exon14	c.C1929T	p.C643C	GGCACAGCAGCAC	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	33	54	0	0.478261	0	A|0.746;G|0.254	0.254	strong	.	AXIN1	290	.	NM_181050	exon7	c.T1827C	p.A609A	CGACTCAGCCTTC	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	99028811	99028811	+	Silent	SNP	G	G	A	rs79255841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	104	208	0	0.509804	0	G|0.976;A|0.024	0.024	strong	MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	NM_002380	exon11	c.G1617A	p.S539S	ACATTCGTGTGTA	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24652350	24652350	+	Silent	SNP	G	G	A	rs377303706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	72	138	0	0.529412	0	.	.	weak	.	IPO4	74	.	NM_024658	exon23	c.C2253T	p.V751V	TGGCACGACTCGG	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95603098	95603098	+	Silent	SNP	G	G	A	rs17023760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	91	166	0	0.505556	0	G|0.947;A|0.053	0.053	strong	.	FGD6	127	.	NM_018351	exon2	c.C1962T	p.L654L	GTCTCCGAGTTGG	.	PASS	Atlas-SNP
TAS2R40	259286	hgsc.bcm.edu	37	7	142919731	142919731	+	Missense_Mutation	SNP	C	C	A	rs10260248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	52	94	0	0.536082	0	C|0.932;A|0.068	0.068	strong	.	TAS2R40	64	.	NM_176882	exon1	c.C560A	p.S187Y	ACTTCTCTGAGAC	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	121929575	121929575	+	Silent	SNP	T	T	C	rs28453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	77	158	0	0.371981	0	T|0.797;C|0.203	0.203	strong	.	DBC1	194	.	NM_014618	exon8	c.A2073G	p.S691S	CATCACTGACGAA	.	PASS	Atlas-SNP
THNSL2	55258	hgsc.bcm.edu	37	2	88478341	88478341	+	Missense_Mutation	SNP	C	C	A	rs34136143	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	204	188	0	1	0	C|0.974;A|0.026	0.026	strong	.	THNSL2	66	.	NM_018271	exon4	c.C611A	p.T204N	TCAAGACTGTGTT	.	PASS	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55815159	55815159	+	Silent	SNP	C	C	A	rs17851415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	49	123	0	0.441441	0	C|0.936;A|0.064	0.064	strong	.	BRSK1	192	.	NM_032430	exon12	c.C1251A	p.T417T	ACCCACCCGACGG	.	PASS	Atlas-SNP
FSD2	123722	hgsc.bcm.edu	37	15	83428192	83428192	+	Missense_Mutation	SNP	C	C	T	rs1108134	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	86	0	0.450549	0	C|0.869;T|0.131	0.131	strong	.	FSD2	45	.	NM_001007122	exon13	c.G2158A	p.E720K	CAAATTCGTGAAG	.	PASS	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139916833	139916833	+	Silent	SNP	T	T	G	rs35590326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	94	132	2	0.630872	0.0151515	T|0.914;G|0.086	0.086	strong	ABCA2,NS,carcinoma,0,1	ABCA2	113	1	NM_212533	exon6	c.A627C	p.A209A	CAAGAGTGCTTGG	.	scavenged	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	172	159	0	0.988506	0	A|0.631;C|0.369	0.369	strong	.	FAM47C	267	.	NM_001013736	exon1	c.A2771C	p.N924T	TCCAGAATGCACC	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88396120	88396120	+	Silent	SNP	G	G	A	rs2919882	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	156	239	0	1	0	G|0.647;A|0.353	0.353	strong	.	SMYD1	95	.	NM_198274	exon6	c.G705A	p.E235E	AATTGAGCTCCGG	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32759183	32759183	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	3	190	1	0.015873	0.00526316	.	.	none	FRY,NS,carcinoma,-1,2	FRY	312	2	NM_023037	exon26	c.C3217T	p.R1073C	TTGACCCGCATGC	.	scavenged	Atlas-SNP
DDX53	168400	hgsc.bcm.edu	37	X	23019317	23019317	+	Missense_Mutation	SNP	G	G	T	rs5925720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	76	0	0.520548	0	G|0.902;T|0.098	0.098	strong	.	DDX53	76	.	NM_182699	exon1	c.G1143T	p.M381I	TAAAATGCTGGAT	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580967	140580967	+	Silent	SNP	T	T	G	rs149572646	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	392	48	256	0	0.122449	0	T|0.998;G|0.002	0.002	strong	.	PCDHB11	162	.	NM_018931	exon1	c.T1620G	p.A540A	CCCGGCTTTGAGC	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33605312	33605312	+	Missense_Mutation	SNP	T	T	C	rs10421769	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	79	0	1	0	T|0.380;C|0.620	0.620	strong	.	GPATCH1	79	.	NM_018025	exon15	c.T2183C	p.L728S	CAGAATTATCCGC	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	43	78	0	0.518072	0	G|0.618;T|0.382	0.382	strong	ATP13A5,NS,carcinoma,0,2	ATP13A5	171	2	NM_198505	exon3	c.C287A	p.S96Y	AGTGTGGATAAGT	.	PASS	Atlas-SNP
CFTR	1080	hgsc.bcm.edu	37	7	117282644	117282644	+	Silent	SNP	A	A	G	rs1800130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	29	89	0	0.345238	0	A|0.927;G|0.073	0.073	strong	.	CFTR	171	.	NM_000492	exon23	c.A3870G	p.P1290P	GATACCACAGGTG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3067278	3067278	+	Silent	SNP	A	A	G	rs2230164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	115	0	1	0	A|0.424;G|0.576	0.576	strong	MYOM1,colon,carcinoma,0,1	MYOM1	192	1	NM_003803	exon38	c.T5040C	p.G1680G	CTTGCCACCTTTC	.	PASS	Atlas-SNP
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	46	136	0	0.353846	0	0|0.003;G|0.509	0.509	strong	.	ZNF280C	63	.	NM_017666	exon15	c.A1851C	p.G617G	GTGAATTCCCCGA	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15532430	15532430	+	Silent	SNP	G	G	A	rs7225221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	142	269	0	0.438272	0	G|0.953;A|0.047	0.047	strong	.	TRIM16	45	.	NM_006470	exon9	c.C1194T	p.T398T	GGGCGTGGTGTTG	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53503934	53503934	+	Silent	SNP	G	G	A	rs1131220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	132	159	0	0.992481	0	G|0.461;A|0.539	0.539	strong	.	RBL2	115	.	NM_005611	exon15	c.G2082A	p.T694T	AGGGACGCCTGGG	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29886341	29886341	+	Silent	SNP	C	C	T	rs61744118	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	135	140	1	0.992647	0.00714286	C|0.990;T|0.010	0.010	strong	.	NEFH	178	.	NM_021076	exon4	c.C2712T	p.P904P	AGTCCCCACCCCA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158618320	158618320	+	Silent	SNP	G	G	A	rs34773716	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	53	82	0	0.6625	0	G|0.988;A|0.012	0.012	strong	SPTA1,NS,carcinoma,-2,1	SPTA1	720	1	NM_003126	exon26	c.C3693T	p.D1231D	TACGAGGTCCCTT	.	PASS	Atlas-SNP
CCDC116	164592	hgsc.bcm.edu	37	22	21988602	21988602	+	Missense_Mutation	SNP	C	C	T	rs861853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	19	31	0	0.475	0	C|0.817;T|0.183	0.183	strong	.	CCDC116	56	.	NM_152612	exon3	c.C364T	p.R122W	GGTGGACGGCGGG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28934681	28934681	+	Missense_Mutation	SNP	A	A	T	rs3752095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	95	162	0	0.5	0	A|0.864;T|0.136	0.136	strong	.	DSG1	176	.	NM_001942	exon15	c.A2522T	p.Y841F	AGTCTTACACCAC	.	PASS	Atlas-SNP
AIRE	326	hgsc.bcm.edu	37	21	45705988	45705988	+	Silent	SNP	T	T	C	rs3746964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	30	85	0	0.405405	0	T|0.716;C|0.284	0.284	strong	.	AIRE	61	.	NM_000383	exon1	c.T99C	p.A33A	GCTGGCTGACCAC	.	PASS	Atlas-SNP
RNF216	54476	hgsc.bcm.edu	37	7	5765034	5765034	+	Silent	SNP	C	C	T	rs77500990	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	79	144	0	0.526667	0	C|0.996;T|0.004	0.004	strong	.	RNF216	71	.	NM_207111	exon8	c.G1425A	p.L475L	TGGTGACAGCTCC	.	PASS	Atlas-SNP
PLA2G1B	5319	hgsc.bcm.edu	37	12	120762765	120762765	+	Silent	SNP	C	C	T	rs5637	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	260	273	0	0.996169	0	C|0.786;T|0.214	0.214	strong	.	PLA2G1B	8	.	NM_000928	exon3	c.G294A	p.S98S	AGAGCACGAGTAT	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117853022	117853022	+	Silent	SNP	C	C	T	rs944510	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	125	143	0	0.992063	0	C|0.530;T|0.470	0.470	strong	TNC,NS,carcinoma,0,1	TNC	282	1	NM_002160	exon2	c.G276A	p.V92V	CCCATCCACTGTG	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16979714	16979714	+	Missense_Mutation	SNP	T	T	C	rs41289305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	36	103	0	0.507042	0	T|0.874;C|0.126	0.126	strong	.	CUBN	515	.	NM_001081	exon39	c.A5803G	p.S1935G	TGGAGCTGAAAGA	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70800475	70800475	+	Missense_Mutation	SNP	C	C	T	rs3761966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	144	268	0	0.56917	0	C|0.667;T|0.333	0.333	strong	.	BDP1	204	.	NM_018429	exon16	c.C2269T	p.R757C	CAATCGCGTAAAG	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888048	52888048	+	Silent	SNP	G	G	A	rs324124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	22	41	0	0.564103	0	G|0.865;A|0.135	0.135	strong	.	ZNF880	45	.	NM_001145434	exon4	c.G1215A	p.E405E	GGGAGAGCAACCT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790868	4790868	+	Missense_Mutation	SNP	T	T	C	rs75972277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	33	83	0	0.39759	0	T|0.955;C|0.045	0.045	strong	.	OR51F1	60	.	NM_001004752	exon1	c.A280G	p.I94V	GACTGATTTCACG	.	PASS	Atlas-SNP
P2RX6	9127	hgsc.bcm.edu	37	22	21377301	21377301	+	Silent	SNP	C	C	A	rs1548411	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	163	176	1	1	0.00568182	C|0.383;A|0.617	0.617	strong	.	.	.	.	NM_005446	exon5	c.C534A	p.P178P	GTGCCCCGTGGAG	.	PASS	Atlas-SNP
DDX59	83479	hgsc.bcm.edu	37	1	200635560	200635560	+	Silent	SNP	T	T	C	rs3795633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	151	141	0	0.993421	0	T|0.871;C|0.129	0.129	strong	.	DDX59	117	.	NM_001031725	exon2	c.A309G	p.P103P	TTCCCCTGGTTCT	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704422	19704422	+	Missense_Mutation	SNP	T	T	A	rs8134187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	65	0	0.468354	0	T|0.954;A|0.046	0.046	strong	.	TMPRSS15	189	.	NM_002772	exon14	c.A1633T	p.S545C	GGTAGCTGTTTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511816	195511816	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	7	416	0	0.0242215	0	.	.	none	MUC4_ENST00000463781,bladder,carcinoma,+1,2	MUC4	1505	2	NM_018406	exon2	c.C6635A	p.T2212N	GGGCTGGTGACAG	.	scavenged	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	38	70	0	0.469136	0	A|0.597;G|0.403	0.403	strong	CD109,caecum,carcinoma,0,1	CD109	170	1	NM_133493	exon21	c.A2390G	p.N797S	CTTCAAATGAAAT	.	PASS	Atlas-SNP
DISP2	85455	hgsc.bcm.edu	37	15	40662501	40662501	+	Silent	SNP	G	G	A	rs4514650	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	31	48	0	0.462687	0	G|0.832;A|0.168	0.168	strong	.	DISP2	86	.	NM_033510	exon8	c.G4188A	p.T1396T	TCACACGTCAGGC	.	PASS	Atlas-SNP
ZNF7	7553	hgsc.bcm.edu	37	8	146068322	146068322	+	Silent	SNP	C	C	T	rs9004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	31	61	0	0.508197	0	C|0.716;T|0.284	0.284	strong	.	ZNF7	62	.	NM_003416	exon5	c.C1830T	p.Y610Y	GTTTTACGAATAT	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77079854	77079854	+	Silent	SNP	A	A	G	rs61729127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	46	63	0	0.541176	0	A|0.956;G|0.044	0.044	strong	.	ENGASE	55	.	NM_001042573	exon10	c.A1263G	p.V421V	GGCGGTAGGGCCC	.	PASS	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	720960	720960	+	Silent	SNP	C	C	T	rs3743912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	21	36	0	0.583333	0	C|0.824;T|0.176	0.176	strong	.	RHOT2	35	.	NM_138769	exon10	c.C708T	p.N236N	CAGGAACGTGGCG	.	PASS	Atlas-SNP
HAGH	3029	hgsc.bcm.edu	37	16	1869907	1869907	+	Silent	SNP	G	G	A	rs17849371	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	28	84	0	0.358974	0	G|0.958;A|0.042	0.042	strong	.	HAGH	20	.	NM_005326	exon4	c.C423T	p.S141S	CAGTGTGGACAGG	.	PASS	Atlas-SNP
C14orf80	283643	hgsc.bcm.edu	37	14	105957446	105957446	+	Missense_Mutation	SNP	G	G	A	rs76864584	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	91	117	0	0.541667	0	G|0.956;A|0.044	0.044	strong	.	C14orf80	19	.	NM_001134877	exon2	c.G7A	p.G3S	ATGTCCGGCCAGC	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	33	63	0	0.507692	0	G|0.855;A|0.145	0.145	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.G1519A	p.A507T	CTGGCCGCCTACC	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46969312	46969312	+	Missense_Mutation	SNP	G	G	A	rs55894256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	33	101	0	0.214286	0	G|0.950;A|0.050	0.050	strong	SYT15_ENST00000416127,NS,carcinoma,0,3	SYT15	165	3	NM_031912	exon2	c.C149T	p.T50I	GCAGCTGTGGTGG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248524974	248524974	+	Missense_Mutation	SNP	A	A	G	rs57795102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	800	387	775	1	0.48375	0.00129032	A|0.925;G|0.075	0.075	strong	OR2T4,NS,adenocarcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.A92G	p.N31S	TGGCCAATATCAC	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	12952293	12952293	+	Silent	SNP	C	C	T	rs658856	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	50	129	0	0.396825	0	C|0.888;T|0.112	0.112	strong	DLC1,caecum,carcinoma,-1,1	DLC1	411	1	NM_182643	exon12	c.G3501A	p.S1167S	GGTTTCCGAGAGT	.	PASS	Atlas-SNP
GGT7	2686	hgsc.bcm.edu	37	20	33451148	33451148	+	Silent	SNP	G	G	A	rs11546155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	96	228	0	0.422908	0	G|0.875;A|0.125	0.125	strong	GGT7,NS,carcinoma,0,2	GGT7	41	2	NM_178026	exon2	c.C373T	p.L125L	TGACCAGCGCCAC	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136507577	136507577	+	Silent	SNP	C	C	T	rs5322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	38	42	0	0.703704	0	C|0.978;T|0.022	0.022	strong	.	DBH	86	.	NM_000787	exon3	c.C735T	p.H245H	GCACCACATTATC	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	37	6	84856409	84856409	+	Silent	SNP	T	T	C	rs9449804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	25	65	0	0.462963	0	T|0.900;C|0.100	0.100	strong	.	KIAA1009	119	.	NM_014895	exon25	c.A3867G	p.K1289K	TACCTCTTTCTGT	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95953517	95953517	+	Missense_Mutation	SNP	G	G	T	rs11568681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	36	86	0	0.4	0	G|0.982;T|0.018	0.018	strong	.	ABCC4	248	.	NM_005845	exon1	c.C52A	p.L18I	AGCAGAGGTTCGC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152547268	152547268	+	Silent	SNP	G	G	A	rs373946448	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	91	164	0	0.535294	0	.	.	weak	.	NEB	1697	.	NM_004543	exon24	c.C2283T	p.A761A	GAGCTGGGCTTGC	.	PASS	Atlas-SNP
RBMXL3	139804	hgsc.bcm.edu	37	X	114424508	114424508	+	Silent	SNP	G	G	T	rs12848233	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	11	11	0	0.647059	0	G|0.915;T|0.085	0.085	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.G504T	p.S168S	GCCGTCGAGCCTG	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	140	29	0	0.809249	0	G|0.614;C|0.386	0.386	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.C663G	p.T221T	GACCTTGGTGCTG	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6094249	6094249	+	Missense_Mutation	SNP	C	C	T	rs62641242	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	82	128	0	0.532468	0	C|0.999;T|0.001	0.001	strong	.	VWF	338	.	NM_000552	exon40	c.G6938A	p.R2313H	TTCTGGCGGAGGC	.	PASS	Atlas-SNP
IL21R	50615	hgsc.bcm.edu	37	16	27460437	27460437	+	Missense_Mutation	SNP	G	G	A	rs3093386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	58	103	0	0.517857	0	G|0.962;A|0.038	0.038	strong	.	IL21R	95	.	NM_181079	exon10	c.G1516A	p.G506S	CTGGCCGGCCTGG	.	PASS	Atlas-SNP
ALDH3A2	224	hgsc.bcm.edu	37	17	19559770	19559770	+	Missense_Mutation	SNP	C	C	T	rs115977487	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	135	219	1	0.509434	0.00456621	C|0.990;T|0.010	0.010	strong	.	ALDH3A2	41	.	NM_001031806	exon4	c.C563T	p.A188V	ACACTGCGGTTGG	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22155629	22155629	+	Missense_Mutation	SNP	A	A	G	rs9937453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	149	279	0	0.498328	0	A|0.627;G|0.373	0.373	strong	VWA3A_ENST00000389398,NS,carcinoma,-1,2	VWA3A	115	2	NM_173615	exon26	c.A2654G	p.N885S	GTCCCAACTGCAC	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132628285	132628285	+	Silent	SNP	G	G	A	rs191101265	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	6	8	0	0.375	0	G|0.968;A|0.032	0.032	strong	.	DDX51	33	.	NM_175066	exon2	c.C474T	p.V158V	GCCGGGGACCAGG	.	PASS	Atlas-SNP
ZNF470	388566	hgsc.bcm.edu	37	19	57085769	57085769	+	Missense_Mutation	SNP	G	G	C	rs10421285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	123	0	1	0	G|0.566;C|0.434	0.434	strong	ZNF470,NS,carcinoma,0,1	ZNF470	103	1	NM_001001668	exon4	c.G67C	p.V23L	GGTTCAGTGACTT	.	PASS	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26092631	26092631	+	Silent	SNP	A	A	G	rs1060822	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	159	142	1	1	0.00704225	A|0.322;G|0.678	0.678	strong	.	NOS2	113	.	NM_000625	exon20	c.T2358C	p.G786G	CAGGATACCTTGG	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713608	32713608	+	Silent	SNP	G	G	A	rs199931222	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	57	436	0	0.133803	0	G|0.998;A|0.002	0.002	weak	HLA-DQA2,colon,carcinoma,+1,1	HLA-DQA2	27	1	NM_020056	exon3	c.G372A	p.T124T	TGTGACGCTGGGT	.	PASS	Atlas-SNP
TTPAL	79183	hgsc.bcm.edu	37	20	43117986	43117986	+	Missense_Mutation	SNP	C	C	G	rs59069332	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	83	125	0	0.576389	0	C|0.976;G|0.024	0.024	strong	.	TTPAL	31	.	NM_001039199	exon5	c.C833G	p.A278G	GCACGGCTGGGGA	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3432586	3432586	+	Silent	SNP	T	T	G	rs146006696	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	31	60	0	0.413333	0	T|0.988;G|0.012	0.012	strong	.	CSMD1	1469	.	NM_033225	exon10	c.A1225C	p.R409R	ATGTTCTCGCTGG	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62029006	62029006	+	Silent	SNP	A	A	G	rs79893125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	332	155	305	1	0.466867	0.00327869	A|0.936;G|0.064	0.064	strong	.	SCN4A	205	.	NM_000334	exon14	c.T2631C	p.D877D	CTTCTCATCCTCG	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	46	103	0	0.505495	0	C|0.485;T|0.515	0.515	strong	FANCA,NS,carcinoma,0,1	FANCA	99	1	NM_000135	exon26	c.G2426A	p.G809D	CCAGCACCAGGTG	.	PASS	Atlas-SNP
ZNF358	140467	hgsc.bcm.edu	37	19	7585762	7585762	+	Missense_Mutation	SNP	G	G	C	rs116797831	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	117	183	0	0.565217	0	G|0.977;C|0.023	0.023	strong	.	ZNF358	41	.	NM_018083	exon2	c.G1634C	p.S545T	CTGTCAGCCCAGC	.	PASS	Atlas-SNP
SLC26A6	65010	hgsc.bcm.edu	37	3	48664473	48664473	+	Missense_Mutation	SNP	C	C	T	rs59643945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	96	208	1	0.548571	0.00480769	C|0.962;T|0.038	0.038	strong	.	SLC26A6	45	.	NM_022911	exon18	c.G1909A	p.D637N	TCTTATCTCCTGA	.	PASS	Atlas-SNP
PRPF18	8559	hgsc.bcm.edu	37	10	13658436	13658436	+	Silent	SNP	G	G	A	rs11258476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	33	84	0	0.44	0	G|0.943;A|0.057	0.057	strong	.	PRPF18	32	.	NM_003675	exon9	c.G831A	p.A277A	AAATGCGCCTTGG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10470764	10470764	+	Missense_Mutation	SNP	T	T	G	rs75814156	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	13	48	0	0.325	0	T|0.984;G|0.016	0.016	strong	RP1L1,NS,carcinoma,+2,1	RP1L1	453	1	NM_178857	exon4	c.A844C	p.N282H	GGGGGTTGCTAGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412541	105412541	+	Missense_Mutation	SNP	C	C	T	rs12433837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	262	2	1	0.00763359	C|0.760;T|0.240	0.240	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G9247A	p.V3083I	CCTTGACATCTAT	.	PASS	Atlas-SNP
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	50	94	0	0.471698	0	A|0.655;C|0.345	0.345	strong	.	ENPP1	108	.	NM_006208	exon4	c.A517C	p.K173Q	AAGGACAAGGGCG	.	PASS	Atlas-SNP
REC8	9985	hgsc.bcm.edu	37	14	24647814	24647814	+	Silent	SNP	T	T	C	rs1885711	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	41	79	0	0.5125	0	T|0.305;C|0.695	0.695	strong	.	REC8	47	.	NM_001048205	exon13	c.T996C	p.P332P	ACAGCCTATGGTG	.	PASS	Atlas-SNP
TAAR2	9287	hgsc.bcm.edu	37	6	132938817	132938817	+	Silent	SNP	G	G	A	rs61745666	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	48	70	0	0.510638	0	A|0.164;G|0.836;T|0.000	0.164	strong	TAAR2,colon,carcinoma,0,1	TAAR2	45	1	NM_001033080	exon2	c.C528T	p.F176F	CACCCCGAAGGCA	.	PASS	Atlas-SNP
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	rs213227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	47	91	0	0.47	0	T|0.958;A|0.042	0.042	strong	.	ZKSCAN3	50	.	NM_024493	exon5	c.T738A	p.H246Q	GAACCATGGCAGC	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84230500	84230500	+	Silent	SNP	A	A	C	rs2303243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	165	180	2	0.993976	0.0111111	A|0.666;C|0.334	0.334	strong	ADAD2,NS,carcinoma,0,1	ADAD2	46	1	NM_139174	exon11	c.A1918C	p.R640R	GCTCGCAGGCAGC	.	scavenged	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45825818	45825818	+	Silent	SNP	C	C	T	rs17004645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	21	55	0	0.456522	0	C|0.993;T|0.007	0.007	strong	TRPM2,NS,carcinoma,+1,1	TRPM2	196	1	NM_003307	exon18	c.C2688T	p.R896R	CGGGCGCGTCATC	.	PASS	Atlas-SNP
TDP1	55775	hgsc.bcm.edu	37	14	90451500	90451500	+	Silent	SNP	A	A	G	rs17126522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	80	153	0	0.493827	0	A|0.938;G|0.062	0.062	strong	.	TDP1	47	.	NM_018319	exon10	c.A1077G	p.P359P	AACCCCAGGACGC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284344	152284344	+	Silent	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	568	29	546	2	0.0510563	0.003663	.	.	none	FLG,NS,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.A3018C	p.G1006G	AGGAGTTCCTGAT	.	scavenged	Atlas-SNP
BPIFC	254240	hgsc.bcm.edu	37	22	32843312	32843312	+	Silent	SNP	G	G	A	rs28733723	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	102	0	0.551282	0	G|0.968;A|0.032	0.032	strong	.	.	.	.	NM_174932	exon3	c.C261T	p.A87A	TGAAAAGGCACTG	.	PASS	Atlas-SNP
OGDH	4967	hgsc.bcm.edu	37	7	44747499	44747499	+	Silent	SNP	G	G	A	rs2070606	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	20	82	0	0.277778	0	G|0.856;A|0.144	0.144	strong	.	OGDH	145	.	NM_002541	exon23	c.G2973A	p.A991A	CCCAGCGGCTGCT	.	PASS	Atlas-SNP
NOXO1	124056	hgsc.bcm.edu	37	16	2030029	2030029	+	Silent	SNP	C	C	T	rs34358073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	46	74	0	0.560976	0	C|0.966;T|0.034	0.034	strong	.	NOXO1	13	.	NM_172168	exon5	c.G570A	p.E190E	CAGGCTCTCCTGG	.	PASS	Atlas-SNP
UBD	10537	hgsc.bcm.edu	37	6	29523670	29523670	+	Missense_Mutation	SNP	C	C	A	rs7757931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	84	149	0	0.509091	0	C|0.831;A|0.169	0.169	strong	.	UBD	13	.	NM_006398	exon2	c.G485T	p.C162F	CCAATACAATAAC	.	PASS	Atlas-SNP
ZMYND8	23613	hgsc.bcm.edu	37	20	45867852	45867852	+	Missense_Mutation	SNP	A	A	G	rs2275801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	23	29	0	1	0	A|0.741;C|0.002	.	strong	.	ZMYND8	166	.	NM_183047	exon15	c.T2315C	p.V772A	CTGCCCACCGTCG	.	PASS	Atlas-SNP
RPH3A	22895	hgsc.bcm.edu	37	12	113312971	113312971	+	Missense_Mutation	SNP	G	G	T	rs2189473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	41	63	0	0.594203	0	G|0.954;T|0.046	0.046	strong	.	RPH3A	98	.	NM_001143854	exon11	c.G879T	p.Q293H	TGGGCAGCCAGGT	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746107	143746107	+	Silent	SNP	C	C	T	rs61747165	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	38	25	0	0.730769	0	C|0.992;T|0.008	0.008	strong	.	.	.	.	NM_003724	exon2	c.G1371A	p.S457S	TGCTGGCGACGTG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512642	4512642	+	Missense_Mutation	SNP	T	T	C	rs60931060	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	51	203	1	0.277174	0.00492611	T|0.935;C|0.065	0.065	strong	PLIN4,NS,carcinoma,+2,1	PLIN4	191	1	NM_001080400	exon3	c.A1288G	p.M430V	AATTCATGGCACC	.	scavenged	Atlas-SNP
RASGRP3	25780	hgsc.bcm.edu	37	2	33774761	33774761	+	Silent	SNP	T	T	C	rs2276590	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	134	322	2	0.428115	0.00621118	T|0.872;C|0.128	0.128	strong	RASGRP3,NS,carcinoma,0,1	RASGRP3	87	1	NM_170672	exon15	c.T1485C	p.H495H	TATCCATAATTTT	.	scavenged	Atlas-SNP
ARHGAP17	55114	hgsc.bcm.edu	37	16	24942272	24942272	+	Missense_Mutation	SNP	T	T	A	rs111463480	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	76	161	0	0.424581	0	T|0.999;A|0.001	0.001	strong	.	ARHGAP17	138	.	NM_001006634	exon19	c.A2348T	p.N783I	TCAGGGTTACCCC	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7184518	7184518	+	Silent	SNP	G	G	A	rs891087	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	56	105	0	0.5	0	A|0.117;C|0.000;G|0.883;T|0.000	0.117	strong	.	INSR	265	.	NM_000208	exon3	c.C783T	p.D261D	CCTGCCGTCCAGG	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	49	81	0	0.644737	0	C|0.765;T|0.235	0.235	strong	.	USHBP1	85	.	NM_031941	exon10	c.G1573A	p.V525M	GGAGCACGTGAGC	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36350474	36350474	+	Missense_Mutation	SNP	G	G	A	rs34494265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	38	53	0	0.558824	0	G|0.982;A|0.018	0.018	strong	.	KIRREL2	170	.	NM_199180	exon5	c.G614A	p.R205Q	TCTGCCGGGCCCG	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20430678	20430678	+	Missense_Mutation	SNP	G	G	A	rs7192210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	219	169	1	1	0.00591716	G|0.904;A|0.096	0.096	strong	.	ACSM5	101	.	NM_017888	exon4	c.G544A	p.E182K	AGTGCCGAATGCC	.	PASS	Atlas-SNP
TTC4	7268	hgsc.bcm.edu	37	1	55188382	55188382	+	Silent	SNP	C	C	T	rs11550481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	46	102	0	0.46	0	C|0.892;T|0.108	0.108	strong	TTC4,NS,carcinoma,0,1	TTC4	21	1	NM_004623	exon5	c.C504T	p.A168A	CTTTGCCGAGGCC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78272294	78272294	+	Missense_Mutation	SNP	C	C	T	rs72849841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	54	146	0	0.375	0	C|0.869;T|0.131	0.131	strong	RNF213_ENST00000456466,colon,carcinoma,-1,3	RNF213	766	3	NM_001256071	exon11	c.C2186T	p.P729L	TCTCACCGTTCCG	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	37	11	33065394	33065394	+	Silent	SNP	C	C	T	rs1064005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	40	80	0	0.465116	0	C|0.583;T|0.417	0.417	strong	.	TCP11L1	40	.	NM_001145541	exon2	c.C75T	p.L25L	AGGCCTCGAAGAT	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133358984	133358984	+	Silent	SNP	A	A	G	rs76963006	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	107	234	0	0.532338	0	A|0.990;G|0.010	0.010	strong	.	GOLGA3	234	.	NM_005895	exon17	c.T3363C	p.L1121L	GCCCGTAAGCTTC	.	PASS	Atlas-SNP
ZNF618	114991	hgsc.bcm.edu	37	9	116812084	116812084	+	Silent	SNP	C	C	T	rs7856141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	24	91	0	0.328767	0	C|0.923;T|0.077	0.077	strong	.	ZNF618	184	.	NM_133374	exon14	c.C2223T	p.N741N	CATCAACGAGGTG	.	PASS	Atlas-SNP
RNF139	11236	hgsc.bcm.edu	37	8	125498547	125498547	+	Silent	SNP	C	C	T	rs3812471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	53	85	0	0.552083	0	C|0.445;T|0.555	0.555	strong	.	RNF139	57	.	NM_007218	exon2	c.C657T	p.Y219Y	AATTTACGGATTA	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116356549	116356549	+	Missense_Mutation	SNP	C	C	G	rs113405588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	42	75	0	0.583333	0	C|0.988;G|0.012	0.012	strong	.	RGS3	251	.	NM_144489	exon1	c.C350G	p.P117R	GGGGCCCTACAGA	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	319	151	317	0	0.473354	0	T|0.667;C|0.333	0.333	strong	.	OR2D3	51	.	NM_001004684	exon1	c.T720C	p.T240T	CTCCACTGTTATC	.	PASS	Atlas-SNP
SYTL5	94122	hgsc.bcm.edu	37	X	37967868	37967868	+	Silent	SNP	T	T	C	rs5918476	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	172	384	0	0.492837	0	T|0.570;C|0.430	0.430	strong	.	SYTL5	72	.	NM_001163334	exon12	c.T1416C	p.Y472Y	GTCATATCTTCTT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467130	10467130	+	Missense_Mutation	SNP	G	G	A	rs138261433	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	24	36	0	0.5	0	G|0.998;A|0.002	0.002	strong	.	RP1L1	453	.	NM_178857	exon4	c.C4478T	p.A1493V	GGTTGGGCCTGCG	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002710	36002710	+	Silent	SNP	C	C	A	rs4806162	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	120	193	0	0.487805	0	C|0.766;A|0.234	0.234	strong	.	DMKN	116	.	NM_001190347	exon4	c.G690T	p.T230T	GGGATTCGTGCAC	.	PASS	Atlas-SNP
OR5J2	282775	hgsc.bcm.edu	37	11	55944501	55944501	+	Missense_Mutation	SNP	G	G	C	rs12279899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	193	316	0	0.453052	0	G|0.979;C|0.021	0.021	strong	.	OR5J2	98	.	NM_001005492	exon1	c.G408C	p.M136I	AGCCATGTCTGAT	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	78	164	0	0.450867	0	T|0.566;C|0.434	0.434	strong	.	NUP88	47	.	NM_002532	exon16	c.A2157G	p.K719K	CTCCTCTTTCAGG	.	PASS	Atlas-SNP
ARHGEF17	9828	hgsc.bcm.edu	37	11	73078685	73078685	+	Missense_Mutation	SNP	G	G	A	rs143114785	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	72	0	0.528571	0	G|0.991;A|0.009	0.009	strong	.	ARHGEF17	117	.	NM_014786	exon21	c.G6052A	p.A2018T	GGCCCCGCCCCTG	.	PASS	Atlas-SNP
FOXN4	121643	hgsc.bcm.edu	37	12	109717697	109717697	+	Silent	SNP	A	A	G	rs10774641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	32	60	0	0.571429	0	A|0.660;G|0.340	0.340	strong	.	FOXN4	74	.	NM_213596	exon10	c.T1333C	p.L445L	TGTCCAAGCTGAA	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131622735	131622735	+	Silent	SNP	T	T	C	rs7302341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	21	34	0	0.403846	0	T|0.416;C|0.584	0.584	strong	.	GPR133	136	.	NM_198827	exon24	c.T2490C	p.S830S	CAGCTCTGCCCGC	.	PASS	Atlas-SNP
AATK	9625	hgsc.bcm.edu	37	17	79095629	79095629	+	Missense_Mutation	SNP	C	C	A	rs7503604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	20	4	0	1	0	C|0.463;A|0.537	0.537	strong	AATK_ENST00000326724,NS,carcinoma,0,2	AATK	102	2	NM_001080395	exon11	c.G2107T	p.G703C	CGTGGCCGCCCGC	.	PASS	Atlas-SNP
FZD3	7976	hgsc.bcm.edu	37	8	28413375	28413375	+	Silent	SNP	C	C	T	rs62001924	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	58	124	0	0.58	0	C|0.984;T|0.016	0.016	strong	.	FZD3	65	.	NM_017412	exon7	c.C1674T	p.T558T	ATCCACCCATGCT	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47086978	47086978	+	Silent	SNP	G	G	A	rs3740294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	386	89	316	0	0.23057	0	G|0.852;A|0.148	0.148	strong	.	PPYR1	54	.	NM_005972	exon3	c.G195A	p.V65V	GTGTGTGACTGTG	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921132	12921132	+	Missense_Mutation	SNP	A	A	G	rs12139550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	103	192	0	0.413655	0	A|0.890;G|0.110	0.110	strong	.	PRAMEF2	85	.	NM_023014	exon4	c.A923G	p.E308G	TAGAAGAGGACTT	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1542697	1542697	+	Silent	SNP	G	G	A	rs3752714	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	137	147	0	1	0	G|0.412;A|0.588	0.588	strong	INTS1,NS,carcinoma,0,1	INTS1	145	1	NM_001080453	exon3	c.C189T	p.A63A	CAACGCGGCCGCC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179586779	179586779	+	Silent	SNP	A	A	G	rs16866469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	58	123	0	0.483333	0	A|0.982;G|0.018	0.018	strong	.	TTN	18412	.	NM_001267550	exon78	c.T22611C	p.H7537H	AGTAACATGACAC	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184573555	184573555	+	Silent	SNP	C	C	T	rs6443999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	77	127	0	0.531034	0	C|0.471;T|0.529	0.529	strong	.	VPS8	109	.	NM_001009921	exon13	c.C1092T	p.Y364Y	AAATTACGTGAAT	.	PASS	Atlas-SNP
RABGGTA	5875	hgsc.bcm.edu	37	14	24736027	24736027	+	Silent	SNP	G	G	A	rs14193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	97	244	0	0.419913	0	T|0.000;G|0.465;A|0.534	0.534	strong	.	RABGGTA	43	.	NM_004581	exon14	c.C1422T	p.R474R	TCGGAGGCGATTG	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	40	74	0	0.588235	0	C|0.971;T|0.029	0.029	strong	.	TH	43	.	NM_199292	exon3	c.G279A	p.S93S	GGGCTCCGAGGGG	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3418391	3418391	+	Silent	SNP	C	C	T	rs4648508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	118	194	0	0.47012	0	C|0.703;T|0.297	0.297	strong	MEGF6,colon,carcinoma,0,2	MEGF6	91	2	NM_001409	exon18	c.G2283A	p.P761P	CCCCGGCGGACAC	.	PASS	Atlas-SNP
OR9A2	135924	hgsc.bcm.edu	37	7	142724062	142724062	+	Missense_Mutation	SNP	C	C	T	rs9885986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	73	160	0	0.445122	0	C|0.909;T|0.091	0.091	strong	.	OR9A2	52	.	NM_001001658	exon1	c.G158A	p.R53H	TGCAGACGTTTAT	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85402610	85402610	+	Silent	SNP	G	G	A	rs34122391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	77	0	0.485437	0	G|0.941;A|0.059	0.059	strong	.	ALPK3	289	.	NM_020778	exon7	c.G4560A	p.E1520E	GGGCGAGGTGGGC	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55450746	55450746	+	Missense_Mutation	SNP	C	C	T	rs61747414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	31	117	0	0.392405	0	C|0.893;T|0.107	0.107	strong	NLRP7_ENST00000328092,NS,carcinoma,+1,2	NLRP7	411	2	NM_001127255	exon4	c.G1441A	p.A481T	CCAGGGCGTAGAA	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124846788	124846788	+	Missense_Mutation	SNP	G	G	C	rs11057592	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	16	41	0	0.380952	0	G|0.973;C|0.027	0.027	strong	.	NCOR2	475	.	NM_006312	exon24	c.C2984G	p.A995G	GGGGGAGCTGGCT	.	PASS	Atlas-SNP
GM2A	2760	hgsc.bcm.edu	37	5	150632832	150632832	+	Missense_Mutation	SNP	G	G	A	rs1048719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	28	49	0	0.424242	0	G|0.952;A|0.048	0.048	strong	.	GM2A	24	.	NM_001167607	exon1	c.G55A	p.A19T	CTCGCGGCCCCTG	.	PASS	Atlas-SNP
QRFP	347148	hgsc.bcm.edu	37	9	133768921	133768921	+	Missense_Mutation	SNP	G	G	A	rs140393161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	38	98	0	0.361905	0	G|0.999;A|0.001	0.001	strong	.	QRFP	14	.	NM_198180	exon1	c.C305T	p.P102L	GCAGCAGGGAGGA	.	PASS	Atlas-SNP
POLR2A	5430	hgsc.bcm.edu	37	17	7412349	7412349	+	Silent	SNP	G	G	A	rs2228134	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	135	262	1	0.537849	0.00381679	G|0.935;A|0.065	0.065	strong	POLR2A,colon,carcinoma,+1,1	POLR2A	157	1	NM_000937	exon21	c.G3552A	p.T1184T	GAGCACGGTGGTG	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121414061	121414061	+	Missense_Mutation	SNP	C	C	T	rs1127412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	138	227	0	0.509225	0	C|0.760;T|0.240	0.240	strong	.	GOLGB1	319	.	NM_001256486	exon13	c.G5309A	p.G1770D	ACATTACCTTCTA	.	PASS	Atlas-SNP
DAGLB	221955	hgsc.bcm.edu	37	7	6461424	6461424	+	Silent	SNP	C	C	T	rs836515	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	47	71	0	0.566265	0	C|0.946;T|0.054	0.054	strong	.	DAGLB	74	.	NM_139179	exon9	c.G1152A	p.T384T	CAGGTCCGTAAGG	.	PASS	Atlas-SNP
KRT71	112802	hgsc.bcm.edu	37	12	52946498	52946498	+	Missense_Mutation	SNP	C	C	T	rs665470	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	117	217	0	0.50431	0	C|0.774;N|0.000	.	strong	.	KRT71	70	.	NM_033448	exon1	c.G364A	p.E122K	GGATCTCGGGGTC	.	PASS	Atlas-SNP
RICTOR	253260	hgsc.bcm.edu	37	5	38960006	38960006	+	Silent	SNP	G	G	A	rs73751814	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	82	136	0	0.518987	0	G|0.993;A|0.007	0.007	strong	.	RICTOR	182	.	NM_152756	exon21	c.C1926T	p.P642P	TCTTTCGGGTTTC	.	PASS	Atlas-SNP
B3GNT4	79369	hgsc.bcm.edu	37	12	122691058	122691058	+	Missense_Mutation	SNP	T	T	C	rs35203505	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	82	194	0	0.438503	0	T|0.944;C|0.056	0.056	strong	.	B3GNT4	35	.	NM_030765	exon3	c.T260C	p.L87P	CCTCTCTGTCCCT	.	PASS	Atlas-SNP
SLC38A3	10991	hgsc.bcm.edu	37	3	50257389	50257389	+	Silent	SNP	G	G	A	rs35742391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	101	180	0	0.531579	0	G|0.914;A|0.086	0.086	strong	.	SLC38A3	22	.	NM_006841	exon15	c.G1383A	p.E461E	GAAGGAGCCTGCA	.	PASS	Atlas-SNP
TMEM37	140738	hgsc.bcm.edu	37	2	120194673	120194673	+	Missense_Mutation	SNP	G	G	A	rs114197773	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	25	38	0	0.462963	0	G|0.973;A|0.027	0.027	strong	.	TMEM37	40	.	NM_183240	exon2	c.G230A	p.G77D	ACCTGGGCCAGGC	.	PASS	Atlas-SNP
SORBS2	8470	hgsc.bcm.edu	37	4	186573817	186573817	+	Silent	SNP	C	C	T	rs61732192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	75	174	1	0.503356	0.00574713	C|0.984;T|0.016	0.016	strong	SORBS2_ENST00000448662,NS,carcinoma,-1,4	SORBS2	300	4	NM_001145673	exon8	c.G870A	p.P290P	CATACCCGGCTTG	.	scavenged	Atlas-SNP
TCEAL3	85012	hgsc.bcm.edu	37	X	102864251	102864251	+	Missense_Mutation	SNP	C	C	G	rs12009847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	389	379	379	1	0.974293	0.00263852	C|0.936;G|0.064	0.064	strong	.	TCEAL3	24	.	NM_001006933	exon3	c.C259G	p.Q87E	GCCTCCCAGGCAA	.	PASS	Atlas-SNP
C18orf56	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	15	17	0	0.46875	0	G|0.684;C|0.316	0.316	strong	.	C18orf56	2	.	NM_001012716	exon1	c.C184G	p.R62G	TCCTGCGAGGGAG	.	PASS	Atlas-SNP
AJUBA	84962	hgsc.bcm.edu	37	14	23444247	23444247	+	Silent	SNP	G	G	A	rs10130692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	49	60	0	0.604938	0	G|0.955;A|0.045	0.045	strong	.	.	.	.	NM_032876	exon5	c.C1306T	p.L436L	CATCCAGGCACTT	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579182	55579182	+	Silent	SNP	A	A	G	rs139708815	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	12	211	0	0.0588235	0	A|1.000;G|0.000	0.000	strong	OR5L1,NS,carcinoma,0,3	OR5L1	145	3	NM_001004738	exon1	c.A240G	p.K80K	GCCAAAAATGTTG	.	PASS	Atlas-SNP
CCNJL	79616	hgsc.bcm.edu	37	5	159707731	159707731	+	Silent	SNP	G	G	A	rs76732875	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	55	0	0.509091	0	G|0.959;A|0.041	0.041	strong	.	CCNJL	36	.	NM_024565	exon3	c.C81T	p.P27P	GAAGGTGGGCAGC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585122	43585122	+	Missense_Mutation	SNP	C	C	T	rs143255979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	160	247	1	0.519481	0.00404858	C|0.978;T|0.022	0.022	strong	.	PSG2	84	.	NM_031246	exon2	c.G341A	p.R114Q	TCCTCCCGGGTGA	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148768130	148768130	+	Silent	SNP	T	T	C	rs16861365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	84	157	0	0.521739	0	T|0.956;C|0.044	0.044	strong	.	HLTF	87	.	NM_139048	exon15	c.A1506G	p.V502V	CAAGTGTACATCT	.	PASS	Atlas-SNP
TRIM36	55521	hgsc.bcm.edu	37	5	114482847	114482847	+	Silent	SNP	T	T	C	rs12109197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	459	209	466	1	0.455338	0.00214592	T|0.998;C|0.002	0.002	strong	.	TRIM36	126	.	NM_018700	exon3	c.A543G	p.E181E	GAAGCATTCATTG	.	PASS	Atlas-SNP
DLAT	1737	hgsc.bcm.edu	37	11	111908137	111908137	+	Missense_Mutation	SNP	G	G	A	rs116125936	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	21	97	0	0.328125	0	G|0.992;A|0.008	0.008	strong	.	DLAT	39	.	NM_001931	exon6	c.G928A	p.E310K	CCAACCGAAGTAA	.	PASS	Atlas-SNP
ATAT1	79969	hgsc.bcm.edu	37	6	30610758	30610758	+	Missense_Mutation	SNP	G	G	T	rs150614928	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	74	142	0	0.573643	0	G|0.988;T|0.012	0.012	strong	.	ATAT1	30	.	NM_024909	exon10	c.G938T	p.G313V	ACCCTGGGGGCAG	.	PASS	Atlas-SNP
DTNBP1	84062	hgsc.bcm.edu	37	6	15533469	15533469	+	Splice_Site	SNP	G	G	A	rs61739410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	45	79	0	0.45	0	G|0.969;A|0.031	0.031	strong	.	DTNBP1	56	.	NM_032122	exon9	c.667+2C>T	.	CCACTCGCCTCGC	.	PASS	Atlas-SNP
MRPL47	57129	hgsc.bcm.edu	37	3	179306775	179306775	+	Missense_Mutation	SNP	C	C	T	rs10513762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	128	1	1	0.0078125	C|0.903;T|0.097	0.097	strong	MRPL47,NS,carcinoma,0,1	MRPL47	31	1	NM_020409	exon7	c.G638A	p.R213H	TTCTCACGTTCCA	.	PASS	Atlas-SNP
C1orf173	127254	hgsc.bcm.edu	37	1	75038963	75038963	+	Missense_Mutation	SNP	C	C	A	rs75061423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	60	121	0	0.47619	0	A|0.022;C|0.978	0.022	strong	.	C1orf173	380	.	NM_001002912	exon14	c.G2431T	p.A811S	TCCACGCCCTCAA	.	PASS	Atlas-SNP
PACS2	23241	hgsc.bcm.edu	37	14	105848891	105848891	+	Silent	SNP	T	T	C	rs4076933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	120	0	1	0	T|0.861;C|0.139	0.139	strong	.	PACS2	75	.	NM_001100913	exon14	c.T1491C	p.L497L	CATCCTTGTCAAC	.	PASS	Atlas-SNP
ITGAV	3685	hgsc.bcm.edu	37	2	187490232	187490232	+	Silent	SNP	G	G	A	rs114767222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	33	95	0	0.388235	0	G|0.992;A|0.008	0.008	strong	.	ITGAV	124	.	NM_001145000	exon4	c.G441A	p.E147E	AACTGAGATGAAA	.	PASS	Atlas-SNP
HTR2A	3356	hgsc.bcm.edu	37	13	47469940	47469940	+	Silent	SNP	G	G	A	rs6313	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	61	0	1	0	G|0.581;A|0.419	0.419	strong	.	HTR2A	98	.	NM_000621	exon2	c.C102T	p.S34S	TTCTCCGGAGTTA	.	PASS	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	51	98	0	0.404762	0	0|0.029;C|0.421	0.421	strong	.	MAGEB10	107	.	NM_182506	exon3	c.T149C	p.F50S	ATGTTTTCCAGAG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444588	20444588	+	Missense_Mutation	SNP	T	T	C	rs2153466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	235	171	0	1	0	T|0.613;C|0.387	0.387	strong	.	OR4K15	82	.	NM_001005486	exon1	c.T911C	p.L304P	TCACGCTTATTTT	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	66	71	0	0.545455	0	G|0.772;A|0.228	0.228	strong	TECPR1,colon,carcinoma,0,1	TECPR1	77	1	NM_015395	exon25	c.C3348T	p.H1116H	GGGCTCGTGAGGC	.	PASS	Atlas-SNP
ZNF611	81856	hgsc.bcm.edu	37	19	53209553	53209553	+	Missense_Mutation	SNP	G	G	A	rs75841962		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	107	185	1	0.554404	0.00540541	.	.	weak	ZNF611,NS,carcinoma,0,1	ZNF611	72	1	NM_030972	exon7	c.C755T	p.P252L	AAATGGGGTATCT	.	PASS	Atlas-SNP
RBCK1	10616	hgsc.bcm.edu	37	20	398175	398175	+	Missense_Mutation	SNP	G	G	C	rs143804674	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	54	85	0	0.574468	0	G|1.000;C|0.000	0.000	strong	.	RBCK1	38	.	NM_031229	exon3	c.G173C	p.W58S	GGCTGTGGGTGAG	.	PASS	Atlas-SNP
NPFFR2	10886	hgsc.bcm.edu	37	4	73012709	73012709	+	Missense_Mutation	SNP	T	T	C	rs61733659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	42	84	0	0.488372	0	T|0.990;C|0.010	0.010	strong	.	NPFFR2	98	.	NM_004885	exon4	c.T749C	p.V250A	GTGTGGTCTACCC	.	PASS	Atlas-SNP
SOWAHA	134548	hgsc.bcm.edu	37	5	132150804	132150804	+	Silent	SNP	G	G	A	rs7719416	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	78	0	0.485437	0	G|0.965;A|0.035	0.035	strong	.	.	.	.	NM_175873	exon1	c.G1491A	p.K497K	CTTGAAGAAGTCG	.	PASS	Atlas-SNP
LRRC36	55282	hgsc.bcm.edu	37	16	67409180	67409180	+	Missense_Mutation	SNP	G	G	A	rs8052655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	24	40	0	0.521739	0	G|0.790;A|0.210	0.210	strong	.	LRRC36	68	.	NM_018296	exon10	c.G1525A	p.G509S	TTGCACGGTTTGG	.	PASS	Atlas-SNP
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138713674	138713674	+	Silent	SNP	C	C	G	rs7800990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	93	0	0.551282	0	C|0.961;G|0.039	0.039	strong	.	ZC3HAV1L	15	.	NM_080660	exon3	c.G534C	p.L178L	GCCATACAGGGCT	.	PASS	Atlas-SNP
GNAI1	2770	hgsc.bcm.edu	37	7	79828573	79828573	+	Silent	SNP	A	A	G	rs6970347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	40	122	0	0.512821	0	A|0.982;G|0.018	0.018	strong	.	GNAI1	44	.	NM_002069	exon4	c.A336G	p.G112G	AGCTGGAGCTGCT	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123894329	123894329	+	Missense_Mutation	SNP	C	C	G	rs79417294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	513	280	475	0	0.545809	0	C|0.948;G|0.052	0.052	strong	OR10G9,NS,carcinoma,0,1	OR10G9	80	1	NM_001001953	exon1	c.C610G	p.L204V	ATTGGGCTAGTGG	.	PASS	Atlas-SNP
KRT38	8687	hgsc.bcm.edu	37	17	39594356	39594356	+	Silent	SNP	G	G	A	rs28550887	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	81	189	0	0.462857	0	G|0.934;A|0.066	0.066	strong	.	KRT38	63	.	NM_006771	exon6	c.C1230T	p.S410S	GTCCTCGCTTTCC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895842	1895842	+	Silent	SNP	T	T	C	rs17853847	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	9	219	0	0.0681818	0	T|0.881;C|0.119	0.119	strong	.	SIRPA	83	.	NM_001040022	exon3	c.T177C	p.S59S	GACCTCTCTGATC	.	PASS	Atlas-SNP
FBXO41	150726	hgsc.bcm.edu	37	2	73490412	73490412	+	Silent	SNP	A	A	G	rs34363861	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	52	0	1	0	A|0.461;G|0.539	0.539	strong	.	FBXO41	82	.	NM_001080410	exon8	c.T2100C	p.H700H	GACCTCATGGCCC	.	PASS	Atlas-SNP
LRRC47	57470	hgsc.bcm.edu	37	1	3701663	3701663	+	Silent	SNP	T	T	C	rs2298227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	62	129	0	0.455882	0	T|0.882;C|0.118	0.118	strong	.	LRRC47	42	.	NM_020710	exon3	c.A1182G	p.P394P	GTCCTGTGGGGGC	.	PASS	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38829702	38829702	+	Missense_Mutation	SNP	C	C	T	rs5743816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	80	207	0	0.379147	0	C|0.931;T|0.069	0.069	strong	.	TLR6	67	.	NM_006068	exon2	c.G1393A	p.V465I	TAGGAACGCTCTT	.	PASS	Atlas-SNP
AFAP1L2	84632	hgsc.bcm.edu	37	10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	rs73365341	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	49	40	0	1	0	G|0.884;A|0.116	0.116	strong	.	AFAP1L2	90	.	NM_032550	exon11	c.C1234T	p.L412F	AGTAGAGGTGGTC	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124135009	124135009	+	Missense_Mutation	SNP	G	G	A	rs2512168	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	168	203	0	0.994083	0	G|0.507;A|0.493	0.493	strong	.	.	.	.	NM_001005198	exon1	c.G287A	p.C96Y	TGTACTGTTTCCT	.	PASS	Atlas-SNP
OR6K6	128371	hgsc.bcm.edu	37	1	158725080	158725080	+	Missense_Mutation	SNP	C	C	T	rs16841001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	87	143	0	0.564935	0	C|0.885;T|0.115	0.115	strong	.	OR6K6	81	.	NM_001005184	exon1	c.C475T	p.R159C	CCACTCCGTTACC	.	PASS	Atlas-SNP
NOV	4856	hgsc.bcm.edu	37	8	120429024	120429024	+	Missense_Mutation	SNP	G	G	A	rs2279112	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	7	7	0	0.538462	0	G|0.709;A|0.291	0.291	strong	.	NOV	51	.	NM_002514	exon2	c.G125A	p.R42Q	CGGGCCGGTGCCC	.	PASS	Atlas-SNP
ZNF610	162963	hgsc.bcm.edu	37	19	52869534	52869534	+	Silent	SNP	G	G	A	rs162119	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	96	104	1	0.989691	0.00961538	A|0.826;G|0.174	0.826	strong	ZNF610,NS,carcinoma,0,1	ZNF610	84	1	NM_001161426	exon6	c.G903A	p.S301S	GTGTTCGGGACTT	.	PASS	Atlas-SNP
GBP5	115362	hgsc.bcm.edu	37	1	89735229	89735229	+	Missense_Mutation	SNP	C	C	G	rs17130763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	72	142	0	0.525547	0	C|0.976;G|0.024	0.024	strong	.	GBP5	65	.	NM_052942	exon3	c.G10C	p.E4Q	GGATCTCTAAAGC	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107547872	107547872	+	Silent	SNP	C	C	T	rs61741359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	54	70	0	0.760563	0	C|0.985;T|0.015	0.015	strong	.	ABCA1	244	.	NM_005502	exon49	c.G6450A	p.P2150P	CAGGTCCGGGTTG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47925609	47925609	+	Silent	SNP	G	G	A	rs78480673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	65	115	0	0.507812	0	G|0.951;A|0.049	0.049	strong	PKD1L1,NS,carcinoma,0,2	PKD1L1	328	2	NM_138295	exon18	c.C2880T	p.L960L	GGCACCGAGTCCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681303	100681303	+	Silent	SNP	T	T	C	rs143516283		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	13	109	0	0.077381	0	.	.	weak	MUC17,rectum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.T6606C	p.P2202P	ATCTCCTACAACT	.	scavenged	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18376780	18376780	+	Missense_Mutation	SNP	T	T	C	rs12462974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	83	127	0	0.542484	0	T|0.861;C|0.139	0.139	strong	.	KIAA1683	190	.	NM_001145304	exon3	c.A1570G	p.T524A	CCACTGTTGGAGA	.	PASS	Atlas-SNP
CRNKL1	51340	hgsc.bcm.edu	37	20	20033194	20033194	+	Silent	SNP	G	G	T	rs145198573	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	68	0	0.486842	0	G|0.996;T|0.004	0.004	strong	.	CRNKL1	101	.	NM_016652	exon2	c.C276A	p.R92R	CTCCTTGCGGCAG	.	PASS	Atlas-SNP
ANKRD34B	340120	hgsc.bcm.edu	37	5	79854667	79854667	+	Missense_Mutation	SNP	A	A	G	rs147745221	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	34	46	0	0.596491	0	A|0.999;G|0.001	0.001	strong	.	ANKRD34B	61	.	NM_001004441	exon5	c.T1172C	p.I391T	TTTCCTATAAGTG	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9886988	9886988	+	Missense_Mutation	SNP	C	C	T	rs34812912	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	58	153	0	0.464	0	C|0.940;T|0.060	0.060	strong	.	TXNDC2	168	.	NM_001098529	exon2	c.C512T	p.P171L	TGAAGCCCAGCCA	.	PASS	Atlas-SNP
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	48	41	0	1	0	G|0.682;A|0.318	0.318	strong	.	SLC46A2	30	.	NM_033051	exon1	c.C126T	p.L42L	CACCACGAGGAGT	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176198	57176198	+	Silent	SNP	T	T	G	rs8108756	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	82	0	0.487805	0	T|0.587;G|0.413	0.413	strong	.	ZNF835	106	.	NM_001005850	exon2	c.A369C	p.S123S	GAACGCTGAACAG	.	PASS	Atlas-SNP
XKR3	150165	hgsc.bcm.edu	37	22	17288849	17288849	+	Missense_Mutation	SNP	A	A	G	rs150400922	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	94	185	0	0.449761	0	A|0.996;G|0.004	0.004	strong	.	XKR3	51	.	NM_175878	exon2	c.T115C	p.F39L	TTGAGAAGATAAT	.	PASS	Atlas-SNP
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	141	0	1	0	T|0.696;C|0.304	0.304	strong	.	BRAF	36346	.	NM_004333	exon16	c.A1929G	p.G643G	AACAATTCCAAAT	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15807830	15807830	+	Silent	SNP	T	T	C	rs593421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	149	140	0	0.605691	0	T|0.770;C|0.230	0.230	strong	.	CYP4F12	89	.	NM_023944	exon13	c.T1510C	p.L504L	CTGGAATTGATCA	.	PASS	Atlas-SNP
HOGA1	112817	hgsc.bcm.edu	37	10	99371344	99371344	+	Silent	SNP	C	C	A	rs12261752	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	50	96	0	0.462963	0	C|0.700;A|0.300	0.300	strong	HOGA1,colon,carcinoma,+2,1	HOGA1	25	1	NM_138413	exon7	c.C912A	p.A304A	CCGCGCCCCCTTG	.	PASS	Atlas-SNP
LETM1	3954	hgsc.bcm.edu	37	4	1834666	1834666	+	Silent	SNP	T	T	C	rs140729898	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	108	233	1	0.497696	0.00429185	T|0.977;C|0.023	0.023	strong	.	LETM1	48	.	NM_012318	exon6	c.A885G	p.E295E	CCCTGTTTCCCGG	.	PASS	Atlas-SNP
C7orf55-LUC7L2	100996928	hgsc.bcm.edu	37	7	139090515	139090515	+	Silent	SNP	A	A	G	rs74758604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	62	139	0	0.466165	0	A|0.981;G|0.019	0.019	strong	LUC7L2,NS,carcinoma,+2,1	.	.	1	NM_001244584	exon6	c.A690G	p.A230A	ACGGGCAAAGAAA	.	PASS	Atlas-SNP
PCED1B	91523	hgsc.bcm.edu	37	12	47629368	47629368	+	Silent	SNP	G	G	T	rs2244818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	19	31	0	0.463415	0	G|0.835;T|0.165	0.165	strong	.	.	.	.	NM_138371	exon2	c.G522T	p.G174G	CACCGGGGGTTTT	.	PASS	Atlas-SNP
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	52	144	0	0.379562	0	G|0.546;A|0.454	0.454	strong	.	PRTN3	9	.	NM_002777	exon3	c.G355A	p.V119I	AACGACGTTCTCC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	11	274	6	0.0376712	0.0218978	.	.	none	PSG2,NS,carcinoma,0,2	PSG2	84	2	NM_031246	exon2	c.G210A	p.G70G	GATTTGCCCTTTG	.	scavenged	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	93	0	0.45614	0	G|0.914;A|0.086	0.086	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C2090T	p.A697V	AGGGGCGCTGCCA	.	PASS	Atlas-SNP
MKRN1	23608	hgsc.bcm.edu	37	7	140158960	140158960	+	Silent	SNP	G	G	A	rs61736379	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	125	198	0	0.480769	0	G|0.993;A|0.007	0.007	strong	.	MKRN1	35	.	NM_013446	exon4	c.C618T	p.A206A	CTCCACGGCGGTT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17250836	17250836	+	Silent	SNP	A	A	G	rs57174186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	31	52	0	0.303922	0	A|0.638;G|0.362	0.362	strong	CROCC,NS,carcinoma,0,3	CROCC	185	3	NM_014675	exon3	c.A213G	p.T71T	GGCCACAGAGATG	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957097	111957097	+	Missense_Mutation	SNP	C	C	G	rs7825	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	44	69	0	0.578947	0	C|0.415;G|0.585	0.585	strong	.	OVGP1	177	.	NM_002557	exon11	c.G2026C	p.E676Q	CTTCTTCATCCAC	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016311	25016311	+	Silent	SNP	G	G	A	rs183458338	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	137	218	0	0.513109	0	G|0.985;A|0.015	0.015	strong	.	GGT1	68	.	NM_013430	exon8	c.G399A	p.A133A	GGTGGCGGTGCCT	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	42	122	0	0.43299	0	C|0.758;A|0.242	0.242	strong	.	LRRN1	82	.	NM_020873	exon2	c.C396A	p.T132T	GATTACCGAGATG	.	PASS	Atlas-SNP
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs4643790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	46	100	0	0.410714	0	G|0.806;A|0.194	0.194	strong	SFRP2,NS,carcinoma,-1,1	SFRP2	45	1	NM_003013	exon1	c.C134T	p.A45V	AGGTTGGCAGGGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9068530	9068530	+	Missense_Mutation	SNP	C	C	T	rs7250080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	138	218	0	0.532819	0	C|0.827;T|0.173	0.173	strong	.	MUC16	4315	.	NM_024690	exon3	c.G18916A	p.V6306M	TCCCCACATTGGC	.	PASS	Atlas-SNP
SPAG7	9552	hgsc.bcm.edu	37	17	4863574	4863574	+	Silent	SNP	G	G	A	rs73343383	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	67	163	0	0.527559	0	G|0.978;A|0.022	0.022	strong	.	SPAG7	22	.	NM_004890	exon4	c.C282T	p.S94S	CCCAAAGGAGAAG	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	37	2	74460685	74460685	+	Silent	SNP	C	C	T	rs3796109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	9	32	0	0.375	0	C|0.917;T|0.083	0.083	strong	.	SLC4A5	215	.	NM_021196	exon18	c.G2439A	p.T813T	AGGCCGCGTTGGC	.	PASS	Atlas-SNP
UGGT2	55757	hgsc.bcm.edu	37	13	96508566	96508566	+	Missense_Mutation	SNP	T	T	A	rs35123499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	88	133	0	0.497175	0	T|0.980;A|0.020	0.020	strong	.	UGGT2	127	.	NM_020121	exon34	c.A3854T	p.Y1285F	AATCCATACTCTT	.	PASS	Atlas-SNP
KNTC1	9735	hgsc.bcm.edu	37	12	123089955	123089955	+	Missense_Mutation	SNP	C	C	T	rs7310898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	71	172	0	0.412791	0	C|0.962;T|0.038	0.038	strong	KNTC1,caecum,carcinoma,0,1	KNTC1	182	1	NM_014708	exon51	c.C5489T	p.P1830L	CAAAACCTGGTGA	.	PASS	Atlas-SNP
LIPN	643418	hgsc.bcm.edu	37	10	90530683	90530683	+	Missense_Mutation	SNP	C	C	T	rs114737713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	76	136	0	0.506667	0	C|0.983;T|0.017	0.017	strong	.	LIPN	28	.	NM_001102469	exon6	c.C754T	p.L252F	AAGATACTCTGGT	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447848	10447848	+	Silent	SNP	T	T	G	rs10021506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	54	107	0	0.469565	0	T|0.883;G|0.117	0.117	strong	.	ZNF518B	116	.	NM_053042	exon3	c.A105C	p.P35P	TCTATTTGGCCGA	.	PASS	Atlas-SNP
HSH2D	84941	hgsc.bcm.edu	37	19	16259623	16259623	+	Silent	SNP	C	C	T	rs8103852	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	100	95	0	0.990099	0	C|0.891;T|0.109	0.109	strong	.	HSH2D	16	.	NM_032855	exon4	c.C63T	p.T21T	GCACACCCAGATG	.	PASS	Atlas-SNP
TBXAS1	6916	hgsc.bcm.edu	37	7	139661964	139661964	+	Missense_Mutation	SNP	C	C	G	rs4529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	55	136	0	0.482456	0	C|0.953;G|0.047	0.047	strong	.	TBXAS1	121	.	NM_001166253	exon10	c.C1207G	p.L403V	ACCTACCTACTGG	.	PASS	Atlas-SNP
APBA2	321	hgsc.bcm.edu	37	15	29397593	29397593	+	Silent	SNP	C	C	T	rs35322773	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	30	61	0	0.517241	0	C|0.980;T|0.020	0.020	strong	.	APBA2	132	.	NM_005503	exon10	c.C1536T	p.I512I	GCTCATCGCCCAG	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21139389	21139389	+	Missense_Mutation	SNP	T	T	C	rs4025981	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	87	0	0.470588	0	T|0.942;C|0.058	0.058	strong	NEBL,NS,carcinoma,0,1	NEBL	199	1	NM_006393	exon11	c.A1051G	p.M351V	CAAGCATTGGCTT	.	PASS	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29443949	29443949	+	Silent	SNP	A	A	G	rs3764211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	24	42	0	0.533333	0	A|0.791;G|0.209	0.209	strong	FAM189A1,NS,carcinoma,0,1	FAM189A1	20	1	NM_015307	exon5	c.T618C	p.D206D	CAGGACATCGGAG	.	PASS	Atlas-SNP
ADORA1	134	hgsc.bcm.edu	37	1	203098275	203098275	+	Silent	SNP	T	T	G	rs2228079	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	38	144	0	0.365385	0	T|0.745;G|0.255	0.255	strong	.	ADORA1	62	.	NM_001048230	exon2	c.T306G	p.A102A	AATTGCTGTGGAC	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46900670	46900670	+	Silent	SNP	C	C	T	rs112723616	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	36	31	0	0.631579	0	C|0.990;T|0.010	0.010	strong	.	COL18A1	129	.	NM_030582	exon12	c.C2049T	p.G683G	GCCCGGCGAGCCA	.	PASS	Atlas-SNP
C1orf109	54955	hgsc.bcm.edu	37	1	38155319	38155319	+	Silent	SNP	C	C	T	rs61731880	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	103	187	0	0.481308	0	C|0.966;T|0.034	0.034	strong	.	C1orf109	13	.	NM_017850	exon2	c.G234A	p.L78L	AGCCACCAGCTGC	.	PASS	Atlas-SNP
DPY19L3	147991	hgsc.bcm.edu	37	19	32930808	32930808	+	Missense_Mutation	SNP	G	G	A	rs139732410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	100	0	0.463636	0	G|0.998;A|0.002	0.002	strong	.	DPY19L3	70	.	NM_001172774	exon8	c.G847A	p.A283T	CTGCCAGCAGTGA	.	PASS	Atlas-SNP
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60036547	60036547	+	Missense_Mutation	SNP	G	G	A	rs35993683	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	27	0	0.444444	0	G|0.989;A|0.011	0.011	strong	.	TNFRSF11A	51	.	NM_003839	exon9	c.G1397A	p.R466H	CAAAACGTGGACC	.	PASS	Atlas-SNP
SI	6476	hgsc.bcm.edu	37	3	164750325	164750325	+	Silent	SNP	A	A	G	rs140829463	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	24	65	0	0.421053	0	A|0.999;G|0.001	0.001	strong	.	SI	500	.	NM_001041	exon24	c.T2721C	p.Y907Y	AGCATCATAAGTG	.	PASS	Atlas-SNP
IFNA16	3449	hgsc.bcm.edu	37	9	21216908	21216908	+	Missense_Mutation	SNP	C	C	G	rs28368163	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	127	329	0	0.423333	0	C|0.973;G|0.027	0.027	strong	.	IFNA16	27	.	NM_002173	exon1	c.G397C	p.A133P	TCAGGGCAATCTC	.	PASS	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434905	42434905	+	Missense_Mutation	SNP	T	T	C	rs144100358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	67	97	0	0.587719	0	T|0.992;C|0.008	0.008	strong	.	PLA2G4F	75	.	NM_213600	exon19	c.A2150G	p.K717R	GTCATCTTCAAGA	.	PASS	Atlas-SNP
IFI30	10437	hgsc.bcm.edu	37	19	18288069	18288069	+	Silent	SNP	A	A	G	rs7125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	193	214	0	1	0	A|0.525;C|0.003	.	strong	IFI30,NS,carcinoma,0,1	IFI30	12	1	NM_006332	exon5	c.A603G	p.P201P	GCCACCACACGAG	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126715075	126715075	+	Silent	SNP	T	T	C	rs3781413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	54	169	0	0.469565	0	T|0.892;C|0.108	0.108	strong	CTBP2,NS,carcinoma,0,1	CTBP2	100	1	NM_022802	exon1	c.A1254G	p.A418A	GGTGGCTGCCGTC	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	122	251	1	0.458647	0.00398406	C|0.865;T|0.135	0.135	strong	.	PLEKHM1	69	.	NM_014798	exon4	c.G468A	p.R156R	AGCATCCCGGAGC	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53993988	53993988	+	Missense_Mutation	SNP	A	A	T	rs56187530		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	382	191	338	0	0.5	0	.	.	weak	ZNF813_ENST00000396403,NS,carcinoma,0,1	ZNF813	81	1	NM_001004301	exon4	c.A502T	p.I168F	AAGTCTATCAACG	.	PASS	Atlas-SNP
MRPL40	64976	hgsc.bcm.edu	37	22	19423250	19423250	+	Missense_Mutation	SNP	G	G	A	rs7575	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	75	157	0	0.517241	0	G|0.776;A|0.224	0.224	strong	.	MRPL40	13	.	NM_003776	exon4	c.G386A	p.R129H	AAGAGCGTAAGAT	.	PASS	Atlas-SNP
FBXW12	285231	hgsc.bcm.edu	37	3	48420987	48420987	+	Missense_Mutation	SNP	A	A	G	rs77256337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	119	214	1	0.540909	0.0046729	A|0.994;G|0.006	0.006	strong	.	FBXW12	44	.	NM_207102	exon7	c.A713G	p.H238R	TTCTACACTGCTC	.	PASS	Atlas-SNP
CRTAC1	55118	hgsc.bcm.edu	37	10	99667840	99667840	+	Silent	SNP	A	A	G	rs35333633	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	75	115	0	0.490196	0	A|0.946;G|0.054	0.054	strong	.	CRTAC1	86	.	NM_001206528	exon6	c.T780C	p.N260N	ATTCTCATTGTCG	.	PASS	Atlas-SNP
EPRS	2058	hgsc.bcm.edu	37	1	220154768	220154768	+	Silent	SNP	C	C	T	rs1061160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	48	86	0	0.461538	0	C|0.645;T|0.355	0.355	strong	.	EPRS	140	.	NM_004446	exon24	c.G3405A	p.Q1135Q	GTGTGACTGTACC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26699822	26699822	+	Silent	SNP	G	G	A	rs2272068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	51	90	0	0.447368	0	G|0.965;A|0.035	0.035	strong	.	OTOF	524	.	NM_194248	exon22	c.C2613T	p.L871L	GGAGAAGAGCAGG	.	PASS	Atlas-SNP
TTF2	8458	hgsc.bcm.edu	37	1	117637966	117637966	+	Silent	SNP	A	A	G	rs34079217	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	96	0	0.401869	0	A|0.964;G|0.036	0.036	strong	.	TTF2	92	.	NM_003594	exon19	c.A3012G	p.Q1004Q	AATTCAAAGAAAT	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73716774	73716774	+	Silent	SNP	G	G	A	rs177393	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	57	91	0	0.471074	0	G|0.667;A|0.333	0.333	strong	.	PAPLN	180	.	NM_173462	exon6	c.G417A	p.T139T	TGGGACGCCCTGC	.	PASS	Atlas-SNP
CDKN1A	1026	hgsc.bcm.edu	37	6	36651971	36651971	+	Missense_Mutation	SNP	C	C	A	rs1801270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	42	67	0	0.567568	0	C|0.812;A|0.188	0.188	strong	.	CDKN1A	27	.	NM_001220778	exon2	c.C93A	p.S31R	GCTGAGCCGCGAC	.	PASS	Atlas-SNP
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10912719	10912719	+	Silent	SNP	G	G	A	rs72777388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	91	0	0.494118	0	G|0.830;A|0.170	0.170	strong	.	ATP6V1C2	73	.	NM_001039362	exon8	c.G621A	p.V207V	CATGGTGGTCCCT	.	PASS	Atlas-SNP
FMR1NB	158521	hgsc.bcm.edu	37	X	147088249	147088249	+	Missense_Mutation	SNP	C	C	T	rs764631	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	55	85	0	0.604396	0	C|0.582;0|0.015	.	strong	.	FMR1NB	51	.	NM_152578	exon3	c.C425T	p.A142V	AGGTGGCAAAGCC	.	PASS	Atlas-SNP
MSL1	339287	hgsc.bcm.edu	37	17	38285681	38285681	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	5	80	0	0.0526316	0	.	.	none	.	MSL1	21	.	NM_001012241	exon4	c.T387C	p.S129S	CCGGTCTTCAGTG	.	PASS	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	563257	563257	+	Silent	SNP	G	G	A	rs34954482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	59	143	0	0.380645	0	G|0.921;A|0.079	0.079	strong	.	RASSF7	22	.	NM_001143994	exon4	c.G891A	p.Q297Q	CATCCAGCAGACC	.	PASS	Atlas-SNP
NF1	4763	hgsc.bcm.edu	37	17	29652884	29652884	+	Silent	SNP	T	T	C	rs10512435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	42	93	0	0.552632	0	T|0.979;C|0.021	0.021	strong	.	NF1	1586	.	NM_001042492	exon37	c.T4882C	p.L1628L	CATGTCTTACTGA	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14291259	14291259	+	Silent	SNP	G	G	A	rs61737132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	63	142	0	0.440559	0	G|0.963;A|0.037	0.037	strong	.	TRIO	305	.	NM_007118	exon5	c.G975A	p.L325L	GCATCTGCACCAG	.	PASS	Atlas-SNP
WDR53	348793	hgsc.bcm.edu	37	3	196281263	196281263	+	Missense_Mutation	SNP	C	C	T	rs61730533	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	549	259	523	1	0.471767	0.00191205	C|0.942;T|0.058	0.058	strong	.	WDR53	26	.	NM_182627	exon4	c.G896A	p.G299D	TTTCCACCCTGCT	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	37	10	70646139	70646139	+	Missense_Mutation	SNP	G	G	A	rs7904300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	42	88	0	0.4	0	G|0.968;A|0.032	0.032	strong	.	STOX1	75	.	NM_152709	exon3	c.G2587A	p.A863T	AGAAAAGCCAGTT	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101090925	101090925	+	Missense_Mutation	SNP	C	C	A	rs115061809	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	72	145	0	0.461538	0	C|0.988;A|0.012	0.012	strong	.	SENP7	170	.	NM_020654	exon7	c.G723T	p.Q241H	CGCAGTCTGCTTT	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48313881	48313881	+	Missense_Mutation	SNP	T	T	C	rs17712299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	30	70	0	0.4	0	T|0.884;C|0.116	0.116	strong	.	ABCA13	1192	.	NM_152701	exon17	c.T4618C	p.F1540L	AATCAGTTTCAAA	.	PASS	Atlas-SNP
LRRC38	126755	hgsc.bcm.edu	37	1	13802437	13802437	+	Silent	SNP	G	G	A	rs3013106	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	156	152	0	0.993631	0	A|0.323;C|0.008	0.323	strong	.	LRRC38	12	.	NM_001010847	exon2	c.C762T	p.S254S	CACACCGGAGAAA	.	PASS	Atlas-SNP
CATSPERG	57828	hgsc.bcm.edu	37	19	38834974	38834974	+	Missense_Mutation	SNP	G	G	A	rs61732182	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	69	117	0	0.543307	0	G|0.997;A|0.003	0.003	strong	.	CATSPERG	121	.	NM_021185	exon6	c.G635A	p.R212Q	GAGACCGGGACAA	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57378198	57378198	+	Silent	SNP	T	T	C	rs1754533	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	143	245	0	0.491409	0	T|0.900;C|0.100	0.100	strong	.	C8A	103	.	NM_000562	exon10	c.T1503C	p.P501P	TGGGCCTTGCTTC	.	PASS	Atlas-SNP
C15orf40	123207	hgsc.bcm.edu	37	15	83680329	83680329	+	Missense_Mutation	SNP	G	G	A	rs17361375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	17	25	0	0.68	0	G|0.855;A|0.145	0.145	strong	.	C15orf40	18	.	NM_001160116	exon1	c.C31T	p.L11F	CCCGAAGGTGCCT	.	PASS	Atlas-SNP
CYP1A2	1544	hgsc.bcm.edu	37	15	75043592	75043592	+	Missense_Mutation	SNP	C	C	A	rs17861157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	119	111	1	1	0.00900901	C|0.973;A|0.027	0.027	strong	.	CYP1A2	70	.	NM_000761	exon3	c.C894A	p.S298R	AGCCAGCGGCAAC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48506642	48506642	+	Missense_Mutation	SNP	A	A	G	rs4917153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	42	82	0	0.442105	0	A|0.777;G|0.223	0.223	strong	.	ABCA13	1192	.	NM_152701	exon44	c.A12905G	p.Q4302R	CACGCCAGTAAGT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254074	39254074	+	Missense_Mutation	SNP	G	G	T	rs78662167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	19	139	0	0.142857	0	G|0.500;T|0.500	0.500	weak	.	KRTAP4-8	57	.	NM_031960	exon1	c.C263A	p.T88N	CAGCAGGTGGGCT	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274172	39274172	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	4	150	0	0.0289855	0	.	.	none	KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	NM_033059	exon1	c.C396A	p.P132P	GCAGGTGGGCTGG	.	scavenged	Atlas-SNP
C9orf173	441476	hgsc.bcm.edu	37	9	140146526	140146526	+	Silent	SNP	G	G	A	rs74822962	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	52	58	0	0.732394	0	G|0.991;A|0.009	0.009	strong	C9orf173,colon,carcinoma,0,1	C9orf173	19	1	NM_001256701	exon3	c.G342A	p.P114P	GAGCCCGTCCGTA	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72020103	72020103	+	Silent	SNP	G	G	A	rs56384440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	70	173	0	0.47619	0	A|0.013;G|0.987	0.013	strong	.	ZFC3H1	172	.	NM_144982	exon22	c.C4254T	p.D1418D	CACCTCGTCCTTG	.	PASS	Atlas-SNP
ITPKC	80271	hgsc.bcm.edu	37	19	41235120	41235120	+	Silent	SNP	A	A	G	rs10420685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	76	0	1	0	A|0.881;G|0.119	0.119	strong	.	ITPKC	36	.	NM_025194	exon3	c.A1269G	p.A423A	CCAGGCAGGAGAG	.	PASS	Atlas-SNP
NUDT9	53343	hgsc.bcm.edu	37	4	88344063	88344063	+	Silent	SNP	G	G	C	rs11937770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	20	37	0	0.952381	0	G|0.895;C|0.105	0.105	strong	.	NUDT9	21	.	NM_001248011	exon1	c.G6C	p.A2A	CATGGCGGGACGC	.	PASS	Atlas-SNP
GFRAL	389400	hgsc.bcm.edu	37	6	55196587	55196587	+	Missense_Mutation	SNP	C	C	T	rs12199003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	36	88	0	0.418605	0	C|0.627;T|0.373	0.373	strong	.	GFRAL	91	.	NM_207410	exon2	c.C97T	p.R33C	TGCTTACGTGATG	.	PASS	Atlas-SNP
GJB4	127534	hgsc.bcm.edu	37	1	35227041	35227041	+	Silent	SNP	C	C	T	rs76188300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	77	148	0	0.463855	0	C|0.964;T|0.036	0.036	strong	.	GJB4	51	.	NM_153212	exon2	c.C186T	p.N62N	CCCCAACGTCTGC	.	PASS	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169853220	169853220	+	Silent	SNP	G	G	A	rs11568377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	84	0	1	0	G|0.935;A|0.065	0.065	strong	.	ABCB11	136	.	NM_003742	exon6	c.C402T	p.I134I	GCTCTCGATGTTC	.	PASS	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	24	58	0	0.533333	0	C|0.794;T|0.206	0.206	strong	.	TEKT3	64	.	NM_031898	exon3	c.G8A	p.R3H	CCTACACGTTCCA	.	PASS	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695612	45695612	+	Silent	SNP	C	C	T	rs1346265	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	35	62	0	0.443038	0	C|0.860;T|0.140	0.140	strong	.	SPATA5L1	40	.	NM_024063	exon1	c.C985T	p.L329L	ACGCTGCTGGACG	.	PASS	Atlas-SNP
PVRL2	5819	hgsc.bcm.edu	37	19	45368805	45368805	+	Silent	SNP	C	C	T	rs34929997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	11	47	0	0.333333	0	C|0.980;T|0.020	0.020	strong	.	PVRL2	58	.	NM_002856	exon2	c.C366T	p.D122D	CCAGGACGCCACG	.	PASS	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41509950	41509950	+	Silent	SNP	G	G	C	rs28399485		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	67	181	0	0.41875	0	.	.	weak	CYP2B6,NS,carcinoma,0,1	CYP2B6	79	1	NM_000767	exon2	c.G216C	p.P72P	GGGACCGAGGCCC	.	PASS	Atlas-SNP
TTYH2	94015	hgsc.bcm.edu	37	17	72227040	72227040	+	Missense_Mutation	SNP	G	G	A	rs150215307	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	59	183	0	0.364198	0	G|0.995;A|0.005	0.005	strong	.	TTYH2	63	.	NM_032646	exon3	c.G316A	p.V106I	GTGGGCGTTGGTT	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96127869	96127869	+	Silent	SNP	T	T	G	rs2276322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	137	154	0	1	0	T|0.394;G|0.606	0.606	strong	.	UNC5C	141	.	NM_003728	exon11	c.A1812C	p.P604P	GACGACTGGGCGG	.	PASS	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	37	2	86709704	86709704	+	Silent	SNP	C	C	T	rs34673273	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	96	144	0	0.518919	0	C|0.969;T|0.031	0.031	strong	.	KDM3A	179	.	NM_001146688	exon18	c.C2809T	p.L937L	AGCATTCTGGGCT	.	PASS	Atlas-SNP
DCAF6	55827	hgsc.bcm.edu	37	1	168013850	168013850	+	Missense_Mutation	SNP	T	T	C	rs11558511	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	79	112	0	0.473054	0	C|0.196;N|0.000	0.196	strong	.	DCAF6	99	.	NM_001198956	exon15	c.T1871C	p.V624A	AGGATGTGACAAA	.	PASS	Atlas-SNP
PLEKHG4	25894	hgsc.bcm.edu	37	16	67318242	67318242	+	Missense_Mutation	SNP	A	A	G	rs8044843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	33	95	0	0.37931	0	A|0.727;G|0.273	0.273	strong	.	PLEKHG4	94	.	NM_001129728	exon12	c.A1574G	p.D525G	AACTGGACCCCCC	.	PASS	Atlas-SNP
MAGED2	10916	hgsc.bcm.edu	37	X	54837277	54837277	+	Missense_Mutation	SNP	G	G	C	rs12014977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	105	150	0	0.535714	0	G|0.973;C|0.027	0.027	strong	.	MAGED2	74	.	NM_201222	exon4	c.G561C	p.E187D	GGAAGAGGATGGC	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	37	6	46977783	46977783	+	Missense_Mutation	SNP	C	C	T	rs45598235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	85	134	0	0.482955	0	C|0.952;T|0.048	0.048	strong	GPR110,NS,carcinoma,0,1	GPR110	102	1	NM_153840	exon11	c.G1388A	p.R463H	AACACACGGCCTC	.	PASS	Atlas-SNP
CHI3L1	1116	hgsc.bcm.edu	37	1	203152851	203152851	+	Missense_Mutation	SNP	C	C	T	rs147131854	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	101	0	0.485437	0	C|0.999;T|0.001	0.001	strong	CHI3L1,colon,carcinoma,0,1	CHI3L1	51	1	NM_001276	exon5	c.G383A	p.R128H	TGGGTGCGCAGAA	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	37	MT	6150	6150	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	8	0	1	0	.	.	none	.	.	.	.	ENST00000361624	exon1	c.G247A	p.V83I	TGACTAGTTCCCC	.	PASS	Atlas-SNP
COG6	57511	hgsc.bcm.edu	37	13	40229957	40229957	+	Missense_Mutation	SNP	T	T	A	rs3812883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	55	92	0	0.56701	0	T|0.567;A|0.433	0.433	strong	.	COG6	49	.	NM_001145079	exon1	c.T94A	p.C32S	ACGACCTGCAACC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28456220	28456220	+	Missense_Mutation	SNP	G	G	A	rs2525916		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	738	15	644	1	0.0203252	0.0015528	.	.	weak	HERC2,NS,carcinoma,0,1	HERC2	501	1	NM_004667	exon44	c.C6997T	p.L2333F	GGGAGAGCAGCGC	.	scavenged	Atlas-SNP
ZNF43	7594	hgsc.bcm.edu	37	19	21991663	21991663	+	Silent	SNP	A	A	G	rs61733114	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	28	52	0	0.571429	0	A|0.968;G|0.032	0.032	strong	.	ZNF43	152	.	NM_001256653	exon4	c.T1203C	p.H401H	TTCAGTATGAATT	.	PASS	Atlas-SNP
FAM166A	401565	hgsc.bcm.edu	37	9	140140188	140140188	+	Silent	SNP	G	G	A	rs112239130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	76	135	0	0.655172	0	G|0.992;A|0.008	0.008	strong	.	FAM166A	44	.	NM_001001710	exon2	c.C174T	p.P58P	GGACATGGGGGAC	.	PASS	Atlas-SNP
GPT	2875	hgsc.bcm.edu	37	8	145729727	145729727	+	Missense_Mutation	SNP	C	C	A	rs1063739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	37	53	0	0.578125	0	A|0.384;C|0.616	0.384	strong	GPT,NS,haematopoietic_neoplasm,-2,1	GPT	31	1	NM_005309	exon1	c.C40A	p.H14N	GTGAGGCATGGAC	.	PASS	Atlas-SNP
USP17L20	100287441	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	977	73	271	0	0.0747185	0	.	.	none	RP11-1286E23.17,NS,carcinoma,0,1	.	.	1	NM_001256861	exon1	c.G984A	p.W328X	TGGGTGGAGTTGT	.	scavenged	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23731426	23731426	+	Silent	SNP	C	C	T	rs13045477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	169	177	1	0.994118	0.00564972	C|0.665;T|0.335	0.335	strong	CST1,NS,carcinoma,0,1	CST1	37	1	NM_001898	exon1	c.G78A	p.E26E	CCTATCCTCCTCC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	111	0	1	0	A|0.682;G|0.318	0.318	strong	.	KRT84	61	.	NM_033045	exon7	c.T1266C	p.D422D	TTTGGCATCACTG	.	PASS	Atlas-SNP
WDR31	114987	hgsc.bcm.edu	37	9	116085148	116085148	+	Silent	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	68	176	0	0.348718	0	.	.	none	.	WDR31	23	.	NM_001012361	exon7	c.T513G	p.L171L	CCACAGAAGCAGG	.	PASS	Atlas-SNP
KLF16	83855	hgsc.bcm.edu	37	19	1854701	1854701	+	Silent	SNP	G	G	A	rs76157530	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	25	30	0	0.581395	0	G|0.989;A|0.011	0.011	strong	.	KLF16	9	.	NM_031918	exon2	c.C516T	p.D172D	CAGCTCGTCGGAG	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48234214	48234214	+	Silent	SNP	C	C	T	rs61745566	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	27	62	0	0.442623	0	C|0.980;T|0.020	0.020	strong	.	ABCC11	177	.	NM_033151	exon14	c.G2055A	p.T685T	GACGACCGTCTTC	.	PASS	Atlas-SNP
WDR19	57728	hgsc.bcm.edu	37	4	39267749	39267749	+	Missense_Mutation	SNP	G	G	A	rs16995209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	66	141	0	0.409938	0	G|0.962;A|0.038	0.038	strong	.	WDR19	96	.	NM_025132	exon29	c.G3250A	p.G1084S	AACGATGGCATGC	.	PASS	Atlas-SNP
PTPN1	5770	hgsc.bcm.edu	37	20	49197955	49197955	+	Silent	SNP	C	C	T	rs74607837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	81	138	0	0.5	0	C|0.980;T|0.020	0.020	strong	.	PTPN1	36	.	NM_002827	exon9	c.C1242T	p.C414C	CATGTGCGTGGCT	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68609647	68609647	+	Missense_Mutation	SNP	G	G	T	rs2271725	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	52	154	0	0.366197	0	G|0.833;T|0.167	0.167	strong	.	ITGA11	110	.	NM_001004439	exon21	c.C2671A	p.Q891K	AGACTTGCTTCTG	.	PASS	Atlas-SNP
SLTM	79811	hgsc.bcm.edu	37	15	59179264	59179264	+	Silent	SNP	G	G	A	rs2124203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	58	83	0	0.495726	0	G|0.937;A|0.063	0.063	strong	SLTM,colon,carcinoma,0,1	SLTM	90	1	NM_024755	exon19	c.C2745T	p.G915G	GGGAGCGCCTCTC	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5391702	5391702	+	Missense_Mutation	SNP	C	C	G	rs3801048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	142	143	0	1	0	C|0.797;G|0.203	0.203	strong	.	TNRC18	311	.	NM_001080495	exon17	c.G5218C	p.E1740Q	GGAATTCTTCGTC	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156085	39156085	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	58	172	0	0.333333	0	.	.	none	KRTAP3-2,rectum,carcinoma,0,1	KRTAP3-2	11	1	NM_031959	exon1	c.C21A	p.R7R	GCAGCTGCGAGAG	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73142296	73142296	+	Missense_Mutation	SNP	C	C	T	rs2973571	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	54	103	0	0.519231	0	C|0.829;T|0.171	0.171	strong	.	.	.	.	NM_001080479	exon12	c.C1631T	p.S544L	TACAGTCGAAGGT	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	5	199	0	0.019685	0	T|1.000;|0.000	.	weak	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon4	c.T928A	p.L310M	GAGGACTTGAAGT	.	scavenged	Atlas-SNP
KRT33A	3883	hgsc.bcm.edu	37	17	39503163	39503163	+	Missense_Mutation	SNP	G	G	A	rs57740817	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	217	210	0	0.951754	0	G|0.333;A|0.667	0.667	weak	KRT33A,colon,carcinoma,0,1	KRT33A	53	1	NM_004138	exon5	c.C809T	p.A270V	ATCTCCGCCTGGT	.	PASS	Atlas-SNP
MRO	83876	hgsc.bcm.edu	37	18	48327815	48327815	+	Silent	SNP	G	G	A	rs2276186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	90	117	0	0.989011	0	G|0.579;A|0.421	0.421	strong	MRO,NS,carcinoma,0,1	MRO	36	1	NM_001127176	exon5	c.C531T	p.A177A	CCTCCCGGCAAAG	.	PASS	Atlas-SNP
TNFSF14	8740	hgsc.bcm.edu	37	19	6669934	6669934	+	Silent	SNP	G	G	A	rs2291668	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	69	100	1	0.50365	0.01	G|0.841;A|0.159	0.159	strong	TNFSF14,NS,carcinoma,-1,1	TNFSF14	40	1	NM_003807	exon2	c.C147T	p.A49A	CAGCCCGGCCCCC	.	scavenged	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	45	88	0	0.445545	0	C|0.329;G|0.000;T|0.671	0.329	strong	MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	NM_054030	exon2	c.A185G	p.N62S	AAGGCGTTCCTGC	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40657700	40657700	+	Missense_Mutation	SNP	C	C	G	rs7308720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	59	97	0	0.5	0	C|0.897;G|0.103	0.103	strong	.	LRRK2	763	.	NM_198578	exon14	c.C1653G	p.N551K	TTTGAACAGGGTA	.	PASS	Atlas-SNP
RGS8	85397	hgsc.bcm.edu	37	1	182640864	182640864	+	Missense_Mutation	SNP	T	T	C	rs680277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	85	278	1	0.377778	0.00359712	T|0.817;C|0.183	0.183	strong	RGS8,NS,carcinoma,0,1	RGS8	51	1	NM_033345	exon2	c.A8G	p.N3S	AAGGTGTTCTGGG	.	PASS	Atlas-SNP
MB	4151	hgsc.bcm.edu	37	22	36007045	36007045	+	Silent	SNP	G	G	A	rs7292	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	160	153	0	0.993789	0	G|0.474;A|0.526	0.526	strong	.	MB	7	.	NM_203377	exon3	c.C204T	p.T68T	GAGCACGGTGGCA	.	PASS	Atlas-SNP
TAGLN	6876	hgsc.bcm.edu	37	11	117075014	117075014	+	Missense_Mutation	SNP	A	A	G	rs12284316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	146	312	1	0.572549	0.00320513	A|0.996;G|0.004	0.004	strong	.	TAGLN	17	.	NM_001001522	exon5	c.A545G	p.N182S	GCAGCAACAGAGG	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6656830	6656830	+	Missense_Mutation	SNP	G	G	A	rs2243563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	24	52	0	0.461538	0	G|0.313;A|0.687	0.687	strong	ZNF853_ENST00000457543,rectum,carcinoma,0,2	ZNF853	32	2	NM_017560	exon2	c.G22A	p.G8R	ACTCCCGGGAATC	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117110112	117110112	+	Missense_Mutation	SNP	T	T	C	rs1265891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	101	138	1	1	0.00724638	T|0.754;C|0.246	0.246	strong	.	AKNA	119	.	NM_030767	exon16	c.A3290G	p.Q1097R	AGTGGCTGGTGCA	.	PASS	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15217535	15217535	+	Silent	SNP	C	C	T	rs144456077	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	312	159	286	0	0.509615	0	C|0.996;T|0.004	0.004	strong	TEKT3,NS,adenocarcinoma,0,1	TEKT3	64	1	NM_031898	exon6	c.G747A	p.A249A	CTGGGACGCTCTG	.	PASS	Atlas-SNP
ZWINT	11130	hgsc.bcm.edu	37	10	58118630	58118630	+	Missense_Mutation	SNP	T	T	C	rs2241666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	268	245	0	0.996283	0	C|0.704;N|0.000	0.704	strong	.	ZWINT	39	.	NM_007057	exon6	c.A559G	p.R187G	ACACCCTGTCAAG	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132240298	132240298	+	Silent	SNP	C	C	T	rs138292408	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	136	360	0	0.45485	0	C|0.942;T|0.058	0.058	strong	.	TUBA3D	60	.	NM_080386	exon5	c.C1230T	p.G410G	CGTGGGCGAAGGC	.	PASS	Atlas-SNP
GPR107	57720	hgsc.bcm.edu	37	9	132854643	132854643	+	Silent	SNP	T	T	C	rs34227818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	126	163	0	0.62069	0	T|0.980;C|0.020	0.020	strong	.	GPR107	30	.	NM_001136557	exon9	c.T846C	p.H282H	GATTCATATCCTT	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	37	15	90164769	90164769	+	Silent	SNP	T	T	C	rs75934760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	26	70	0	0.472727	0	T|0.973;C|0.027	0.027	strong	.	.	.	.	NM_152259	exon19	c.T3300C	p.P1100P	GGTACCTGCAGCT	.	PASS	Atlas-SNP
MOGS	7841	hgsc.bcm.edu	37	2	74688884	74688884	+	Missense_Mutation	SNP	G	G	A	rs13405869	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	47	126	0	0.398305	0	G|0.980;A|0.020	0.020	strong	.	MOGS	58	.	NM_006302	exon4	c.C2032T	p.R678W	GGGGCCGACCCAC	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82764924	82764924	+	Missense_Mutation	SNP	C	C	T	rs138200846	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	83	159	0	0.535484	0	C|0.995;T|0.005	0.005	strong	.	PCLO	1506	.	NM_014510	exon3	c.G1942A	p.G648R	GATCCCCGCCTAG	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28211921	28211921	+	Silent	SNP	G	G	A	rs1800411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	61	144	1	0.403974	0.00694444	G|0.543;A|0.457	0.457	strong	OCA2,NS,carcinoma,-2,1	OCA2	173	1	NM_000275	exon15	c.C1551T	p.C517C	AACAAGGCAAATC	.	scavenged	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559849	140559849	+	Missense_Mutation	SNP	G	G	A	rs17096961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	73	130	0	0.489933	0	G|0.827;A|0.173	0.173	strong	.	PCDHB8	199	.	NM_019120	exon1	c.G2234A	p.S745N	CCGGGAGCCTGTC	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31342744	31342744	+	Silent	SNP	C	C	T	rs1035705	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	133	236	0	0.525692	0	C|0.456;T|0.544	0.544	strong	.	TRPM1	183	.	NM_001252020	exon11	c.G1356A	p.T452T	CTTCTCCGTGGCT	.	PASS	Atlas-SNP
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	Silent	SNP	A	A	G	rs1065178	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	297	225	2	0.996644	0.00888889	A|0.622;G|0.378	0.378	strong	.	.	.	.	NM_001206650	exon2	c.T132C	p.I44I	GGTTAAAATCACA	.	PASS	Atlas-SNP
UCK1	83549	hgsc.bcm.edu	37	9	134404337	134404337	+	Silent	SNP	G	G	A	rs11557925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	20	34	0	0.571429	0	G|0.976;A|0.024	0.024	strong	.	UCK1	29	.	NM_001261451	exon5	c.C612T	p.C204C	CGGCAGGCAGAAC	.	PASS	Atlas-SNP
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	116	0	1	0	C|0.772;T|0.228	0.228	strong	.	ZNF17	49	.	NM_006959	exon3	c.C693T	p.S231S	CAACTCCGACCTT	.	PASS	Atlas-SNP
CCDC138	165055	hgsc.bcm.edu	37	2	109429277	109429277	+	Missense_Mutation	SNP	G	G	C	rs58170568	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	76	165	0	0.466258	0	G|0.993;C|0.007	0.007	strong	.	CCDC138	49	.	NM_144978	exon9	c.G935C	p.R312T	TGCAGAGGAAGTA	.	PASS	Atlas-SNP
ISOC1	51015	hgsc.bcm.edu	37	5	128442644	128442644	+	Silent	SNP	T	T	C	rs3734161	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	129	166	1	1	0.0060241	T|0.931;C|0.069	0.069	strong	.	ISOC1	26	.	NM_016048	exon4	c.T639C	p.H213H	GACTCATGTGTGC	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12409535	12409535	+	Silent	SNP	A	A	G	rs3801366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	87	196	0	0.467742	0	A|0.851;G|0.149	0.149	strong	.	VWDE	123	.	NM_001135924	exon12	c.T2397C	p.S799S	GAGGCCAGAGGGA	.	PASS	Atlas-SNP
CXorf57	55086	hgsc.bcm.edu	37	X	105883826	105883826	+	Missense_Mutation	SNP	T	T	G	rs5962707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	419	145	406	0	0.346062	0	0|0.014;G|0.148	0.148	strong	.	CXorf57	107	.	NM_018015	exon10	c.T1779G	p.I593M	AGAAATTCAAGAA	.	PASS	Atlas-SNP
FPR1	2357	hgsc.bcm.edu	37	19	52249702	52249702	+	Silent	SNP	G	G	T	rs2070746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	33	41	0	0.622642	0	G|0.682;T|0.318	0.318	strong	.	FPR1	64	.	NM_001193306	exon3	c.C546A	p.P182P	GGTCCAGGGCGAA	.	PASS	Atlas-SNP
NPSR1	387129	hgsc.bcm.edu	37	7	34917759	34917759	+	Missense_Mutation	SNP	C	C	T	rs13230135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	146	224	0	0.506944	0	C|0.987;T|0.013	0.013	strong	.	NPSR1	134	.	NM_207173	exon9	c.C1097T	p.T366I	AGGGTACTTGGCC	.	PASS	Atlas-SNP
SULT1A1	6817	hgsc.bcm.edu	37	16	28617413	28617413	+	Missense_Mutation	SNP	A	A	G	rs28374453	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	83	516	0	0.306273	0	A|0.974;G|0.026	0.026	strong	SULT1A1_ENST00000350842,NS,carcinoma,0,10	SULT1A1	53	10	NM_177534	exon6	c.T739C	p.F247L	CCATGAACTCCTG	.	scavenged	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136535746	136535746	+	Missense_Mutation	SNP	C	C	T	rs61685718	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	41	107	0	0.344538	0	C|0.987;T|0.013	0.013	strong	SARDH,colon,carcinoma,0,1	SARDH	112	1	NM_007101	exon19	c.G2455A	p.A819T	GGCCTGCGGCCCG	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95076665	95076665	+	Missense_Mutation	SNP	C	C	G	rs2236344	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	56	75	0	0.565657	0	C|0.939;G|0.061	0.061	strong	.	NOL8	118	.	NM_017948	exon7	c.G2242C	p.V748L	CACTCACATCTGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281039	152281039	+	Missense_Mutation	SNP	G	G	A	rs7522925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	952	502	517	1	0.527311	0.00193424	G|0.716;A|0.284	0.284	strong	.	FLG	900	.	NM_002016	exon3	c.C6323T	p.A2108V	CTGGGCGCAGACT	.	PASS	Atlas-SNP
PCDHGB5	56101	hgsc.bcm.edu	37	5	140778256	140778256	+	Missense_Mutation	SNP	G	G	A	rs6867460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	50	94	0	0.45045	0	G|0.804;A|0.196	0.196	strong	.	.	.	.	NM_018925	exon1	c.G562A	p.G188S	CAGGATGGTAGTA	.	PASS	Atlas-SNP
MAGEB2	4113	hgsc.bcm.edu	37	X	30237003	30237003	+	Silent	SNP	C	C	T	rs2074793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	75	191	0	0.441176	0	C|0.599;0|0.003	.	strong	.	MAGEB2	133	.	NM_002364	exon2	c.C306T	p.S102S	AACATCCACTAAG	.	PASS	Atlas-SNP
TMEM105	284186	hgsc.bcm.edu	37	17	79287477	79287477	+	Missense_Mutation	SNP	G	G	A	rs9916085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	65	121	0	0.454545	0	G|0.882;A|0.118	0.118	strong	.	TMEM105	19	.	NM_178520	exon3	c.C364T	p.R122W	CACCCCGGCCCCA	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909099	123909099	+	Missense_Mutation	SNP	G	G	T	rs59358830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	183	471	5	0.429577	0.0106157	G|0.962;T|0.038	0.038	strong	OR10G7,NS,carcinoma,0,1	OR10G7	103	1	NM_001004463	exon1	c.C610A	p.L204I	CCACTAGCCCAAT	.	scavenged	Atlas-SNP
SMURF2	64750	hgsc.bcm.edu	37	17	62567987	62567987	+	Silent	SNP	G	G	A	rs34788315	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	92	205	0	0.505495	0	G|0.964;A|0.036	0.036	strong	.	SMURF2	63	.	NM_022739	exon10	c.C945T	p.F315F	GTCAACGAAATAA	.	PASS	Atlas-SNP
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	16	50	0	0.333333	0	A|0.841;G|0.159	0.159	strong	.	GPR149	134	.	NM_001038705	exon1	c.T483C	p.S161S	CAGCAGACTGGCT	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	63	106	0	0.557522	0	T|0.576;C|0.424	0.424	strong	.	ABCC1	156	.	NM_004996	exon9	c.T1062C	p.N354N	CGTGAATGACACG	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	82	167	0	0.506173	0	T|0.910;G|0.090	0.090	strong	.	TMEM232	57	.	NM_001039763	exon5	c.A498C	p.A166A	TACCTTTGCTAGC	.	PASS	Atlas-SNP
LCLAT1	253558	hgsc.bcm.edu	37	2	30863092	30863092	+	Silent	SNP	C	C	T	rs12467646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	68	139	0	0.482269	0	C|0.872;T|0.128	0.128	strong	.	LCLAT1	51	.	NM_182551	exon7	c.C852T	p.H284H	CTTTCACGTCCAC	.	PASS	Atlas-SNP
WIF1	11197	hgsc.bcm.edu	37	12	65514266	65514266	+	Silent	SNP	T	T	C	rs7301320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	64	176	0	0.460432	0	T|0.221;C|0.779	0.779	strong	.	WIF1	96	.	NM_007191	exon2	c.A219G	p.A73A	CTGTTGTGCTTTT	.	PASS	Atlas-SNP
OAF	220323	hgsc.bcm.edu	37	11	120097551	120097551	+	Silent	SNP	G	G	A	rs873058	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	45	85	0	0.642857	0	G|0.982;A|0.018	0.018	strong	.	OAF	12	.	NM_178507	exon3	c.G393A	p.A131A	GCAGGCGGAGGAG	.	PASS	Atlas-SNP
SOWAHA	134548	hgsc.bcm.edu	37	5	132149593	132149593	+	Missense_Mutation	SNP	G	G	A	rs114865630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	12	4	0	0.75	0	G|0.964;A|0.036	0.036	strong	.	.	.	.	NM_175873	exon1	c.G280A	p.G94S	CCCTTCGGCCCCC	.	PASS	Atlas-SNP
C17orf50	146853	hgsc.bcm.edu	37	17	34091078	34091078	+	Missense_Mutation	SNP	C	C	G	rs4795087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	35	85	0	0.538462	0	C|0.698;G|0.302	0.302	strong	.	C17orf50	4	.	NM_145272	exon2	c.C66G	p.D22E	CGAGGACGCGGAG	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	648916	648916	+	Silent	SNP	T	T	C	rs12942598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	38	80	0	0.387755	0	T|0.974;C|0.026	0.026	strong	.	GEMIN4	116	.	NM_015721	exon2	c.A2367G	p.T789T	AAAAAGTGTGGCT	.	PASS	Atlas-SNP
FRYL	285527	hgsc.bcm.edu	37	4	48588742	48588742	+	Silent	SNP	C	C	T	rs34558821	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	56	55	0	0.982456	0	C|0.516;T|0.484	0.484	strong	.	FRYL	242	.	NM_015030	exon19	c.G1644A	p.G548G	TCTTTCCCCCCTG	.	PASS	Atlas-SNP
MBOAT1	154141	hgsc.bcm.edu	37	6	20109842	20109842	+	Missense_Mutation	SNP	T	T	C	rs2065649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	47	113	0	0.460784	0	T|0.949;C|0.051	0.051	strong	.	MBOAT1	48	.	NM_001080480	exon12	c.A1348G	p.I450V	AGCTGATGGTCGG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15784377	15784377	+	Missense_Mutation	SNP	C	C	T	rs16995376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	73	112	0	0.352657	0	C|0.775;T|0.225	0.225	strong	.	CYP4F12	89	.	NM_023944	exon2	c.C38T	p.P13L	TCAGACCGGTGGC	.	PASS	Atlas-SNP
CXorf64	100130613	hgsc.bcm.edu	37	X	125955199	125955199	+	Missense_Mutation	SNP	T	T	C	rs4289953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	108	186	0	0.639053	0	0|0.026;C|0.181	0.181	strong	.	.	.	.	NM_001122716	exon2	c.T578C	p.M193T	TAGTAATGGAGGT	.	PASS	Atlas-SNP
FAAH	2166	hgsc.bcm.edu	37	1	46876488	46876488	+	Silent	SNP	G	G	C	rs74783386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	80	168	0	0.454545	0	G|0.998;C|0.002	0.002	strong	.	FAAH	36	.	NM_001441	exon11	c.G1278C	p.L426L	GCAGCTGCCAAGG	.	PASS	Atlas-SNP
CEACAM8	1088	hgsc.bcm.edu	37	19	43098931	43098931	+	Missense_Mutation	SNP	C	C	A	rs28367882	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	33	85	0	0.515625	0	C|0.939;A|0.061	0.061	strong	.	CEACAM8	44	.	NM_001816	exon1	c.G50T	p.G17V	AGGAGCCCCTGCC	.	PASS	Atlas-SNP
PPP4R1	9989	hgsc.bcm.edu	37	18	9562042	9562042	+	Missense_Mutation	SNP	C	C	T	rs2306134	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	152	169	0	0.993464	0	C|0.730;T|0.270	0.270	strong	PPP4R1_ENST00000400556,NS,carcinoma,+1,1	PPP4R1	63	1	NM_001042388	exon13	c.G1778A	p.S593N	GAATCGCTGTGAA	.	PASS	Atlas-SNP
MED22	6837	hgsc.bcm.edu	37	9	136208405	136208405	+	Missense_Mutation	SNP	C	C	T	rs145653063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	39	106	0	0.33913	0	C|0.989;T|0.011	0.011	strong	.	MED22	13	.	NM_133640	exon5	c.G553A	p.A185T	CAGGGGCTGCCAC	.	PASS	Atlas-SNP
GMNC	647309	hgsc.bcm.edu	37	3	190578566	190578566	+	Missense_Mutation	SNP	A	A	G	rs13075089	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	70	116	0	0.538462	0	A|0.589;G|0.411	0.411	strong	.	GMNC	12	.	NM_001146686	exon2	c.T85C	p.S29P	CACTAGATTCTGA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207782931	207782931	+	Missense_Mutation	SNP	A	A	G	rs6691117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	105	0	1	0	A|0.601;G|0.399	0.399	strong	.	CR1	354	.	NM_000651	exon37	c.A6193G	p.I2065V	GAGATCATCAGAT	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	63113968	63113968	+	Missense_Mutation	SNP	T	T	C	rs61743961	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	47	0	0.428571	0	T|0.959;C|0.041	0.041	strong	DOCK7,NS,carcinoma,0,1	DOCK7	184	1	NM_001271999	exon6	c.A541G	p.M181V	TTGACATTGAACG	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73566094	73566094	+	Missense_Mutation	SNP	G	G	C	rs115026154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	62	87	0	0.62	0	G|0.977;C|0.023	0.023	strong	.	LLGL2	155	.	NM_004524	exon15	c.G1632C	p.Q544H	GGAGCAGGTGGAG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15794423	15794423	+	Silent	SNP	C	C	T	rs114945576	byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	52	124	0	0.275132	0	C|0.990;T|0.010	0.010	strong	.	CYP4F12	89	.	NM_023944	exon7	c.C768T	p.F256F	GCGCTTCCACAGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417765	105417765	+	Silent	SNP	A	A	C	rs2894636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	263	389	1	0.996212	0.00257069	A|0.831;C|0.169	0.169	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T4023G	p.S1341S	TGGGGCAGACACC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224099	248224099	+	Missense_Mutation	SNP	T	T	C	rs79225254	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	483	222	466	0	0.459627	0	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.T116C	p.I39T	CTCTAATTGGAAA	.	PASS	Atlas-SNP
KCNMB2	10242	hgsc.bcm.edu	37	3	178560581	178560581	+	Silent	SNP	A	A	C	rs6443583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	155	0	1	0	A|0.352;C|0.648	0.648	strong	.	KCNMB2	35	.	NM_005832	exon6	c.A564C	p.T188T	CCTAACAAAACTC	.	PASS	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	155	124	0	1	0	C|0.765;T|0.235	0.235	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.G1011A	p.V337V	GCTCTGCACGTCG	.	PASS	Atlas-SNP
GGT7	2686	hgsc.bcm.edu	37	20	33447314	33447314	+	Missense_Mutation	SNP	C	C	T	rs61319953	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	34	76	0	0.485714	0	C|0.971;T|0.029	0.029	strong	.	GGT7	41	.	NM_178026	exon7	c.G946A	p.V316I	CAAGTACATCCAG	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221057662	221057662	+	Silent	SNP	G	G	A	rs3738182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	91	183	0	0.489247	0	G|0.810;A|0.190	0.190	strong	.	HLX	67	.	NM_021958	exon4	c.G1083A	p.E361E	TGGCGAGCAGGAC	.	PASS	Atlas-SNP
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	7	174	0	0.0338164	0	.	.	none	OR52E8,NS,carcinoma,0,1	OR52E8	54	1	NM_001005168	exon1	c.C475T	p.L159L	TGTACAGGCTCCT	.	scavenged	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20680718	20680718	+	Missense_Mutation	SNP	G	G	A	rs2072751	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	100	214	0	0.429185	0	G|0.772;A|0.228	0.228	strong	.	VWA5B1	44	.	NM_001039500	exon22	c.G3610A	p.E1204K	AATCTCGAGTTCA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	169993977	169993977	+	Silent	SNP	C	C	T	rs34029982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	113	0	0.479167	0	C|0.992;T|0.008	0.008	strong	.	LRP2	751	.	NM_004525	exon76	c.G13545A	p.G4515G	CTGCTTCCCCATT	.	PASS	Atlas-SNP
ZNF467	168544	hgsc.bcm.edu	37	7	149462055	149462055	+	Silent	SNP	G	G	A	rs863021	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	8	4	0	0.470588	0	G|0.947;A|0.053	0.053	strong	.	ZNF467	50	.	NM_207336	exon5	c.C1536T	p.S512S	GGGGCGGCTGCCA	.	PASS	Atlas-SNP
NUFIP2	57532	hgsc.bcm.edu	37	17	27620934	27620934	+	Silent	SNP	G	G	A	rs1054145	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	525	275	476	0	0.52381	0	G|0.981;A|0.019	0.019	strong	NUFIP2,NS,carcinoma,-2,1	NUFIP2	60	1	NM_020772	exon1	c.C144T	p.H48H	ATGATGGTGGTGG	.	PASS	Atlas-SNP
CKM	1158	hgsc.bcm.edu	37	19	45815033	45815033	+	Silent	SNP	G	G	T	rs17875616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	32	65	0	0.516129	0	G|0.928;T|0.072	0.072	strong	CKM,rectum,carcinoma,0,2	CKM	40	2	NM_001824	exon5	c.C627A	p.R209R	CCAGTCGCGGGCC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	3	113	1	0.0214286	0.00884956	.	.	none	CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	NM_153610	exon2	c.A7974G	p.V2658V	TCTAGTATTAGAA	.	scavenged	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20852817	20852817	+	Missense_Mutation	SNP	G	G	A	rs1760903	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	118	103	0	0.991597	0	G|0.428;A|0.572	0.572	strong	.	TEP1	224	.	NM_007110	exon22	c.C3163T	p.R1055C	TCCGACGTGCGGC	.	PASS	Atlas-SNP
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	76	212	0	0.460606	0	G|0.639;A|0.361	0.361	strong	.	ANKRD17	214	.	NM_032217	exon29	c.C6609T	p.L2203L	GACACTGAGGACT	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100512919	100512919	+	Missense_Mutation	SNP	C	C	G	rs17599091	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	60	117	0	0.4	0	C|0.964;G|0.036	0.036	strong	.	MTTP	127	.	NM_000253	exon7	c.C730G	p.Q244E	TTCCTACAAACCA	.	PASS	Atlas-SNP
CER1	9350	hgsc.bcm.edu	37	9	14722477	14722477	+	Missense_Mutation	SNP	G	G	C	rs3747532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	156	208	0	1	0	G|0.572;C|0.428	0.428	strong	.	CER1	41	.	NM_005454	exon1	c.C194G	p.A65G	CTGGTGGCTACAA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129904477	129904477	+	Missense_Mutation	SNP	C	C	T	rs11591817	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	447	228	439	1	0.510067	0.0022779	C|0.798;T|0.202	0.202	strong	.	MKI67	363	.	NM_002417	exon13	c.G5627A	p.R1876Q	TTGGGCCGTTGCT	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132628281	132628281	+	Missense_Mutation	SNP	C	C	T	rs78871841	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	6	8	0	0.375	0	C|0.962;T|0.038	0.038	strong	.	DDX51	33	.	NM_175066	exon2	c.G478A	p.G160S	CCAGGCCGGGGAC	.	PASS	Atlas-SNP
CD36	948	hgsc.bcm.edu	37	7	80300449	80300449	+	Nonsense_Mutation	SNP	T	T	G	rs3211938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	49	0	1	0	T|0.967;G|0.033	0.033	strong	.	CD36	185	.	NM_001127444	exon8	c.T975G	p.Y325X	ATCATATGGTGTG	.	PASS	Atlas-SNP
LRRC8B	23507	hgsc.bcm.edu	37	1	90049088	90049088	+	Silent	SNP	G	G	A	rs35903285	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	43	67	0	0.457447	0	G|0.976;A|0.024	0.024	strong	.	LRRC8B	49	.	NM_015350	exon5	c.G879A	p.V293V	TGATGTGCAGGCT	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	37	5	40998760	40998760	+	Silent	SNP	C	C	T	rs61745464	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	56	118	0	0.478632	0	C|0.936;T|0.064	0.064	strong	.	.	.	.	NM_173489	exon41	c.G4605A	p.L1535L	GCTGGTCAAATTG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367092	128367092	+	Silent	SNP	G	G	A	rs777432	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	51	113	0	0.447368	0	G|0.692;A|0.308	0.308	strong	MYO7B_ENST00000428314,colon,carcinoma,0,2	MYO7B	359	2	NM_001080527	exon23	c.G2826A	p.S942S	GGAATCGAAGACC	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23745723	23745723	+	Silent	SNP	G	G	A	rs11844797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	67	155	0	0.5	0	G|0.948;A|0.052	0.052	strong	.	HOMEZ	80	.	NM_020834	exon2	c.C714T	p.N238N	TGACTGGTTGGGA	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61960961	61960961	+	Missense_Mutation	SNP	T	T	C	rs6011740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	14	39	0	0.451613	0	T|0.949;C|0.051	0.051	strong	.	COL20A1	137	.	NM_020882	exon35	c.T3806C	p.M1269T	GTCAGATGGGCAG	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011571	46011571	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	21	280	0	0.0615836	0	.	.	none	.	KRTAP10-6	57	.	NM_198688	exon1	c.C795A	p.P265P	CTGGCAGGGGGAG	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104059542	104059542	+	Missense_Mutation	SNP	G	G	A	rs2243682	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	78	0	0.514706	0	G|0.855;A|0.145	0.145	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon39	c.C6269T	p.T2090M	CTTTCCGTAAGGT	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	27	48	0	0.586957	0	C|0.605;T|0.395	0.395	strong	.	SP140L	68	.	NM_138402	exon13	c.C1129T	p.P377S	AATCCTCCAAGAA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547068	132547068	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	3	94	0	0.032967	0	.	.	none	EP400,NS,carcinoma,0,2	EP400	370	2	NM_015409	exon47	c.G8156A	p.R2719K	TTCTCAGGCAGCA	.	scavenged	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10312792	10312792	+	Silent	SNP	C	C	T	rs73275411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	134	316	0	0.533865	0	C|0.976;T|0.024	0.024	strong	.	MYH8	346	.	NM_002472	exon16	c.G1701A	p.Q567Q	GGGCTTCTGGAAG	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	84	137	1	0.525	0.00729927	C|0.834;T|0.166	0.166	strong	WDFY4,colon,carcinoma,0,1	WDFY4	205	1	NM_020945	exon23	c.C4119T	p.G1373G	CATTGGCGGGCCT	.	scavenged	Atlas-SNP
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692173	31692173	+	Missense_Mutation	SNP	C	C	T	rs78165499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	114	231	0	0.581633	0	C|0.988;T|0.012	0.012	strong	.	KRTAP26-1	58	.	NM_203405	exon1	c.G181A	p.G61S	GTTCACCGCAGGT	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32032397	32032397	+	Missense_Mutation	SNP	G	G	T	rs4955216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	74	152	0	0.503401	0	G|0.644;T|0.356	0.356	strong	.	ZNF860	96	.	NM_001137674	exon2	c.G1826T	p.R609L	CACATCGCATTAG	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27324844	27324844	+	Silent	SNP	G	G	A	rs2565061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	42	126	0	0.381818	0	G|0.788;A|0.212	0.212	strong	.	CHRNA2	48	.	NM_000742	exon5	c.C351T	p.D117D	TTTGTAGTCGCTC	.	PASS	Atlas-SNP
PLA1A	51365	hgsc.bcm.edu	37	3	119331874	119331874	+	Silent	SNP	C	C	T	rs2272270	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	38	40	0	0.535211	0	C|0.759;T|0.241	0.241	strong	.	PLA1A	65	.	NM_015900	exon5	c.C573T	p.P191P	GGACCCCGCTGGA	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs61742867	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	56	142	0	0.321839	0	C|0.029;G|0.971	0.971	strong	PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	NM_018930	exon1	c.C1383G	p.R461R	CGTCCGCGAGAAC	.	scavenged	Atlas-SNP
E2F4	1874	hgsc.bcm.edu	37	16	67229827	67229827	+	Silent	SNP	C	C	T	rs3730404	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	63	118	0	0.547826	0	C|0.949;T|0.051	0.051	strong	.	E2F4	25	.	NM_001950	exon7	c.C951T	p.S317S	CAGCAGCAGCAGC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604694	140604694	+	Silent	SNP	G	G	A	rs76971158	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	119	194	0	0.481781	0	G|0.978;A|0.022	0.022	strong	PCDHB14,caecum,carcinoma,0,1	PCDHB14	132	1	NM_018934	exon1	c.G1617A	p.P539P	GTCCCCGGCGTTG	.	PASS	Atlas-SNP
COL1A2	1278	hgsc.bcm.edu	37	7	94027699	94027699	+	Silent	SNP	T	T	C	rs1801182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	80	0	0.493333	0	T|0.823;C|0.177	0.177	strong	.	COL1A2	240	.	NM_000089	exon3	c.T87C	p.T29T	GGAAACTGTAAGA	.	PASS	Atlas-SNP
TRIM48	79097	hgsc.bcm.edu	37	11	55029787	55029787	+	Missense_Mutation	SNP	G	G	A	rs12799381	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	82	162	0	0.509317	0	G|0.891;A|0.109	0.109	strong	TRIM48_ENST00000417545,caecum,carcinoma,+1,2	TRIM48	149	2	NM_024114	exon1	c.G44A	p.R15Q	CCCAGCGGTGAGT	.	PASS	Atlas-SNP
TTF2	8458	hgsc.bcm.edu	37	1	117618024	117618024	+	Missense_Mutation	SNP	G	G	C	rs17036832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	58	120	0	0.491525	0	A|0.000;C|0.019;G|0.980	0.019	strong	.	TTF2	92	.	NM_003594	exon5	c.G818C	p.S273T	CAATAAGCAAGCC	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51204996	51204996	+	Silent	SNP	C	C	T	rs11376	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	216	219	1	1	0.00456621	C|0.452;T|0.548	0.548	strong	.	NIN	475	.	NM_020921	exon27	c.G5637A	p.Q1879Q	TTCCAACTGACGG	.	PASS	Atlas-SNP
NAA25	80018	hgsc.bcm.edu	37	12	112471090	112471090	+	Missense_Mutation	SNP	G	G	T	rs12298022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	106	88	0	0.972477	0	G|0.868;T|0.132	0.132	strong	.	NAA25	105	.	NM_024953	exon23	c.C2743A	p.L915I	CAATTAGATGTGT	.	PASS	Atlas-SNP
ADAMTS8	11095	hgsc.bcm.edu	37	11	130284495	130284495	+	Silent	SNP	C	C	T	rs142963990	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	127	258	1	0.468635	0.00387597	C|0.996;T|0.004	0.004	strong	.	ADAMTS8	172	.	NM_007037	exon5	c.G1497A	p.T499T	GCACGGCGTGCCG	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133486988	133486988	+	Silent	SNP	C	C	T	rs7845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	36	78	0	0.444444	0	C|0.985;G|0.000;T|0.015	0.015	strong	.	TF	116	.	NM_001063	exon13	c.C1602T	p.Y534Y	ATACTACGGCTAC	.	PASS	Atlas-SNP
MFSD9	84804	hgsc.bcm.edu	37	2	103334969	103334969	+	Silent	SNP	G	G	A	rs1052431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	52	103	0	0.504854	0	G|0.653;A|0.347	0.347	strong	.	MFSD9	56	.	NM_032718	exon6	c.C1335T	p.G445G	CACAGCGCCCAGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548026	32548026	+	Missense_Mutation	SNP	G	G	C	rs9269744	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	61	431	0	0.184848	0	G|0.500;C|0.500	0.500	strong	.	HLA-DRB1	41	.	NM_002124	exon5	c.C785G	p.T262R	TTACCTGTTGGCT	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15795939	15795939	+	Silent	SNP	A	A	G	rs61729075	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	71	157	0	0.275194	0	A|0.981;G|0.019	0.019	strong	.	CYP4F12	89	.	NM_023944	exon9	c.A1047G	p.E349E	CCCAGAATACCAG	.	PASS	Atlas-SNP
OSBP2	23762	hgsc.bcm.edu	37	22	31091064	31091064	+	Silent	SNP	C	C	T	rs41279967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	38	59	0	0.655172	0	C|0.888;T|0.112	0.112	strong	.	OSBP2	52	.	NM_030758	exon1	c.C168T	p.P56P	CCAGCCCGTGCCC	.	PASS	Atlas-SNP
ZDHHC1	29800	hgsc.bcm.edu	37	16	67440289	67440289	+	Silent	SNP	C	C	T	rs8058306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	71	138	0	0.440994	0	C|0.924;T|0.076	0.076	strong	.	ZDHHC1	28	.	NM_013304	exon3	c.G66A	p.T22T	CGGTGCCGTCCAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515030	195515030	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	436	23	143	0	0.0527523	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G3421T	p.D1141Y	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3846802	3846802	+	Silent	SNP	A	A	G	rs758641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	105	0	1	0	A|0.605;G|0.395	0.395	strong	.	ATP2A3	148	.	NM_174956	exon11	c.T1302C	p.Y434Y	CTTCTCATACACA	.	PASS	Atlas-SNP
CFC1B	653275	hgsc.bcm.edu	37	2	131356322	131356322	+	Missense_Mutation	SNP	C	C	T	rs201431919	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	797	540	1076	0	0.677541	0	C|0.969;T|0.031	0.031	strong	CFC1,fourth_ventricle,glioma,0,1	.	.	1	NM_001079530	exon3	c.G140A	p.R47Q	GACTGTCGGTGCT	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100731896	100731896	+	Silent	SNP	T	T	C	rs61730716	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	20	49	0	0.384615	0	T|0.922;C|0.078	0.078	strong	.	TRIM56	123	.	NM_030961	exon3	c.T1303C	p.L435L	CAGACCTTGGAGG	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	815593	815593	+	Missense_Mutation	SNP	G	G	C	rs115279916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	65	60	0	0.555556	0	G|0.985;C|0.015	0.015	strong	.	MSLN	109	.	NM_005823	exon10	c.G771C	p.Q257H	GGGCCAGCCCATC	.	PASS	Atlas-SNP
OR6C4	341418	hgsc.bcm.edu	37	12	55945265	55945265	+	Silent	SNP	A	A	G	rs74093226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	120	0	0.491379	0	A|0.951;G|0.049	0.049	strong	.	OR6C4	34	.	NM_001005494	exon1	c.A255G	p.T85T	GACAACAGGAAAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	16	148	0	0.111111	0	T|0.994;C|0.006	0.006	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3996C	p.Y1332Y	AACTTATAGTGAA	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22473646	22473646	+	Missense_Mutation	SNP	A	A	C	rs143150726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	44	113	0	0.37931	0	A|0.998;C|0.002	0.002	strong	.	KIAA1967	72	.	NM_021174	exon14	c.A1730C	p.E577A	AGGAGGAGGCGGC	.	PASS	Atlas-SNP
GBE1	2632	hgsc.bcm.edu	37	3	81586149	81586149	+	Silent	SNP	G	G	A	rs2229520	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	49	107	0	0.385827	0	G|0.987;A|0.013	0.013	strong	.	GBE1	111	.	NM_000158	exon13	c.C1716T	p.D572D	AAGGTCGTCGTCA	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100466441	100466441	+	Missense_Mutation	SNP	G	G	A	rs2075756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	93	156	0	0.58125	0	G|0.746;A|0.254	0.254	strong	.	TRIP6	45	.	NM_003302	exon4	c.G688A	p.V230I	GCTGGGGTCTCTG	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1634225	1634225	+	Missense_Mutation	SNP	G	G	A	rs8060532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	24	41	0	0.55814	0	G|0.969;A|0.031	0.031	strong	.	IFT140	128	.	NM_014714	exon11	c.C1352T	p.A451V	TTGGTGGCAAACA	.	PASS	Atlas-SNP
PRPH2	5961	hgsc.bcm.edu	37	6	42689940	42689940	+	Missense_Mutation	SNP	G	G	A	rs61755770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	68	94	0	0.561983	0	G|0.994;A|0.006	0.006	strong	.	PRPH2	47	.	NM_000322	exon1	c.C133T	p.L45F	TTCGGAGTTCAAT	.	PASS	Atlas-SNP
S1PR5	53637	hgsc.bcm.edu	37	19	10625067	10625067	+	Silent	SNP	A	A	C	rs6511701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	67	56	0	1	0	A|0.222;C|0.778	0.778	strong	S1PR5,NS,carcinoma,0,1	S1PR5	33	1	NM_030760	exon2	c.T621G	p.A207A	ACAGATAGCGGCC	.	PASS	Atlas-SNP
DCTN1	1639	hgsc.bcm.edu	37	2	74597937	74597937	+	Missense_Mutation	SNP	G	G	T	rs13420401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	73	113	0	0.528986	0	G|0.954;T|0.046	0.046	strong	.	DCTN1	110	.	NM_004082	exon10	c.C859A	p.L287M	CCTCCAGCGCCTC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138378308	138378308	+	Missense_Mutation	SNP	G	G	A	rs35142799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	107	120	0	0.727891	0	G|0.994;A|0.006	0.006	strong	.	.	.	.	NM_014811	exon4	c.G1952A	p.G651D	GGGAGGGCACCGC	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132218075	132218075	+	Missense_Mutation	SNP	C	C	T	rs61748102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	66	142	0	0.445946	0	C|0.981;T|0.019	0.019	strong	.	DNAJC13	253	.	NM_015268	exon37	c.C4262T	p.A1421V	TGCCTGCGGCTAC	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79700648	79700648	+	Silent	SNP	C	C	T	rs149171291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	101	243	1	0.459091	0.00411523	C|0.997;T|0.003	0.003	strong	.	PHIP	177	.	NM_017934	exon20	c.G2256A	p.R752R	TTCTGACCTGTAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1252708	1252708	+	Silent	SNP	G	G	C	rs2735709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	68	122	0	0.515152	0	G|0.443;C|0.557	0.557	strong	.	MUC5B	473	.	NM_002458	exon14	c.G1596C	p.L532L	AGGCCTGGGGCTG	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3613239	3613239	+	Missense_Mutation	SNP	C	C	T	rs8057436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	20	24	0	0.625	0	C|0.969;T|0.031	0.031	strong	.	NLRC3	103	.	NM_178844	exon5	c.G1699A	p.V567M	GCAACACGTTGAT	.	PASS	Atlas-SNP
TOMM70A	9868	hgsc.bcm.edu	37	3	100084432	100084432	+	Silent	SNP	G	G	A	rs277644	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	105	255	0	0.458515	0	G|0.834;A|0.166	0.166	strong	.	TOMM70A	65	.	NM_014820	exon12	c.C1803T	p.Y601Y	TAATCCGTATTTC	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42465713	42465713	+	Missense_Mutation	SNP	C	C	T	rs9562362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	40	76	0	0.444444	0	C|0.775;T|0.225	0.225	strong	.	.	.	.	NM_015058	exon5	c.G494A	p.R165H	GCTGCACGAACTG	.	PASS	Atlas-SNP
DCST2	127579	hgsc.bcm.edu	37	1	155006091	155006091	+	Silent	SNP	A	A	G	rs10908453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	122	121	1	0.99187	0.00826446	A|0.513;G|0.487	0.487	strong	.	DCST2	80	.	NM_144622	exon1	c.T87C	p.G29G	GGTAAAACCTCCC	.	PASS	Atlas-SNP
EXOC5	10640	hgsc.bcm.edu	37	14	57676330	57676330	+	Silent	SNP	G	G	T	rs1804820	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	82	162	0	0.503067	0	G|0.765;T|0.235	0.235	strong	.	EXOC5	45	.	NM_006544	exon17	c.C1893A	p.A631A	ACAAATGGCCAAC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81232426	81232426	+	Missense_Mutation	SNP	A	A	C	rs9934856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	111	245	0	0.546798	0	A|0.984;C|0.016;G|0.000	0.016	strong	.	PKD1L2	361	.	NM_001076780	exon7	c.T1384G	p.L462V	GCTCCAAATGGTC	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919794	28919794	+	Missense_Mutation	SNP	C	C	A	rs8091117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	118	156	0	1	0	C|0.806;A|0.194	0.194	strong	.	DSG1	176	.	NM_001942	exon11	c.C1493A	p.T498N	CGAACACTAAAAT	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254622	3254622	+	Missense_Mutation	SNP	G	G	A	rs8045183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	126	243	1	0.504	0.00411523	G|0.966;A|0.034	0.034	strong	.	OR1F1	36	.	NM_012360	exon1	c.G376A	p.V126M	GTCGCCGTGTGCC	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3010298	3010298	+	Missense_Mutation	SNP	A	A	G	rs28383623	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	77	123	0	0.487342	0	A|0.960;G|0.040	0.040	strong	.	NQO2	21	.	NM_000904	exon3	c.A47G	p.K16R	AACCCAAGTCTTT	.	PASS	Atlas-SNP
TSKU	25987	hgsc.bcm.edu	37	11	76507403	76507403	+	Missense_Mutation	SNP	G	G	A	rs11236938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	67	88	0	0.587719	0	G|0.913;A|0.087	0.087	strong	.	TSKU	26	.	NM_015516	exon2	c.G743A	p.S248N	CGCCCAGTGGCTT	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17447237	17447237	+	Silent	SNP	C	C	G	rs115898475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	33	64	0	0.6	0	C|0.994;G|0.006	0.006	strong	.	GAB4	95	.	NM_001037814	exon6	c.G1041C	p.V347V	CAGGCCCACAAGC	.	PASS	Atlas-SNP
TMED7-TICAM2	100302736	hgsc.bcm.edu	37	5	114916763	114916763	+	Missense_Mutation	SNP	C	C	T	rs113049216	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	68	122	0	0.459459	0	C|0.989;T|0.011	0.011	strong	.	.	.	.	NM_001164468	exon4	c.G698A	p.S233N	TCCACGCTCTGAG	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	175998246	175998246	+	Silent	SNP	T	T	C	rs17078320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	57	100	0	0.548077	0	T|0.732;C|0.268	0.268	strong	.	CDHR2	152	.	NM_017675	exon6	c.T348C	p.D116D	GGAAGATAGAAAC	.	PASS	Atlas-SNP
PTPLAD1	51495	hgsc.bcm.edu	37	15	65863917	65863917	+	Missense_Mutation	SNP	A	A	C	rs2279854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	125	259	0	0.408497	0	A|0.949;C|0.051	0.051	strong	.	PTPLAD1	23	.	NM_016395	exon9	c.A805C	p.M269L	ATTGACATGGATT	.	PASS	Atlas-SNP
PPAN	56342	hgsc.bcm.edu	37	19	10221804	10221804	+	Missense_Mutation	SNP	G	G	T	rs200927331	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	7	8	0	0.5	0	.	.	weak	.	PPAN	43	.	NM_020230	exon12	c.G1385T	p.G462V	GGCGAGGCCGGGG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1546906	1546906	+	Silent	SNP	C	C	T	rs11907593	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	51	71	0	0.69863	0	C|0.984;T|0.016	0.016	strong	.	SIRPB1	83	.	NM_006065	exon5	c.G1092A	p.A364A	AGCCAGCGCTGCT	.	PASS	Atlas-SNP
EFTUD1	79631	hgsc.bcm.edu	37	15	82533686	82533686	+	Silent	SNP	T	T	G	rs11548681	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	58	123	0	0.456693	0	T|0.969;G|0.031	0.031	strong	.	EFTUD1	74	.	NM_024580	exon5	c.A303C	p.S101S	TACTTCTGAGGAA	.	PASS	Atlas-SNP
DGKZ	8525	hgsc.bcm.edu	37	11	46388024	46388024	+	Missense_Mutation	SNP	G	G	A	rs11827702	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	26	23	0	0.590909	0	G|0.968;A|0.032	0.032	strong	.	DGKZ	199	.	NM_001105540	exon2	c.G218A	p.R73Q	GCCGCCGGCGCTC	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127231765	127231765	+	Missense_Mutation	SNP	C	C	T	rs76434769	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	140	134	1	0.979021	0.00746269	C|0.977;T|0.023	0.023	strong	.	GPR144	33	.	NM_001161808	exon16	c.C2497T	p.R833C	GCCCGCCGCCGTG	.	PASS	Atlas-SNP
TMEM176A	55365	hgsc.bcm.edu	37	7	150500832	150500832	+	Missense_Mutation	SNP	C	C	T	rs76937000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	50	0	0.506667	0	C|0.977;T|0.023	0.023	strong	.	TMEM176A	35	.	NM_018487	exon5	c.C467T	p.S156L	CCAGCTCGAGTGA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512934	4512934	+	Silent	SNP	A	A	G	rs199854884	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	70	377	0	0.28	0	A|0.989;G|0.011	0.011	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T996C	p.N332N	GGCCACATTCATG	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241834944	241834944	+	Silent	SNP	T	T	C	rs4468809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	59	140	0	0.42446	0	T|0.497;C|0.503	0.503	strong	.	C2orf54	14	.	NM_001085437	exon1	c.A471G	p.V157V	GGCTGCTACCAGC	.	PASS	Atlas-SNP
LDLRAD4	753	hgsc.bcm.edu	37	18	13645310	13645310	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	3	118	0	0.0277778	0	.	.	none	C18orf1_ENST00000359446,NS,carcinoma,0,2	.	.	2	NM_181482	exon6	c.G521A	p.R174Q	AGCTCCGGGACCC	.	scavenged	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	37	11	51412370	51412370	+	Missense_Mutation	SNP	T	T	A	rs149177099	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	38	94	0	0.431818	0	T|0.990;A|0.010	0.010	strong	OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	NM_001005272	exon1	c.A26T	p.E9V	ACAAATTCTGTAA	.	PASS	Atlas-SNP
GSK3B	2932	hgsc.bcm.edu	37	3	119720980	119720980	+	Silent	SNP	T	T	A	rs34002644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	59	104	0	0.464567	0	T|0.938;A|0.062	0.062	strong	GSK3B_ENST00000316626,colon,carcinoma,-1,2	GSK3B	119	2	NM_002093	exon2	c.A195T	p.G65G	AAATGATCCATTT	.	PASS	Atlas-SNP
NFAM1	150372	hgsc.bcm.edu	37	22	42783070	42783070	+	Silent	SNP	G	G	A	rs34963472	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	37	38	0	0.606557	0	G|0.880;A|0.120	0.120	strong	.	NFAM1	12	.	NM_145912	exon5	c.C678T	p.R226R	GGTCTCGCGGCGC	.	PASS	Atlas-SNP
ACCS	84680	hgsc.bcm.edu	37	11	44089352	44089352	+	Missense_Mutation	SNP	G	G	A	rs33952257	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	79	112	0	0.50641	0	G|0.754;A|0.246	0.246	strong	.	ACCS	64	.	NM_032592	exon2	c.G175A	p.D59N	TCCTCTGATACCT	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579078	55579078	+	Missense_Mutation	SNP	A	A	T	rs2869020	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	107	238	1	0.44958	0.00420168	A|0.976;T|0.024	0.024	strong	.	OR5L1	145	.	NM_001004738	exon1	c.A136T	p.I46F	GGCATGATTGCAC	.	PASS	Atlas-SNP
CRAT	1384	hgsc.bcm.edu	37	9	131860421	131860421	+	Silent	SNP	G	G	A	rs16930895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	17	53	0	0.459459	0	G|0.943;A|0.057	0.057	strong	.	CRAT	43	.	NM_000755	exon11	c.C1335T	p.Y445Y	CTGTCCGTAGATC	.	PASS	Atlas-SNP
RBM11	54033	hgsc.bcm.edu	37	21	15599354	15599354	+	Missense_Mutation	SNP	G	G	A	rs139439630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	160	342	0	0.443213	0	G|0.988;A|0.012	0.012	strong	.	RBM11	41	.	NM_144770	exon5	c.G586A	p.D196N	CCAAGTGACTCTG	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72350412	72350412	+	Missense_Mutation	SNP	G	G	A	rs2271535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	8	4	0	0.444444	0	G|0.631;A|0.369	0.369	strong	KIF19,NS,carcinoma,0,1	KIF19	102	1	NM_153209	exon18	c.G2420A	p.R807H	CAGAGCGCAGCAG	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931099	116931099	+	Missense_Mutation	SNP	G	G	A	rs2241671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	90	157	0	0.703125	0	G|0.596;A|0.404	0.404	strong	COL27A1,NS,carcinoma,0,1	COL27A1	200	1	NM_032888	exon3	c.G1264A	p.A422T	CGTCCCGCAGAGA	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14784389	14784389	+	Missense_Mutation	SNP	G	G	A	rs41265306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	73	147	0	0.45625	0	G|0.928;A|0.072	0.072	strong	.	FREM1	261	.	NM_144966	exon25	c.C4421T	p.T1474I	GAGACAGTCACCT	.	PASS	Atlas-SNP
PGM2	55276	hgsc.bcm.edu	37	4	37857342	37857342	+	Silent	SNP	G	G	C	rs11554509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	69	168	0	0.469388	0	G|0.826;C|0.174	0.174	strong	.	PGM2	45	.	NM_018290	exon13	c.G1716C	p.L572L	AGAGCTGTGTGCC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	23	374	0	0.0839416	0	A|0.864;T|0.136	0.136	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.T31A	p.C11S	TCATGCAGGAGCC	.	PASS	Atlas-SNP
SULT1C3	442038	hgsc.bcm.edu	37	2	108875270	108875270	+	Missense_Mutation	SNP	G	G	A	rs61743196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	44	101	0	0.511628	0	G|0.978;A|0.022	0.022	strong	.	SULT1C3	53	.	NM_001008743	exon5	c.G607A	p.E203K	TTCTACGAGGATA	.	PASS	Atlas-SNP
SNX31	169166	hgsc.bcm.edu	37	8	101586133	101586133	+	Missense_Mutation	SNP	T	T	C	rs2022923	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	50	107	0	0.49505	0	T|0.551;C|0.449	0.449	strong	SNX31,NS,carcinoma,0,1	SNX31	66	1	NM_152628	exon14	c.A1283G	p.D428G	CAGTCATCTTTAG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940462	144940462	+	Silent	SNP	G	G	A	rs56146920	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	11	174	0	0.0555556	0	G|0.500;A|0.500	0.500	weak	.	EPPK1	199	.	NM_031308	exon1	c.C6960T	p.S2320S	GAAGAGGGAGATC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6585670	6585670	+	Silent	SNP	C	C	T	rs16915423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	110	211	1	0.511628	0.00473934	C|0.905;T|0.095	0.095	strong	.	DNHD1	198	.	NM_144666	exon32	c.C10392T	p.D3464D	ACTGGACGAGTGG	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007679	6007679	+	Missense_Mutation	SNP	C	C	T	rs61742092	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	70	164	0	0.4375	0	A|0.000;C|0.988;T|0.012	0.012	strong	OR52L1_ENST00000332249,NS,carcinoma,-1,2	OR52L1	100	2	NM_001005173	exon1	c.G482A	p.C161Y	CCGATGCACCCTA	.	PASS	Atlas-SNP
NOP16	51491	hgsc.bcm.edu	37	5	175811133	175811133	+	Missense_Mutation	SNP	T	T	C	rs1065212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	36	37	0	1	0	T|0.896;C|0.104	0.104	strong	.	NOP16	26	.	NM_001256539	exon5	c.A548G	p.E183G	GCCAGCTCCTCTG	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377436	49377436	+	Missense_Mutation	SNP	G	G	C	rs556052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	173	173	0	1	0	G|0.568;C|0.432	0.432	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G946C	p.A316P	GTCAAGGCTTTGG	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103514939	103514939	+	Silent	SNP	C	C	T	rs4150316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	69	111	0	0.575	0	C|0.959;T|0.041	0.041	strong	.	.	.	.	NM_001204425	exon16	c.C2802T	p.H934H	TGTTCACGTGGGG	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	31	70	0	0.407895	0	G|0.696;A|0.304	0.304	strong	.	NDRG4	29	.	NM_001130487	exon13	c.G921A	p.T307T	CACTACGACCTTC	.	PASS	Atlas-SNP
SAG	6295	hgsc.bcm.edu	37	2	234255548	234255548	+	Missense_Mutation	SNP	T	T	C	rs1046976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	42	59	0	0.482759	0	T|0.869;C|0.131	0.131	strong	.	SAG	77	.	NM_000541	exon16	c.T1208C	p.V403A	ATGACGTTGATGA	.	PASS	Atlas-SNP
CYP3A7	1551	hgsc.bcm.edu	37	7	99317993	99317993	+	Silent	SNP	G	G	A	rs45466796	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	142	251	0	0.474916	0	G|0.983;A|0.017	0.017	strong	.	CYP3A7	59	.	NM_000765	exon4	c.C261T	p.P87P	CATGTCGGGATCT	.	PASS	Atlas-SNP
IFITM2	10581	hgsc.bcm.edu	37	11	309127	309127	+	Missense_Mutation	SNP	A	A	G	rs1059091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	447	447	410	0	1	0	A|0.607;C|0.000;G|0.393	0.393	strong	.	IFITM2	21	.	NM_006435	exon2	c.A361G	p.I121V	CTGCTCATCATCA	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160464289	160464289	+	Silent	SNP	G	G	A	rs894817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	85	0	0.468354	0	G|0.650;A|0.350	0.350	strong	.	IGF2R	251	.	NM_000876	exon12	c.G1590A	p.G530G	ACGAGGGTGTCCC	.	PASS	Atlas-SNP
ABI3	51225	hgsc.bcm.edu	37	17	47295165	47295165	+	Missense_Mutation	SNP	G	G	A	rs137924898	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	28	64	0	0.474576	0	G|0.997;A|0.003	0.003	strong	.	ABI3	35	.	NM_016428	exon3	c.G350A	p.R117Q	TCCAGCGGCTGCC	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	134	0	1	0	A|0.478;G|0.521	0.521	strong	DSC3,NS,carcinoma,0,1	DSC3	225	1	NM_024423	exon12	c.T1797C	p.P599P	TTCATCAGGATCA	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59480969	59480969	+	Missense_Mutation	SNP	A	A	G	rs472177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	29	66	0	0.39726	0	A|0.824;G|0.176	0.176	strong	.	OR10V1	40	.	NM_001005324	exon1	c.T350C	p.V117A	ATGACTACCAGCA	.	PASS	Atlas-SNP
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	136	213	0	0.546185	0	G|0.724;A|0.276	0.276	strong	.	DNAJB8	34	.	NM_153330	exon3	c.C15T	p.Y5Y	CACTTCGTAGTAG	.	PASS	Atlas-SNP
TIFA	92610	hgsc.bcm.edu	37	4	113199075	113199075	+	Silent	SNP	A	A	G	rs701759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	85	0	1	0	A|0.344;G|0.656	0.656	strong	.	TIFA	15	.	NM_052864	exon2	c.T498C	p.Y166Y	GAGCGAATAAGTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416685	105416685	+	Silent	SNP	C	C	G	rs2582506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	258	243	0	0.996139	0	C|0.401;G|0.599	0.599	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G5103C	p.L1701L	GGTCTTCAGGTCC	.	PASS	Atlas-SNP
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	80	140	0	0.506329	0	A|0.912;C|0.088	0.088	strong	.	EBNA1BP2	37	.	NM_001159936	exon10	c.T1044G	p.P348P	TTTTCCAGGTCTC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140605092	140605092	+	Missense_Mutation	SNP	C	C	G	rs76671799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	40	0	0.439394	0	C|0.978;G|0.022	0.022	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C2015G	p.P672R	ACCTGCCGCTCCC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	64	170	0	0.299065	0	T|0.881;C|0.119	0.119	strong	WNK2_ENST00000297954,NS,carcinoma,+1,2	WNK2	277	2	NM_006648	exon3	c.T1011C	p.S337S	TGGGTCTGTGAAG	.	PASS	Atlas-SNP
IFITM3	10410	hgsc.bcm.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs199749095	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	8	134	1	0.0467836	0.00746269	G|0.936;T|0.064	0.064	strong	IFITM3,caecum,carcinoma,0,13	IFITM3	132	13	NM_021034	exon1	c.C208A	p.P70T	AGCAGGGGTTCAT	.	scavenged	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21769193	21769193	+	Missense_Mutation	SNP	C	C	A	rs1040904	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	13	14	0	0.764706	0	C|0.941;A|0.059	0.059	strong	.	RPGRIP1	213	.	NM_020366	exon3	c.C287A	p.P96Q	CGGCGCCGCTCTC	.	PASS	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	37	7	143088592	143088592	+	Silent	SNP	G	G	A	rs56307701	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	84	134	0	0.48	0	G|0.988;A|0.013	0.013	strong	.	EPHA1	193	.	NM_005232	exon18	c.C2889T	p.H963H	CTTCTGGTGCCCG	.	PASS	Atlas-SNP
NOL11	25926	hgsc.bcm.edu	37	17	65732093	65732093	+	Silent	SNP	A	A	G	rs3760227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	91	123	0	0.486631	0	A|0.903;G|0.097	0.097	strong	.	NOL11	48	.	NM_015462	exon9	c.A1008G	p.S336S	AGTGTCATCATTA	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117068826	117068826	+	Silent	SNP	G	G	A	rs1249762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	31	62	0	0.424658	0	G|0.974;A|0.026	0.026	strong	.	COL27A1	200	.	NM_032888	exon58	c.G4965A	p.V1655V	GCTGGTGCTGGAC	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127821207	127821207	+	Silent	SNP	G	G	A	rs1137845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	52	105	0	0.514852	0	G|0.772;T|0.015	.	strong	.	BIN1	85	.	NM_139345	exon9	c.C714T	p.Y238Y	GTTGACGTAGAAA	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13753517	13753517	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	24	218	0	0.111111	0	.	.	none	DNAH5,NS,carcinoma,+1,1	DNAH5	868	1	NM_001369	exon63	c.T10697A	p.M3566K	ATCAACATCTCAC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7043335	7043335	+	Missense_Mutation	SNP	A	A	G	rs9950267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	135	160	0	0.985401	0	A|0.939;G|0.061	0.061	strong	.	LAMA1	458	.	NM_005559	exon8	c.T1046C	p.L349S	GTATTCAAACTTT	.	PASS	Atlas-SNP
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	65	103	0	0.560345	0	C|0.898;T|0.102	0.102	strong	.	MANSC1	38	.	NM_018050	exon2	c.G163A	p.V55I	TATATACGGGCTC	.	PASS	Atlas-SNP
PRKD3	23683	hgsc.bcm.edu	37	2	37505105	37505105	+	Silent	SNP	T	T	G	rs10460527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	76	141	0	0.47205	0	T|0.827;G|0.173	0.173	strong	PRKD3_ENST00000379066,NS,carcinoma,0,2	PRKD3	170	2	NM_005813	exon8	c.A1200C	p.L400L	CCTCATTAGCGGA	.	PASS	Atlas-SNP
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	73	0	0.460674	0	A|0.824;G|0.176	0.176	strong	NKX1-2_ENST00000440536,NS,carcinoma,0,2	NKX1-2	6	2	NM_001146340	exon2	c.T819C	p.N273N	GAGGACATTGGCC	.	PASS	Atlas-SNP
OR4E2	26686	hgsc.bcm.edu	37	14	22133416	22133416	+	Silent	SNP	A	A	G	rs12717305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	161	0	1	0	A|0.520;G|0.480	0.480	strong	.	OR4E2	44	.	NM_001001912	exon1	c.A120G	p.S40S	GCTTTCAGGGAAC	.	PASS	Atlas-SNP
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	73	162	0	0.496599	0	G|0.902;A|0.098	0.098	strong	FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	NM_145246	exon11	c.C752T	p.S251F	GCAGAAGATAATC	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80260014	80260014	+	Silent	SNP	T	T	C	rs8026803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	53	128	0	0.445378	0	T|0.622;C|0.378	0.378	strong	.	BCL2A1	28	.	NM_001114735	exon2	c.A441G	p.T147T	CATAGGTGTGTGA	.	PASS	Atlas-SNP
ZNF678	339500	hgsc.bcm.edu	37	1	227842405	227842405	+	Missense_Mutation	SNP	C	C	A	rs61283390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	52	62	0	0.577778	0	C|0.987;A|0.013	0.013	strong	.	ZNF678	137	.	NM_178549	exon4	c.C619A	p.P207T	GAGAAACCCTACA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277717	152277717	+	Silent	SNP	C	C	A	rs9436066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	415	414	512	2	0.99759	0.00390625	C|0.695;A|0.305	0.305	strong	.	FLG	900	.	NM_002016	exon3	c.G9645T	p.V3215V	CTGGCTCACACTG	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	37	20	47838020	47838020	+	Missense_Mutation	SNP	C	C	T	rs114928867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	59	115	0	0.468254	0	C|0.997;T|0.003	0.003	strong	.	DDX27	74	.	NM_017895	exon2	c.C218T	p.A73V	AAAAAGCTTTGGG	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3747910	3747910	+	Missense_Mutation	SNP	G	G	A	rs10408494	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	80	100	0	0.571429	0	G|0.950;A|0.050	0.050	strong	.	TJP3	79	.	NM_001267561	exon19	c.G2468A	p.G823D	AGGGCGGCGCGTA	.	PASS	Atlas-SNP
TRIM15	89870	hgsc.bcm.edu	37	6	30139971	30139971	+	Missense_Mutation	SNP	G	G	C	rs115649931	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	32	41	0	0.561404	0	G|0.990;C|0.010	0.010	strong	.	TRIM15	34	.	NM_033229	exon7	c.G1243C	p.V415L	CGCGGCGTGAGAG	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1052086	1052086	+	Silent	SNP	G	G	A	rs61576791	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	44	91	0	0.431373	0	G|0.938;A|0.062	0.062	strong	.	ABCA7	174	.	NM_019112	exon22	c.G3108A	p.T1036T	CCTGACGCTGGTG	.	PASS	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	37	2	210559960	210559960	+	Silent	SNP	G	G	T	rs2239672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	88	0	0.509804	0	G|0.883;T|0.117	0.117	strong	.	MAP2	372	.	NM_002374	exon7	c.G3066T	p.V1022V	TTCAGTGCCAGAG	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1642700	1642700	+	Missense_Mutation	SNP	G	G	A	rs61747875	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	53	130	0	0.40458	0	G|0.990;A|0.010	0.010	strong	.	PXDN	255	.	NM_012293	exon21	c.C4124T	p.T1375I	GAGCGTGTGCTGA	.	PASS	Atlas-SNP
STRADA	92335	hgsc.bcm.edu	37	17	61787892	61787892	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	121	0	0.482517	0	.	.	none	.	STRADA	27	.	NM_001003787	exon8	c.G540A	p.L180L	GGCCTTCAGCACC	.	PASS	Atlas-SNP
GIGYF1	64599	hgsc.bcm.edu	37	7	100285476	100285476	+	Missense_Mutation	SNP	C	C	T	rs77794375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	56	128	0	0.380952	0	C|0.942;T|0.058	0.058	strong	.	GIGYF1	113	.	NM_022574	exon3	c.G196A	p.A66T	CCGCGGCGAACTC	.	PASS	Atlas-SNP
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236097	67236097	+	Missense_Mutation	SNP	A	A	T	rs1060575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	32	52	0	0.421053	0	A|0.878;N|0.000	.	strong	.	TCTEX1D1	27	.	NM_152665	exon3	c.A147T	p.E49D	TATGGAAGAACCC	.	PASS	Atlas-SNP
ANKLE2	23141	hgsc.bcm.edu	37	12	133331459	133331459	+	Missense_Mutation	SNP	G	G	C	rs7968520	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	61	101	0	0.54955	0	G|0.917;C|0.083	0.083	strong	.	ANKLE2	76	.	NM_015114	exon2	c.C442G	p.Q148E	CAGCCTGATCAGT	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121576518	121576518	+	Missense_Mutation	SNP	C	C	G	rs201833154	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	73	136	0	0.51773	0	.	.	weak	C6orf170,colon,carcinoma,-2,1	C6orf170	146	1	NM_152730	exon17	c.G1974C	p.E658D	AGAACCCTCTACT	.	PASS	Atlas-SNP
FCRLB	127943	hgsc.bcm.edu	37	1	161697072	161697072	+	Missense_Mutation	SNP	G	G	C	rs72704099	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	82	88	1	1	0.0113636	G|0.770;C|0.230	0.230	strong	FCRLB,NS,carcinoma,0,1	FCRLB	35	1	NM_001002901	exon6	c.G901C	p.A301P	GCCCCAGCTCCAT	.	scavenged	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031135	32031135	+	Silent	SNP	A	A	G	rs6419811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	70	234	0	0.429448	0	A|0.567;G|0.433	0.433	strong	ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	NM_001137674	exon2	c.A564G	p.S188S	TTCCTCAGTTCTA	.	PASS	Atlas-SNP
ZNF268	10795	hgsc.bcm.edu	37	12	133780309	133780309	+	Missense_Mutation	SNP	G	G	T	rs36127550	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	3	0	1	0	G|0.858;T|0.142	0.142	strong	ZNF268,NS,carcinoma,0,1	ZNF268	71	1	NM_001165881	exon6	c.G2037T	p.L679F	TAGTTTGAAGTCC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10470130	10470130	+	Missense_Mutation	SNP	C	C	T	rs79401306	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	11	24	0	0.333333	0	C|0.987;T|0.013	0.013	strong	.	RP1L1	453	.	NM_178857	exon4	c.G1478A	p.R493Q	GCTTTCCGCTCAG	.	PASS	Atlas-SNP
GYPA	2993	hgsc.bcm.edu	37	4	145041720	145041720	+	Missense_Mutation	SNP	A	A	G	rs7682260	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	30	181	29	0.153061	0.160221	A|0.519;G|0.481	0.481	strong	GYPA,NS,carcinoma,0,1	GYPA	27	1	NM_002099	exon2	c.T59C	p.L20S	GTACTTAATGCTG	.	scavenged	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	65	0	0.521277	0	C|0.699;T|0.301	0.301	strong	AZI1_ENST00000450824,NS,carcinoma,0,2	AZI1	145	2	NM_014984	exon15	c.G1824A	p.A608A	GCTCAGCGCCTTC	.	PASS	Atlas-SNP
CAPN9	10753	hgsc.bcm.edu	37	1	230895340	230895340	+	Missense_Mutation	SNP	C	C	A	rs28359608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	115	85	0	0.991379	0	C|0.861;A|0.139	0.139	strong	.	CAPN9	116	.	NM_006615	exon3	c.C366A	p.S122R	CCAAAGCTTTGGC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036971	33036971	+	Silent	SNP	C	C	T	rs2308928	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	146	0	1	0	C|0.695;T|0.305	0.305	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.G453A	p.T151T	CAGCCACGTGACG	.	PASS	Atlas-SNP
PDP1	54704	hgsc.bcm.edu	37	8	94935623	94935623	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	117	159	0	0.529412	0	.	.	none	PDP1,caecum,carcinoma,-2,1	PDP1	97	1	NM_001161780	exon3	c.A1411G	p.I471V	CAGCCAATAGCTG	.	PASS	Atlas-SNP
RGS10	6001	hgsc.bcm.edu	37	10	121275099	121275099	+	Silent	SNP	G	G	A	rs11550215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	128	269	0	0.512	0	G|0.951;A|0.049	0.049	strong	.	RGS10	14	.	NM_001005339	exon4	c.C321T	p.N107N	CTCCACGTTGACC	.	PASS	Atlas-SNP
EBI3	10148	hgsc.bcm.edu	37	19	4236996	4236996	+	Missense_Mutation	SNP	G	G	A	rs4740	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	81	0	1	0	A|0.399;C|0.003	0.399	strong	.	EBI3	15	.	NM_005755	exon5	c.G601A	p.V201I	TACTACGTCCAAG	.	PASS	Atlas-SNP
TSPAN18	90139	hgsc.bcm.edu	37	11	44948263	44948263	+	Silent	SNP	C	C	T	rs34695714	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	65	107	0	0.524194	0	C|0.972;T|0.028	0.028	strong	TSPAN18,colon,carcinoma,+1,1	TSPAN18	38	1	NM_130783	exon8	c.C654T	p.Y218Y	GACCTACGTCTAC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	695	306	778	2	0.440288	0.00257069	T|0.769;C|0.231	0.231	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.T189C	p.I63I	GGTCATTTTTGTG	.	PASS	Atlas-SNP
ZNF737	100129842	hgsc.bcm.edu	37	19	20727932	20727932	+	Silent	SNP	G	G	A	rs33926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	15	38	0	0.517241	0	G|0.431;A|0.569	0.569	strong	.	ZNF737	50	.	NM_001159293	exon4	c.C1077T	p.H359H	TATCTTGTGTGTA	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43528932	43528932	+	Missense_Mutation	SNP	C	C	T	rs111739483	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	133	226	0	0.480144	0	C|0.977;T|0.023	0.023	strong	.	PSG11	57	.	NM_002785	exon2	c.G341A	p.R114Q	TCCTCCCGGGTGA	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6015011	6015011	+	Silent	SNP	T	T	C	rs343500	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	75	0	0.483516	0	T|0.882;C|0.118	0.118	strong	RANBP6,NS,carcinoma,0,1	RANBP6	127	1	NM_012416	exon1	c.A597G	p.T199T	GGATAATGTCCTG	.	PASS	Atlas-SNP
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	102	226	1	0.5	0.00442478	C|0.856;T|0.144	0.144	strong	.	UPK1A	23	.	NM_007000	exon1	c.C26T	p.A9V	CGGAGGCCGAGAA	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48175235	48175235	+	Missense_Mutation	SNP	G	G	T	rs16945874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	53	85	0	0.481818	0	G|0.841;T|0.159	0.159	strong	.	ABCC12	190	.	NM_033226	exon3	c.C305A	p.A102E	ACCCTTGCTACCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412066	105412066	+	Missense_Mutation	SNP	C	C	T	rs77154428	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	135	252	3	0.366848	0.0119048	C|0.547;T|0.453	0.453	strong	AHNAK2_ENST00000333244,NS,carcinoma,-1,2	AHNAK2	719	2	NM_138420	exon7	c.G9722A	p.R3241H	CCCTTGCGATCTA	.	scavenged	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	45001398	45001398	+	Silent	SNP	G	G	A	rs10423647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	20	32	0	0.454545	0	G|0.906;A|0.094	0.094	strong	.	ZNF180	103	.	NM_013256	exon2	c.C70T	p.L24L	CCTCCAGGCACAG	.	PASS	Atlas-SNP
CRIP1	1396	hgsc.bcm.edu	37	14	105954682	105954682	+	Silent	SNP	C	C	G	rs1128308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	72	170	0	0.553846	0	C|0.834;G|0.166	0.166	strong	.	CRIP1	1	.	NM_001311	exon4	c.C150G	p.P50P	CAAACCCTACTGC	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	37	8	140743460	140743460	+	Silent	SNP	G	G	A	rs148857575	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	76	0	0.505882	0	G|0.998;A|0.002	0.002	strong	.	TRAPPC9	114	.	NM_031466	exon23	c.C3585T	p.S1195S	CTGGCCGGACGGC	.	PASS	Atlas-SNP
BRCA1	672	hgsc.bcm.edu	37	17	41245643	41245643	+	Silent	SNP	A	A	G	rs369373293		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	61	122	0	0.448529	0	.	.	weak	.	BRCA1	304	.	NM_007300	exon10	c.T1905C	p.N635N	AGTACAATTAGGT	.	PASS	Atlas-SNP
TMBIM6	7009	hgsc.bcm.edu	37	12	50153060	50153060	+	Silent	SNP	A	A	G	rs12310796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	58	142	0	0.453125	0	A|0.993;G|0.007	0.007	strong	.	TMBIM6	26	.	NM_001098576	exon8	c.A744G	p.Q248Q	TACTCAACTCATT	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	91	1	1	0.010989	G|0.744;A|0.256	0.256	strong	ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	NM_001007231	exon6	c.G756A	p.Q252Q	GAGCCAGTACGAA	.	scavenged	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46652929	46652929	+	Silent	SNP	G	G	A	rs6008365	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	38	49	0	0.513514	0	G|0.739;A|0.261	0.261	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C6291T	p.S2097S	ATACACGGACACA	.	PASS	Atlas-SNP
FLT3LG	2323	hgsc.bcm.edu	37	19	49977929	49977929	+	Silent	SNP	A	A	G	rs75750998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	357	183	285	0	0.512605	0	A|0.974;G|0.026	0.026	strong	.	FLT3LG	22	.	NM_001204503	exon1	c.A33G	p.T11T	CCCAACAGTGCGT	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939674	12939674	+	Silent	SNP	C	C	G	rs72474510	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	44	141	0	0.335878	0	C|0.879;G|0.121	0.121	strong	PRAMEF4,NS,carcinoma,0,2	PRAMEF4	62	2	NM_001009611	exon4	c.G1128C	p.L376L	GCGGCTCAGGGCA	.	scavenged	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	37	7	42004897	42004897	+	Silent	SNP	G	G	C	rs35448119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	41	100	0	0.465909	0	G|0.984;C|0.016	0.016	strong	.	GLI3	312	.	NM_000168	exon15	c.C3774G	p.L1258L	CCTGTTGAGACAG	.	PASS	Atlas-SNP
KCNK12	56660	hgsc.bcm.edu	37	2	47748487	47748487	+	Silent	SNP	G	G	A	rs77883212	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	35	86	0	0.432099	0	G|0.986;A|0.014	0.014	strong	.	KCNK12	11	.	NM_022055	exon2	c.C852T	p.I284I	GAGCAGGATGAAG	.	PASS	Atlas-SNP
ERN1	2081	hgsc.bcm.edu	37	17	62137893	62137893	+	Missense_Mutation	SNP	T	T	C	rs79107850	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	64	135	0	0.426667	0	T|0.990;C|0.010	0.010	strong	.	ERN1	102	.	NM_001433	exon11	c.A1142G	p.N381S	AGATTGTTGGGAA	.	PASS	Atlas-SNP
OC90	729330	hgsc.bcm.edu	37	8	133036743	133036743	+	Silent	SNP	A	A	G	rs11991659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	20	52	0	0.588235	0	A|0.952;G|0.048	0.048	strong	OC90_ENST00000262283,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,2	OC90	163	2	NM_001080399	exon14	c.T1419C	p.P473P	ATGAAGAGGCCCG	.	PASS	Atlas-SNP
TNFSF8	944	hgsc.bcm.edu	37	9	117668142	117668142	+	Silent	SNP	C	C	T	rs3181195	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	51	148	0	0.312883	0	C|0.661;T|0.339	0.339	strong	TNFSF8,colon,carcinoma,-1,1	TNFSF8	34	1	NM_001252290	exon3	c.G276A	p.R92R	TGGAGCCCTTTTC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919623	12919623	+	Silent	SNP	C	C	T	rs75838083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	152	341	1	0.470588	0.00293255	C|0.897;T|0.103	0.103	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.C363T	p.A121A	CTGGGCCCTGTCC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179610695	179610695	+	Missense_Mutation	SNP	C	C	T	rs72648915	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	47	97	0	0.47	0	C|0.961;T|0.039	0.039	strong	.	TTN	18412	.	NM_133379	exon46	c.G16432A	p.V5478M	CTATCACAGCAAA	.	PASS	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	37	9	37731007	37731007	+	Silent	SNP	C	C	T	rs2274324	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	81	125	0	0.613636	0	C|0.942;T|0.058	0.058	strong	.	FRMPD1	237	.	NM_014907	exon9	c.C765T	p.D255D	ACATGACTACCGC	.	PASS	Atlas-SNP
CLSPN	63967	hgsc.bcm.edu	37	1	36202585	36202585	+	Missense_Mutation	SNP	G	G	A	rs35490896	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	65	157	0	0.496183	0	G|0.935;A|0.065	0.065	strong	.	CLSPN	248	.	NM_022111	exon24	c.C3839T	p.S1280L	TTTCTTGAATTTC	.	PASS	Atlas-SNP
SLC22A20	440044	hgsc.bcm.edu	37	11	64981472	64981472	+	Silent	SNP	G	G	C	rs239258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	33	77	0	0.478261	0	G|0.614;C|0.386	0.386	strong	SLC22A20,NS,carcinoma,0,6	SLC22A20	36	6	NM_001004326	exon1	c.G129C	p.T43T	CTTCACGGCCGCT	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206658404	206658404	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	56	162	0	0.459016	0	.	.	none	.	IKBKE	77	.	NM_001193322	exon14	c.C1498T	p.R500W	AGGCTGCGGACTG	.	PASS	Atlas-SNP
EDC4	23644	hgsc.bcm.edu	37	16	67911517	67911517	+	Silent	SNP	T	T	C	rs8060686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	60	130	0	0.550459	0	T|0.669;C|0.331	0.331	strong	.	EDC4	101	.	NM_014329	exon6	c.T747C	p.C249C	CTGCTGTGAGGAG	.	PASS	Atlas-SNP
GTPBP3	84705	hgsc.bcm.edu	37	19	17450038	17450038	+	Silent	SNP	C	C	T	rs11880362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	23	43	0	0.489362	0	C|0.972;T|0.028	0.028	strong	.	GTPBP3	40	.	NM_133644	exon5	c.C867T	p.P289P	TGGACCCCCCAAT	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	103	236	1	0.420408	0.00423729	C|0.771;T|0.229	0.229	strong	KRTAP16-1,NS,carcinoma,+2,1	KRTAP16-1	12	1	NM_001146182	exon1	c.G412A	p.V138I	CACAAACGGTGGC	.	scavenged	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120569877	120569877	+	Silent	SNP	T	T	G	rs2305129	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	55	126	0	0.404412	0	T|0.887;G|0.113	0.113	strong	ENPP2,larynx,carcinoma,+2,1	ENPP2	254	1	NM_006209	exon26	c.A2632C	p.R878R	GCACCCTAGCTGT	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2535613	2535613	+	Silent	SNP	C	C	A	rs4648562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	78	173	0	0.404145	0	C|0.594;A|0.406	0.406	strong	.	MMEL1	64	.	NM_033467	exon10	c.G924T	p.V308V	CTCCAGCACCTGC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10469817	10469817	+	Silent	SNP	G	G	A	rs6996950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	35	68	0	0.397727	0	G|0.198;A|0.799	0.799	strong	.	RP1L1	453	.	NM_178857	exon4	c.C1791T	p.G597G	CTCGGTGCCCTGT	.	PASS	Atlas-SNP
KHDRBS2	202559	hgsc.bcm.edu	37	6	62442604	62442604	+	Silent	SNP	A	A	G	rs10484690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	79	176	0	0.44382	0	A|0.601;G|0.399	0.399	strong	.	KHDRBS2	103	.	NM_152688	exon7	c.T876C	p.Y292Y	GGTCGCATAGCTG	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6656897	6656897	+	Missense_Mutation	SNP	A	A	G	rs1806552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	40	44	0	1	0	A|0.289;G|0.711	0.711	strong	ZNF853_ENST00000457543,NS,carcinoma,+1,2	ZNF853	32	2	NM_017560	exon2	c.A89G	p.Q30R	AACTTCAATGTCT	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048640	33048640	+	Missense_Mutation	SNP	A	A	G	rs1042140	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	14	47	0	0.28	0	A|0.758;C|0.000;G|0.242;T|0.000	0.242	strong	.	HLA-DPB1	28	.	NM_002121	exon2	c.A292G	p.K98E	GAGGAGAAGCGGG	.	PASS	Atlas-SNP
IGLL1	3543	hgsc.bcm.edu	37	22	23922281	23922281	+	Missense_Mutation	SNP	C	C	T	rs116760479	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	33	78	0	0.370787	0	C|0.980;T|0.020	0.020	strong	.	IGLL1	27	.	NM_020070	exon1	c.G97A	p.V33M	TTACCACGGCCAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105407798	105407798	+	Missense_Mutation	SNP	T	T	C	rs4465542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	110	0	0.992308	0	T|0.466;C|0.534	0.534	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A13990G	p.T4664A	GAAATGTGGAAGT	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169510380	169510380	+	Silent	SNP	G	G	A	rs9287090	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	611	311	530	1	0.509002	0.00188679	G|0.758;A|0.242	0.242	strong	.	F5	301	.	NM_000130	exon13	c.C3948T	p.L1316L	CTGACCGAGGGCT	.	PASS	Atlas-SNP
MRPS24	64951	hgsc.bcm.edu	37	7	43906544	43906544	+	Silent	SNP	C	C	T	rs9154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	28	55	0	0.411765	0	C|0.953;T|0.047	0.047	strong	MRPS24,colon,carcinoma,-1,2	MRPS24	9	2	NM_032014	exon4	c.G258A	p.T86T	CTCCACCGTTCGC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547093	+	Silent	SNP	A	A	G	rs28513925	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	10	123	0	0.0847458	0	A|0.500;G|0.500	0.500	weak	EP400,NS,carcinoma,0,15	EP400	370	15	NM_015409	exon47	c.A8181G	p.Q2727Q	GCAACAACAGCAG	.	scavenged	Atlas-SNP
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983483	2983483	+	Silent	SNP	C	C	G	rs2074362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	48	60	0	0.505263	0	C|0.704;G|0.296	0.296	strong	.	FLYWCH1	27	.	NM_020912	exon5	c.C1146G	p.L382L	GACTCTCACCAGG	.	PASS	Atlas-SNP
KBTBD12	166348	hgsc.bcm.edu	37	3	127642814	127642814	+	Missense_Mutation	SNP	G	G	C	rs61268888	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	92	180	0	0.455446	0	G|0.846;C|0.154	0.154	strong	.	KBTBD12	41	.	NM_207335	exon1	c.G910C	p.V304L	GATCCTGTATCAC	.	PASS	Atlas-SNP
ZBED4	9889	hgsc.bcm.edu	37	22	50280688	50280688	+	Silent	SNP	A	A	C	rs9627781	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	34	66	0	0.515152	0	A|0.939;C|0.061	0.061	strong	.	ZBED4	102	.	NM_014838	exon2	c.A3378C	p.P1126P	CCCCCCAAGCATC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15795690	15795690	+	Missense_Mutation	SNP	G	G	C	rs61729079	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	48	96	0	0.317881	0	G|0.981;C|0.019	0.019	strong	.	CYP4F12	89	.	NM_023944	exon8	c.G983C	p.G328A	TGTTTGGAGGTGA	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38145841	38145841	+	Missense_Mutation	SNP	C	C	T	rs147388235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	522	236	469	1	0.452107	0.0021322	C|0.985;T|0.015	0.015	strong	.	RPGR	175	.	NM_001034853	exon15	c.G2411A	p.R804K	TCCCCTCTCCCCT	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31242869	31242869	+	Silent	SNP	G	G	A	rs201738430	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	762	74	759	2	0.0971129	0.00263505	G|0.889;A|0.111	0.111	strong	DDX11_ENST00000407793,NS,carcinoma,0,16	DDX11	188	16	NM_030653	exon9	c.G930A	p.E310E	GCAGGAGAAGCAG	.	scavenged	Atlas-SNP
MICAL1	64780	hgsc.bcm.edu	37	6	109767930	109767930	+	Missense_Mutation	SNP	G	G	T	rs9320288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	261	263	1	1	0.00380228	G|0.502;T|0.498	0.498	strong	.	MICAL1	79	.	NM_022765	exon18	c.C2273A	p.A758E	CCTTCCGCTTTGT	.	PASS	Atlas-SNP
C20orf201	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	Silent	SNP	C	C	G	rs6010717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	31	39	1	0.455882	0.025641	C|0.368;G|0.632	0.632	strong	C20orf201,NS,carcinoma,0,1	C20orf201	4	1	NM_001007125	exon2	c.G678C	p.A226A	CTCAGTCGCCGTC	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491840	110491840	+	Missense_Mutation	SNP	C	C	G	rs1783147	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	43	95	0	0.52439	0	C|0.626;G|0.374	0.374	strong	.	PKHD1L1	522	.	NM_177531	exon54	c.C9150G	p.H3050Q	ACCTCACCCAGGG	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	617804	617804	+	Silent	SNP	G	G	A	rs144281668	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	58	128	0	0.417266	0	G|0.999;A|0.001	0.001	strong	.	POLRMT	91	.	NM_005035	exon18	c.C3468T	p.H1156H	AGCTGCGTGAGTC	.	PASS	Atlas-SNP
USP14	9097	hgsc.bcm.edu	37	18	166819	166819	+	Silent	SNP	T	T	C	rs563155	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	26	41	0	0.464286	0	T|0.812;C|0.188	0.188	strong	.	USP14	41	.	NM_001037334	exon3	c.T195C	p.N65N	AAAAAATGTAAGT	.	PASS	Atlas-SNP
SPTAN1	6709	hgsc.bcm.edu	37	9	131362361	131362361	+	Silent	SNP	T	T	C	rs945831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	93	202	0	0.406114	0	T|0.963;C|0.037	0.037	strong	.	SPTAN1	266	.	NM_003127	exon27	c.T3546C	p.D1182D	ATAGGATGAAACT	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152320501	152320501	+	Silent	SNP	T	T	C	rs7566841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	50	113	0	0.625	0	T|0.981;C|0.019	0.019	strong	.	RIF1	244	.	NM_018151	exon30	c.T4467C	p.T1489T	GAAGACTCTTGGG	.	PASS	Atlas-SNP
CNNM1	26507	hgsc.bcm.edu	37	10	101120671	101120671	+	Silent	SNP	G	G	A	rs61735150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	75	0	0.494624	0	G|0.992;A|0.008	0.008	strong	CNNM1_ENST00000356713,NS,carcinoma,0,2	CNNM1	101	2	NM_020348	exon3	c.G1797A	p.T599T	GGACACGGAGATG	.	PASS	Atlas-SNP
MESP2	145873	hgsc.bcm.edu	37	15	90320000	90320000	+	Missense_Mutation	SNP	G	G	A	rs28462216	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	36	0	1	0	G|0.940;A|0.060	0.060	strong	.	MESP2	20	.	NM_001039958	exon1	c.G412A	p.V138M	TCGGCCGTGCTGG	.	PASS	Atlas-SNP
KIAA0947	23379	hgsc.bcm.edu	37	5	5464237	5464237	+	Missense_Mutation	SNP	A	A	C	rs10065646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	23	43	0	0.534884	0	A|0.932;C|0.068	0.068	strong	.	KIAA0947	301	.	NM_015325	exon13	c.A4790C	p.Q1597P	AAACTCAAAGAAG	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610394	38610394	+	Missense_Mutation	SNP	G	G	A	rs140119542	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	33	61	0	0.5	0	G|1.000;A|0.000	0.000	strong	SIPA1L3,caecum,carcinoma,0,1	SIPA1L3	150	1	NM_015073	exon9	c.G2740A	p.G914R	TACTGCGGGGATG	.	PASS	Atlas-SNP
ADAT3	113179	hgsc.bcm.edu	37	19	1912986	1912986	+	Silent	SNP	C	C	T	rs76159002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	22	11	0	1	0	C|0.816;T|0.184	0.184	strong	ADAT3,NS,haematopoietic_neoplasm,0,1	ADAT3	15	1	NM_138422	exon2	c.C940T	p.L314L	ATGGCCCTGGTGC	.	PASS	Atlas-SNP
ZNF765	91661	hgsc.bcm.edu	37	19	53911786	53911786	+	Silent	SNP	G	G	A	rs10407020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	51	0	0.428571	0	G|0.951;A|0.049	0.049	strong	.	ZNF765	61	.	NM_001040185	exon4	c.G978A	p.P326P	GAAACCGTACAAG	.	PASS	Atlas-SNP
KIRREL	55243	hgsc.bcm.edu	37	1	158057633	158057633	+	Silent	SNP	C	C	G	rs36008419	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	108	1	1	0.00925926	C|0.762;G|0.238	0.238	strong	KIRREL_ENST00000368173,NS,carcinoma,0,2	KIRREL	346	2	NM_018240	exon6	c.C750G	p.P250P	CAACCCCGAGATC	.	PASS	Atlas-SNP
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	277	19	288	13	0.0685921	0.0451389	A|1.000;G|0.000	0.000	weak	OR8B3,NS,carcinoma,0,1	OR8B3	36	1	NM_001005467	exon1	c.T321C	p.F107F	GATGACAAAAAAG	.	scavenged	Atlas-SNP
ACER2	340485	hgsc.bcm.edu	37	9	19450598	19450598	+	Silent	SNP	G	G	C	rs7855739	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	328	282	1	0.993939	0.0035461	G|0.933;C|0.067	0.067	strong	.	ACER2	24	.	NM_001010887	exon6	c.G792C	p.L264L	CCTCCTGTGTGCC	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786845	75786845	+	Silent	SNP	T	T	C	rs62250105	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	47	46	0	0.465347	0	T|0.250;C|0.750	0.750	strong	.	ZNF717	160	.	NM_001128223	exon5	c.A1929G	p.G643G	TTTCTCTCCTGTG	.	PASS	Atlas-SNP
PDIA4	9601	hgsc.bcm.edu	37	7	148701245	148701245	+	Missense_Mutation	SNP	C	C	T	rs61739277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	78	208	0	0.445714	0	C|0.992;T|0.008	0.008	strong	.	PDIA4	57	.	NM_004911	exon10	c.G1579A	p.V527I	CCTTGACGGGTCC	.	PASS	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	128844838	128844838	+	Silent	SNP	A	A	G	rs28630040	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	39	74	0	0.46988	0	A|0.892;G|0.108	0.108	strong	.	ADAMTS19	216	.	NM_133638	exon3	c.A798G	p.T266T	CATAACAGGTCAC	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	710966	710966	+	Missense_Mutation	SNP	G	G	A	rs7860464	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	103	0	0.451613	0	G|0.843;A|0.157	0.157	strong	.	KANK1	231	.	NM_001256876	exon7	c.G200A	p.R67Q	AGAGGCGGAAGCC	.	PASS	Atlas-SNP
PRPF8	10594	hgsc.bcm.edu	37	17	1554770	1554770	+	Silent	SNP	A	A	G	rs1802491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	41	98	0	0.506173	0	A|0.777;G|0.223	0.223	strong	.	PRPF8	169	.	NM_006445	exon41	c.T6588C	p.H2196H	CTTGGCATGGGTG	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	59	106	0	0.504274	0	T|0.781;C|0.219	0.219	strong	ADAM32,NS,carcinoma,0,1	ADAM32	70	1	NM_145004	exon16	c.T1743C	p.T581T	CATAACTGTAGAC	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52995127	52995127	+	Missense_Mutation	SNP	C	C	T	rs61747194	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	21	45	0	0.456522	0	C|0.987;T|0.013	0.013	strong	.	KRT72	70	.	NM_001146225	exon1	c.G110A	p.R37Q	TTGACCCGGGCCC	.	PASS	Atlas-SNP
USP19	10869	hgsc.bcm.edu	37	3	49149020	49149020	+	Missense_Mutation	SNP	T	T	C	rs13321689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	39	65	0	0.609375	0	T|0.972;C|0.028	0.028	strong	.	USP19	158	.	NM_001199161	exon21	c.A3130G	p.T1044A	CACTGGTGCTGGG	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43893072	43893072	+	Silent	SNP	G	G	A	rs55877445		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	128	328	0	0.380952	0	.	.	weak	.	STRC	58	.	NM_153700	exon25	c.C4842T	p.F1614F	TGACCTGAACTCC	.	PASS	Atlas-SNP
ZBTB37	84614	hgsc.bcm.edu	37	1	173839435	173839435	+	Silent	SNP	G	G	A	rs9425761	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	89	170	0	0.463542	0	G|0.875;A|0.125	0.125	strong	.	ZBTB37	38	.	NM_032522	exon3	c.G72A	p.Q24Q	AAACCAGTTGCGC	.	PASS	Atlas-SNP
ABAT	18	hgsc.bcm.edu	37	16	8868776	8868776	+	Silent	SNP	C	C	A	rs1641022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	105	0	0.456311	0	C|0.674;A|0.326	0.326	strong	.	ABAT	46	.	NM_001127448	exon13	c.C984A	p.V328V	CGAGGTCCAGACC	.	PASS	Atlas-SNP
ERI2	112479	hgsc.bcm.edu	37	16	20802172	20802172	+	Missense_Mutation	SNP	C	C	T	rs2301770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	68	173	0	0.450331	0	C|0.906;T|0.094	0.094	strong	.	ERI2	50	.	NM_080663	exon9	c.G815A	p.G272D	AAATACCCAAATT	.	PASS	Atlas-SNP
SRGAP2D	100996712	hgsc.bcm.edu	37	1	206574931	206574931	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1642	188	1644	1	0.114495	0.000608273	.	.	none	SRGAP2_ENST00000414007,NS,carcinoma,0,3	.	.	3	NM_001271887	exon4	c.G521A	p.R174H	AGCAGCGCCTCAT	.	scavenged	Atlas-SNP
DDX59	83479	hgsc.bcm.edu	37	1	200635550	200635550	+	Missense_Mutation	SNP	T	T	C	rs3795634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	148	135	0	0.993289	0	T|0.871;C|0.129	0.129	strong	.	DDX59	117	.	NM_001031725	exon2	c.A319G	p.I107V	CACAGATGGGTTC	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118512719	118512719	+	Missense_Mutation	SNP	G	G	T	rs140504036	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	49	59	0	1	0	G|0.999;T|0.001	0.001	strong	.	SPAG17	263	.	NM_206996	exon46	c.C6347A	p.P2116Q	CTGGGTGGGGGCT	.	PASS	Atlas-SNP
NAT10	55226	hgsc.bcm.edu	37	11	34133767	34133767	+	Silent	SNP	G	G	A	rs36003235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	77	168	0	0.472393	0	G|0.996;A|0.004	0.004	strong	.	NAT10	78	.	NM_024662	exon4	c.G369A	p.L123L	TGTGCTGCAGGTG	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19377881	19377881	+	Missense_Mutation	SNP	G	G	A	rs138502172	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	599	62	566	3	0.103506	0.00530035	G|0.973;A|0.027	0.027	strong	OR11H12,NS,carcinoma,0,1	OR11H12	58	1	NM_001013354	exon1	c.G288A	p.M96I	CAAGATGTTGGTC	.	scavenged	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	109	126	0	0.707792	0	G|0.732;A|0.268	0.268	strong	.	DMBT1	677	.	NM_007329	exon20	c.G2343A	p.S781S	CACGTCGGCCCCA	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163266	163266	+	Missense_Mutation	SNP	C	C	G	rs3810867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	103	112	0	0.990385	0	C|0.689;G|0.311	0.311	strong	.	PLEKHG4B	167	.	NM_052909	exon11	c.C2011G	p.R671G	ACCCTGCGCCCAG	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12409263	12409263	+	Missense_Mutation	SNP	C	C	A	rs17165906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	95	239	1	0.458937	0.0041841	C|0.841;A|0.159	0.159	strong	.	VWDE	123	.	NM_001135924	exon12	c.G2669T	p.C890F	TTGGGGCATTTTA	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4016943	4016943	+	Silent	SNP	A	A	G	rs2230741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	45	94	0	0.6	0	A|0.856;G|0.144	0.144	strong	.	ADCY9	151	.	NM_001116	exon11	c.T2895C	p.S965S	CACCGAACTATTG	.	PASS	Atlas-SNP
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	94	0	0.528571	0	C|0.947;G|0.053	0.053	strong	.	TBC1D15	99	.	NM_022771	exon13	c.C1383G	p.S461S	ACTTTCCCCTCTT	.	PASS	Atlas-SNP
CXorf36	79742	hgsc.bcm.edu	37	X	45051111	45051111	+	Missense_Mutation	SNP	C	C	T	rs1132201	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	79	126	0	0.478788	0	0|0.013;T|0.348	0.348	strong	.	CXorf36	53	.	NM_176819	exon2	c.G383A	p.R128K	CAGATTCTCCTGT	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	53907906	53907906	+	Missense_Mutation	SNP	A	A	C	rs16966320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	33	118	0	0.4125	0	A|0.863;C|0.137	0.137	strong	.	WDR72	177	.	NM_182758	exon15	c.T2497G	p.S833A	TCAAAGAAATTCC	.	PASS	Atlas-SNP
ASPG	374569	hgsc.bcm.edu	37	14	104559922	104559922	+	Missense_Mutation	SNP	C	C	G	rs1744284	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	115	1	0.990654	0.00869565	C|0.634;G|0.366	0.366	strong	.	ASPG	34	.	NM_001080464	exon3	c.C286G	p.L96V	GTTTGCCTTGCCC	.	PASS	Atlas-SNP
TMEM102	284114	hgsc.bcm.edu	37	17	7339903	7339903	+	Missense_Mutation	SNP	C	C	G	rs76805816	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	62	89	0	0.473282	0	C|0.967;G|0.033	0.033	strong	.	TMEM102	11	.	NM_178518	exon3	c.C605G	p.A202G	ACGAGGCGCCGGT	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135745648	135745648	+	Missense_Mutation	SNP	G	G	A	rs113683052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	45	119	0	0.424528	0	G|0.989;A|0.011	0.011	strong	.	.	.	.	NM_025052	exon7	c.C794T	p.P265L	GCTCCCGGAGGCT	.	PASS	Atlas-SNP
CLDND2	125875	hgsc.bcm.edu	37	19	51870771	51870771	+	Missense_Mutation	SNP	C	C	A	rs61737052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	101	179	0	0.526042	0	C|0.949;A|0.051	0.051	strong	.	CLDND2	11	.	NM_152353	exon3	c.G370T	p.V124F	AGAAGACGTTGTT	.	PASS	Atlas-SNP
OR51L1	119682	hgsc.bcm.edu	37	11	5020542	5020542	+	Silent	SNP	A	A	T	rs368384016		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	423	203	374	0	0.479905	0	.	.	weak	.	OR51L1	60	.	NM_001004755	exon1	c.A330T	p.T110T	ATTCACATTCCTG	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61897542	61897542	+	Silent	SNP	G	G	A	rs145875137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	20	42	0	0.5	0	G|0.996;A|0.004	0.004	strong	.	INCENP	122	.	NM_001040694	exon4	c.G543A	p.Q181Q	TGAGCAGCATGTC	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101718965	101718965	+	Missense_Mutation	SNP	G	G	A	rs62513921	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	74	145	0	0.334842	0	.	.	weak	PABPC1,NS,carcinoma,+2,2	PABPC1	76	2	NM_002568	exon11	c.C1516T	p.R506C	CGGTGCGGACAGC	.	PASS	Atlas-SNP
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	15	21	0	0.454545	0	C|0.815;G|0.185	0.185	strong	.	SNTB2	22	.	NM_006750	exon1	c.C441G	p.P147P	CTTCCCCGGGCTG	.	PASS	Atlas-SNP
EPB41L3	23136	hgsc.bcm.edu	37	18	5416221	5416221	+	Missense_Mutation	SNP	C	C	T	rs9966357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	87	145	0	0.520958	0	C|0.945;T|0.055	0.055	strong	.	EPB41L3	222	.	NM_012307	exon13	c.G1663A	p.A555T	CCAAGGCGGGCTC	.	PASS	Atlas-SNP
MS4A6A	64231	hgsc.bcm.edu	37	11	59943082	59943082	+	Silent	SNP	C	C	T	rs138028890	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	64	94	0	0.581818	0	C|0.997;T|0.003	0.003	strong	.	MS4A6A	85	.	NM_001247999	exon6	c.G426A	p.V142V	GCTATGCACCTGA	.	PASS	Atlas-SNP
SH3BP1	23616	hgsc.bcm.edu	37	22	38035851	38035851	+	Silent	SNP	A	A	G	rs13055139	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	42	107	0	0.385321	0	A|0.816;G|0.184	0.184	strong	.	SH3BP1	41	.	NM_018957	exon1	c.A57G	p.G19G	CTTGGGACGGTGA	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3656625	3656625	+	Missense_Mutation	SNP	G	G	A	rs79842542	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	146	261	2	0.572549	0.00766284	G|0.937;A|0.063	0.063	strong	SLX4,NS,carcinoma,+1,2	SLX4	173	2	NM_032444	exon3	c.C610T	p.R204C	CTGTGCGGGGTTT	.	scavenged	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263645	263645	+	Silent	SNP	C	C	T	rs200761914	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	14	322	8	0.0436137	0.0248447	C|0.981;T|0.019	0.019	strong	C17orf97_ENST00000360127,NS,carcinoma,+2,2	C17orf97	76	2	NM_001013672	exon2	c.C1011T	p.P337P	CCACCCCGACCCC	.	scavenged	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79083120	79083120	+	Missense_Mutation	SNP	G	G	A	rs61732944	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	35	166	0	0.259259	0	G|0.438;A|0.562	0.562	strong	.	ADAMTS7	142	.	NM_014272	exon6	c.C920T	p.T307M	TGGTGCGTGATCT	.	PASS	Atlas-SNP
CST7	8530	hgsc.bcm.edu	37	20	24939590	24939590	+	Silent	SNP	G	G	C	rs1056033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	34	70	0	0.441558	0	G|0.504;C|0.496	0.496	strong	.	CST7	14	.	NM_003650	exon3	c.G270C	p.L90L	TATGCTGGAGGTG	.	PASS	Atlas-SNP
CNRIP1	25927	hgsc.bcm.edu	37	2	68546449	68546449	+	Silent	SNP	G	G	A	rs13025842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	29	86	0	0.527273	0	G|0.780;A|0.220	0.220	strong	.	CNRIP1	45	.	NM_001111101	exon1	c.C84T	p.D28D	CTGCCCGTCCACC	.	PASS	Atlas-SNP
RNH1	6050	hgsc.bcm.edu	37	11	499120	499120	+	Missense_Mutation	SNP	G	G	A	rs17585	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	82	0	0.494737	0	G|0.891;A|0.109	0.109	strong	.	RNH1	24	.	NM_203384	exon5	c.C509T	p.P170L	AAGTCCGGCTTGG	.	PASS	Atlas-SNP
PDPN	10630	hgsc.bcm.edu	37	1	13910417	13910417	+	Silent	SNP	C	C	T	rs355025	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	67	122	0	0.540323	0	C|0.526;T|0.474	0.474	strong	PDPN,NS,carcinoma,0,1	PDPN	44	1	NM_006474	exon1	c.C117T	p.P39P	GGCCCCCCCACCG	.	PASS	Atlas-SNP
NOS1AP	9722	hgsc.bcm.edu	37	1	162335256	162335256	+	Silent	SNP	C	C	T	rs348624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	53	108	0	0.473214	0	C|0.779;T|0.221	0.221	strong	.	NOS1AP	139	.	NM_014697	exon9	c.C1002T	p.R334R	GGCTCGCGTGCAT	.	PASS	Atlas-SNP
TAAR1	134864	hgsc.bcm.edu	37	6	132967032	132967032	+	Silent	SNP	T	T	G	rs73775159	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	144	221	0	0.529412	0	T|0.989;G|0.011	0.011	strong	.	TAAR1	41	.	NM_138327	exon1	c.A111C	p.T37T	AACGAGTGTGGTC	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27472936	27472936	+	Missense_Mutation	SNP	C	C	T	rs3755652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	124	198	0	0.506122	0	C|0.843;T|0.157	0.157	strong	.	SLC4A7	119	.	NM_003615	exon7	c.G976A	p.E326K	GACTCTCTTGGGA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103398300	103398300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	27	207	0	0.118943	0	.	.	none	.	.	.	.	NM_001146197	exon4	c.C4747T	p.L1583F	TGACAAGCTCATT	.	PASS	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	37	6	43307861	43307861	+	Missense_Mutation	SNP	G	G	A	rs10948072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	100	128	0	0.990099	0	G|0.847;A|0.153	0.153	strong	.	ZNF318	175	.	NM_014345	exon10	c.C3875T	p.T1292I	CTTGGGGTCACCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417102	105417102	+	Silent	SNP	T	T	C	rs2248966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	302	302	1	0.980519	0.00331126	T|0.517;C|0.483	0.483	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A4686G	p.P1562P	GCCCTCTGGGAGT	.	PASS	Atlas-SNP
RNF122	79845	hgsc.bcm.edu	37	8	33408901	33408901	+	Silent	SNP	C	C	G	rs3735949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	60	124	0	0.461538	0	C|0.864;G|0.136	0.136	strong	.	RNF122	17	.	NM_024787	exon3	c.G189C	p.L63L	GTTCCGCAGTTTG	.	PASS	Atlas-SNP
ABCB10	23456	hgsc.bcm.edu	37	1	229683264	229683264	+	Silent	SNP	G	G	A	rs3738187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	143	115	0	1	0	G|0.690;A|0.310	0.310	strong	.	ABCB10	71	.	NM_012089	exon3	c.C903T	p.S301S	GCCTACGGAAGCC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	8	50	0	0.126984	0	A|0.830;C|0.170	0.170	strong	ATXN1,colon,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.T633G	p.H211Q	CTGCTGATGCTGA	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31294343	31294343	+	Missense_Mutation	SNP	A	A	T	rs12898290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	81	0	0.5	0	A|0.933;T|0.067	0.067	strong	.	TRPM1	183	.	NM_001252020	exon27	c.T4611A	p.H1537Q	CTCTTTATGCTCA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Silent	SNP	A	A	G	rs7966348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	82	105	0	0.630769	0	A|0.823;G|0.177	0.177	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon10	c.T1275C	p.Y425Y	CCTACCATATTTG	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	20	48	0	0.416667	0	A|0.793;T|0.207	0.207	strong	.	UBR2	134	.	NM_001184801	exon5	c.A552T	p.S184S	TTTATCAGAAGAT	.	PASS	Atlas-SNP
TSPAN2	10100	hgsc.bcm.edu	37	1	115604798	115604798	+	Silent	SNP	C	C	T	rs10776795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	315	145	323	1	0.460317	0.00309598	C|0.686;T|0.314	0.314	strong	TSPAN2,NS,carcinoma,0,1	TSPAN2	37	1	NM_005725	exon3	c.G228A	p.G76G	GCAGCACCCGAAG	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47607785	47607785	+	Missense_Mutation	SNP	G	G	A	rs2056900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	56	106	0	0.4375	0	G|0.768;A|0.232	0.232	strong	.	CYP4A22	60	.	NM_001010969	exon4	c.G388A	p.G130S	GGGTACGGCTTGC	.	PASS	Atlas-SNP
SPDYE4	388333	hgsc.bcm.edu	37	17	8661641	8661641	+	Silent	SNP	C	C	T	rs72848106	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	27	50	0	0.54	0	C|0.967;T|0.033	0.033	strong	SPDYE4,NS,carcinoma,-1,2	SPDYE4	22	2	NM_001128076	exon1	c.G60A	p.T20T	CCGTACCGTTGTG	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48594973	48594973	+	Missense_Mutation	SNP	G	G	A	rs75706684	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	100	169	0	0.510204	0	G|0.970;A|0.030	0.030	strong	MYCBPAP,NS,NS,0,1	MYCBPAP	135	1	NM_032133	exon4	c.G511A	p.D171N	AGCTTCGATGGCA	.	PASS	Atlas-SNP
PPIG	9360	hgsc.bcm.edu	37	2	170493784	170493784	+	Silent	SNP	T	T	C	rs114584157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	44	137	0	0.357724	0	T|0.997;C|0.003	0.003	strong	.	PPIG	100	.	NM_004792	exon14	c.T2016C	p.N672N	TCATAATAGCTCA	.	PASS	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	135	232	0	0.521236	0	C|0.949;T|0.051	0.051	strong	.	CHRD	149	.	NM_003741	exon3	c.C280T	p.P94S	AGGGGCCCTGGCA	.	PASS	Atlas-SNP
KRTAP22-2	100288287	hgsc.bcm.edu	37	21	31962649	31962649	+	Silent	SNP	G	G	A	rs78392137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	79	123	0	0.530201	0	G|0.990;A|0.010	0.010	strong	.	KRTAP22-2	6	.	NM_001164434	exon1	c.C45T	p.C15C	ATAGCTGCAACCA	.	PASS	Atlas-SNP
FAM211B	388886	hgsc.bcm.edu	37	22	24984261	24984261	+	Nonsense_Mutation	SNP	G	G	A	rs201281973	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	106	195	0	0.527363	0	G|1.000;A|0.000	0.000	strong	C22orf36,colon,carcinoma,0,1	.	.	1	NM_207644	exon3	c.C343T	p.R115X	GCTGTCGGCAGAT	.	PASS	Atlas-SNP
NIPAL2	79815	hgsc.bcm.edu	37	8	99205612	99205612	+	Splice_Site	SNP	C	C	T	rs3735887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	197	239	0	1	0	C|0.467;T|0.533	0.533	strong	.	NIPAL2	23	.	NM_024759	exon12	c.1067+1G>A	.	CACTCACCTCCAA	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56459614	56459614	+	Missense_Mutation	SNP	G	G	C	rs306506	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	93	0	1	0	G|0.334;C|0.665	0.665	strong	.	NLRP8	225	.	NM_176811	exon1	c.G346C	p.V116L	TGTGTTGTAGTCC	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78437182	78437182	+	Silent	SNP	G	G	A	rs689369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	123	256	0	0.49004	0	G|0.814;A|0.186	0.186	strong	.	.	.	.	NM_001098816	exon23	c.C3492T	p.D1164D	GGACGCGTCAATT	.	PASS	Atlas-SNP
CMPK2	129607	hgsc.bcm.edu	37	2	7003680	7003680	+	Silent	SNP	T	T	C	rs77719173	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	52	97	0	0.368794	0	T|0.968;C|0.032	0.032	strong	.	CMPK2	30	.	NM_001256478	exon2	c.A705G	p.A235A	AAGCACTGCCCGG	.	PASS	Atlas-SNP
ALG1	56052	hgsc.bcm.edu	37	16	5132586	5132586	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	7	98	0	0.0636364	0	.	.	none	ALG1,NS,carcinoma,0,1	ALG1	35	1	NM_019109	exon11	c.C1099G	p.H367D	TGTCTGCACACGT	.	scavenged	Atlas-SNP
RAB8A	4218	hgsc.bcm.edu	37	19	16238279	16238279	+	Silent	SNP	C	C	T	rs1043308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	59	132	0	0.41844	0	A|0.000;C|0.710;G|0.000;T|0.290	0.290	strong	.	RAB8A	19	.	NM_005370	exon5	c.C357T	p.L119L	GATACTCGGGAAC	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19166243	19166243	+	Silent	SNP	G	G	A	rs12075191	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	108	176	0	0.529412	0	G|0.950;A|0.050	0.050	strong	.	TAS1R2	134	.	NM_152232	exon6	c.C2370T	p.I790I	GTCCACGATGGTG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	62	113	0	0.462687	0	C|0.734;T|0.266	0.266	strong	.	HLA-G	90	.	NM_002127	exon4	c.C351T	p.H117H	TTCTCACACCCTC	.	PASS	Atlas-SNP
RNF186	54546	hgsc.bcm.edu	37	1	20141283	20141283	+	Silent	SNP	C	C	T	rs1541184	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	67	106	0	0.577586	0	C|0.912;T|0.088	0.088	strong	.	RNF186	14	.	NM_019062	exon1	c.G312A	p.A104A	CACCACCGCCTCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513439	195513439	+	Missense_Mutation	SNP	G	G	A	rs200271894		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	521	145	518	0	0.278311	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C5012T	p.S1671F	GCTGAGGAAGTGC	.	PASS	Atlas-SNP
DDX53	168400	hgsc.bcm.edu	37	X	23019346	23019346	+	Missense_Mutation	SNP	G	G	T	rs5926203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	96	0	1	0	G|0.686;0|0.012	.	strong	.	DDX53	76	.	NM_182699	exon1	c.G1172T	p.R391M	AGATAAGGAAGAT	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55755491	55755491	+	Missense_Mutation	SNP	C	C	T	rs2135720	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	52	116	0	0.472727	0	C|0.754;T|0.246	0.246	strong	PCDH15_ENST00000417177,NS,carcinoma,-1,4	PCDH15	1715	4	NM_001142763	exon22	c.G2801A	p.R934Q	TATATTCGTTTAC	.	PASS	Atlas-SNP
DEF8	54849	hgsc.bcm.edu	37	16	90032296	90032296	+	Silent	SNP	T	T	G	rs11861894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	63	122	0	0.577982	0	T|0.861;G|0.139	0.139	strong	.	DEF8	28	.	NM_207514	exon13	c.T1464G	p.T488T	CACCACTTGTCCC	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	18	67	0	0.375	0	C|0.250;G|0.750	0.750	weak	PRR21,pharynx,carcinoma,0,4	PRR21	53	4	NM_001080835	exon1	c.G348C	p.S116S	CATGGACGAAGGG	.	scavenged	Atlas-SNP
IL34	146433	hgsc.bcm.edu	37	16	70690989	70690989	+	Missense_Mutation	SNP	G	G	C	rs8046424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	124	0	1	0	G|0.354;C|0.646	0.646	strong	.	IL34	26	.	NM_152456	exon5	c.G367C	p.E123Q	GAGGTGGAGACGC	.	PASS	Atlas-SNP
TMEM198	130612	hgsc.bcm.edu	37	2	220414019	220414019	+	Silent	SNP	T	T	C	rs13023533	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	199	210	0	0.985148	0	T|0.559;C|0.441	0.441	strong	TMEM198,NS,carcinoma,0,2	TMEM198	36	2	NM_001005209	exon4	c.T888C	p.P296P	AGACCCTGCTTAT	.	PASS	Atlas-SNP
IFNA14	3448	hgsc.bcm.edu	37	9	21239578	21239578	+	Silent	SNP	C	C	T	rs141933410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	429	43	360	0	0.100233	0	C|0.999;G|0.000;T|0.001	0.001	strong	.	IFNA14	29	.	NM_002172	exon1	c.G357A	p.L119L	GGCTTCCAGGTCA	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103518036	103518036	+	Silent	SNP	A	A	G	rs55686372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	29	61	0	0.460317	0	A|0.995;G|0.005	0.005	strong	.	.	.	.	NM_001204425	exon17	c.A3336G	p.Q1112Q	AGTGCAAAGTGTG	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6621677	6621677	+	Silent	SNP	C	C	G	rs147252633	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	88	204	0	0.486188	0	C|0.994;G|0.006	0.006	strong	.	MAN2B2	80	.	NM_015274	exon18	c.C2838G	p.S946S	GGGGTCCGTGGTG	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88500822	88500822	+	Missense_Mutation	SNP	C	C	G	rs77490207	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	31	62	0	0.516667	0	C|0.988;G|0.012	0.012	strong	.	ZNF469	121	.	NM_001127464	exon2	c.C6860G	p.P2287R	CCCCGCCCCACAC	.	PASS	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40462780	40462780	+	Silent	SNP	G	G	A	rs1801389	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	50	114	0	0.480769	0	G|0.879;A|0.121	0.121	strong	.	BUB1B	71	.	NM_001211	exon4	c.G282A	p.K94K	TGGGAAGGAGAGT	.	PASS	Atlas-SNP
LIFR	3977	hgsc.bcm.edu	37	5	38510768	38510768	+	Silent	SNP	T	T	C	rs141925289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	118	0	0.439024	0	T|0.997;C|0.003	0.003	strong	.	LIFR	348	.	NM_002310	exon7	c.A789G	p.V263V	TGAGCCTACAAGT	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	127	259	0	0.430508	0	C|0.738;T|0.262	0.262	strong	.	HLA-G	90	.	NM_002127	exon6	c.C942T	p.G314G	TGCTGGCCTGGTT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90497589	90497589	+	Missense_Mutation	SNP	A	A	C	rs4707569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	26	18	0	1	0	A|0.832;C|0.168	0.168	strong	.	MDN1	478	.	NM_014611	exon8	c.T1318G	p.F440V	CAAAAAACTGAAA	.	PASS	Atlas-SNP
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37730017	37730017	+	Missense_Mutation	SNP	G	G	A	rs16887092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	113	114	0	1	0	G|0.890;A|0.110	0.110	strong	.	RAB11FIP1	105	.	NM_001002814	exon4	c.C2303T	p.A768V	TCTTCAGCTGCAT	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1003439	1003439	+	Missense_Mutation	SNP	G	G	A	rs55646937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	1	0	1	0	G|0.903;A|0.097	0.097	strong	.	GRIN3B	46	.	NM_138690	exon2	c.G737A	p.R246H	GTGCCCGTCGGGT	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35435006	35435006	+	Missense_Mutation	SNP	G	G	A	rs1345658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	133	112	0	0.992537	0	G|0.345;T|0.003	.	strong	.	ZNF30	44	.	NM_001099438	exon5	c.G1139A	p.R380K	GCGGGAGAACCTT	.	PASS	Atlas-SNP
SLC27A2	11001	hgsc.bcm.edu	37	15	50474766	50474766	+	Missense_Mutation	SNP	A	A	C	rs1648348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	11	58	0	0.215686	0	A|0.412;C|0.588	0.588	strong	.	SLC27A2	50	.	NM_003645	exon1	c.A142C	p.K48Q	TACGGGAAGCGGC	.	PASS	Atlas-SNP
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237783	239237783	+	Missense_Mutation	SNP	C	C	T	rs34723381	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	55	142	0	0.416667	0	C|0.950;T|0.050	0.050	strong	.	TRAF3IP1	58	.	NM_015650	exon5	c.C715T	p.R239W	AGGGAGCGGGACA	.	PASS	Atlas-SNP
CSTL1	128817	hgsc.bcm.edu	37	20	23424660	23424660	+	Silent	SNP	G	G	C	rs12625959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	43	92	0	0.383929	0	G|0.837;C|0.163	0.163	strong	.	CSTL1	30	.	NM_138283	exon3	c.G309C	p.L103L	CCCCCTGCAAAGC	.	PASS	Atlas-SNP
THBD	7056	hgsc.bcm.edu	37	20	23029971	23029971	+	Silent	SNP	G	G	T	rs201268201	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	30	32	0	0.75	0	G|0.999;T|0.001	0.001	strong	.	THBD	26	.	NM_000361	exon1	c.C171A	p.G57G	TAGGTGGCCCCGC	.	PASS	Atlas-SNP
IRX4	50805	hgsc.bcm.edu	37	5	1880891	1880891	+	Missense_Mutation	SNP	C	C	T	rs2232376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	44	70	0	0.494382	0	T|0.195;G|0.006	0.195	strong	IRX4,colon,carcinoma,0,1	IRX4	45	1	NM_016358	exon3	c.G355A	p.A119T	CGGCAGCGGCTGG	.	PASS	Atlas-SNP
RABGAP1L	9910	hgsc.bcm.edu	37	1	174219724	174219724	+	Missense_Mutation	SNP	A	A	G	rs7339904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	56	97	0	0.538462	0	A|0.914;G|0.086	0.086	strong	.	RABGAP1L	103	.	NM_014857	exon6	c.A829G	p.S277G	ACCTTCAGTGTCT	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140640703	140640703	+	Missense_Mutation	SNP	G	G	T	rs61747885	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	79	0	0.526882	0	G|0.877;T|0.123	0.123	strong	.	MAML3	192	.	NM_018717	exon6	c.C3179A	p.P1060H	GCTGGGGGCTGGC	.	PASS	Atlas-SNP
UCP3	7352	hgsc.bcm.edu	37	11	73717254	73717254	+	Silent	SNP	A	A	G	rs1800006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	65	0	1	0	A|0.651;G|0.349	0.349	strong	.	UCP3	31	.	NM_003356	exon3	c.T297C	p.Y99Y	GGAGTCATAGAGG	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36788479	36788479	+	Missense_Mutation	SNP	A	A	G	rs16885577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	21	66	0	0.381818	0	A|0.799;G|0.201	0.201	strong	.	KCNU1	359	.	NM_001031836	exon25	c.A2747G	p.N916S	TCTACAATTATCA	.	PASS	Atlas-SNP
RASA1	5921	hgsc.bcm.edu	37	5	86681125	86681125	+	Silent	SNP	A	A	T	rs137898246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	68	115	0	0.557377	0	A|1.000;G|0.000;T|0.000	0.000	strong	.	RASA1	213	.	NM_002890	exon22	c.A2766T	p.P922P	TTCTCCATCTCCT	.	PASS	Atlas-SNP
MRPL47	57129	hgsc.bcm.edu	37	3	179322385	179322385	+	Missense_Mutation	SNP	A	A	C	rs2339844	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	58	0	1	0	A|0.897;C|0.103	0.103	strong	.	MRPL47	31	.	NM_020409	exon1	c.T28G	p.C10G	TCCTACAAAGAAG	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231256812	231256812	+	Silent	SNP	A	A	G	rs7559665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	83	155	0	0.482558	0	A|0.801;G|0.199	0.199	strong	.	SP140L	68	.	NM_138402	exon12	c.A975G	p.A325A	CTTGGCAAAGTGT	.	PASS	Atlas-SNP
PPP1R9A	55607	hgsc.bcm.edu	37	7	94540416	94540416	+	Missense_Mutation	SNP	A	A	G	rs10230714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	132	0	1	0	A|0.847;G|0.153	0.153	strong	.	PPP1R9A	264	.	NM_017650	exon2	c.A991G	p.M331V	AAGGCAATGCCAA	.	PASS	Atlas-SNP
PRPH2	5961	hgsc.bcm.edu	37	6	42666244	42666244	+	Missense_Mutation	SNP	A	A	C	rs140406696	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	76	0	0.487805	0	A|1.000;C|0.000	0.000	weak	.	PRPH2	47	.	NM_000322	exon3	c.T830G	p.V277G	ATGGTCACCTGGT	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43244485	43244485	+	Missense_Mutation	SNP	G	G	C	rs11880551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	50	0	1	0	G|0.782;C|0.218	0.218	strong	.	PSG3	82	.	NM_021016	exon1	c.C52G	p.L18V	GCAGGAGCCCCTT	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18376509	18376509	+	Missense_Mutation	SNP	G	G	A	rs16982285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	66	152	0	0.442953	0	G|0.854;A|0.146	0.146	strong	KIAA1683_ENST00000392413,colon,carcinoma,0,2	KIAA1683	190	2	NM_001145304	exon3	c.C1841T	p.A614V	GTTTTCGCCTGTT	.	PASS	Atlas-SNP
SLC7A3	84889	hgsc.bcm.edu	37	X	70146475	70146475	+	Missense_Mutation	SNP	G	G	C	rs6525447	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	191	165	0	0.994792	0	0|0.018;C|0.306	0.306	strong	.	SLC7A3	76	.	NM_032803	exon10	c.C1522G	p.L508V	TCCACAGCAGGTC	.	PASS	Atlas-SNP
ZBTB9	221504	hgsc.bcm.edu	37	6	33423698	33423698	+	Missense_Mutation	SNP	C	C	G	rs9469425	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	35	82	0	0.603448	0	C|0.921;G|0.079	0.079	strong	.	ZBTB9	23	.	NM_152735	exon2	c.C821G	p.A274G	TTCCTGCCCCTCC	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170342	58170342	+	Missense_Mutation	SNP	C	C	T	rs11229411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	81	0	0.449438	0	C|0.676;T|0.324	0.324	strong	OR5B3,NS,carcinoma,0,1	OR5B3	65	1	NM_001005469	exon1	c.G541A	p.A181T	TGACTGCTGGAAT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115412793	115412793	+	Silent	SNP	A	A	G	rs3737322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	54	99	0	0.428571	0	A|0.676;G|0.324	0.324	strong	.	NRAP	208	.	NM_001261463	exon6	c.T471C	p.Y157Y	TTCTGTATATTCC	.	PASS	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	37	13	33017158	33017158	+	Missense_Mutation	SNP	G	G	T	rs17077569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	84	181	0	0.525	0	G|0.943;T|0.057	0.057	strong	N4BP2L2_ENST00000399396,NS,carcinoma,0,3	N4BP2L2	90	3	NM_033111	exon7	c.C1516A	p.R506S	CGATACGACTCTG	.	PASS	Atlas-SNP
TSC22D1	8848	hgsc.bcm.edu	37	13	45148257	45148257	+	Missense_Mutation	SNP	G	G	A	rs9525983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	83	143	0	0.522013	0	G|0.926;A|0.074	0.074	strong	.	TSC22D1	88	.	NM_183422	exon1	c.C1954T	p.P652S	AAGCAGGATTTTG	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	130007381	130007381	+	Missense_Mutation	SNP	T	T	C	rs11761888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	144	329	0	0.458599	0	C|0.239;T|0.761	0.239	strong	.	CPA5	61	.	NM_080385	exon11	c.T1007C	p.L336S	GCCGATTGCTGGA	.	PASS	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88903774	88903774	+	Missense_Mutation	SNP	G	G	A	rs7435825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	85	186	0	0.467033	0	G|0.958;A|0.042	0.042	strong	.	SPP1	35	.	NM_001251830	exon8	c.G710A	p.S237N	AGGACAGTTATGA	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73566469	73566469	+	Missense_Mutation	SNP	C	C	T	rs150412778	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	58	102	0	0.557692	0	C|0.989;T|0.011	0.011	strong	.	LLGL2	155	.	NM_004524	exon16	c.C1915T	p.P639S	GAGGGCCCACTCT	.	PASS	Atlas-SNP
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259822	71259822	+	Missense_Mutation	SNP	A	A	G	rs10792769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	329	327	292	0	0.993921	0	A|0.819;G|0.181	0.181	strong	.	KRTAP5-9	19	.	NM_005553	exon1	c.A119G	p.Y40C	CCGTCTACTGCTG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379802	31379802	+	Missense_Mutation	SNP	A	A	G	rs41546915		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	39	129	0	0.493671	0	.	.	weak	.	MICA	21	.	NM_001177519	exon4	c.A692G	p.Y231C	GCTTCTATCCCCG	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12433347	12433347	+	Missense_Mutation	SNP	C	C	T	rs17165995	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	118	100	0	0.991597	0	C|0.794;T|0.206	0.206	strong	.	VWDE	123	.	NM_001135924	exon2	c.G116A	p.R39H	TCAAAACGGACAC	.	PASS	Atlas-SNP
TUBGCP6	85378	hgsc.bcm.edu	37	22	50667859	50667859	+	Silent	SNP	A	A	G	rs6010211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	86	158	0	0.413462	0	A|0.936;G|0.064	0.064	strong	.	TUBGCP6	132	.	NM_020461	exon4	c.T1264C	p.L422L	TGTACAAAGAGTC	.	PASS	Atlas-SNP
MICAL1	64780	hgsc.bcm.edu	37	6	109768295	109768295	+	Silent	SNP	G	G	A	rs910730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	64	72	0	1	0	G|0.464;A|0.536	0.536	strong	.	MICAL1	79	.	NM_022765	exon17	c.C2208T	p.Y736Y	CTGCTCGTAGCCA	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101748356	101748356	+	Missense_Mutation	SNP	A	A	G	rs2075663	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	76	0	1	0	A|0.472;C|0.000;G|0.528	0.528	strong	.	COL15A1	211	.	NM_001855	exon3	c.A610G	p.M204V	ATCTTCATGGGCA	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16352401	16352401	+	Missense_Mutation	SNP	T	T	C	rs8123195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	65	161	0	0.492424	0	T|0.940;C|0.060	0.060	strong	.	KIF16B	305	.	NM_001199866	exon21	c.A3356G	p.N1119S	TAAGCATTGATCC	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9044674	9044674	+	Silent	SNP	G	G	A	rs11741186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	52	90	0	0.553191	0	G|0.950;A|0.050	0.050	strong	.	SEMA5A	236	.	NM_003966	exon22	c.C2916T	p.I972I	CACGGCGATCATG	.	PASS	Atlas-SNP
MACC1	346389	hgsc.bcm.edu	37	7	20198440	20198440	+	Missense_Mutation	SNP	G	G	A	rs975263	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	50	108	0	0.555556	0	G|0.652;N|0.000	.	strong	.	MACC1	99	.	NM_182762	exon5	c.C1544T	p.S515L	AGATTCGAGAGTC	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	37	19	498524	498524	+	Silent	SNP	A	A	G	rs2302217	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	89	1	1	0.011236	A|0.429;G|0.571	0.571	strong	MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	NM_130760	exon3	c.A366G	p.P122P	CTCCCCAGCAGCC	.	scavenged	Atlas-SNP
SPANXE	171489	hgsc.bcm.edu	37	X	140785714	140785714	+	Missense_Mutation	SNP	C	C	G	rs5953618	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1176	235	633	1	0.19983	0.00157978	C|1.000;|0.000	.	weak	.	.	.	.	NM_145665	exon2	c.G202C	p.V68L	CATTCACCAGTTC	.	PASS	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36930795	36930795	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	54	93	0	0.415385	0	.	.	none	.	PI16	50	.	NM_001199159	exon6	c.A677T	p.D226V	CATCAGACTCTAG	.	PASS	Atlas-SNP
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000616	52000616	+	Missense_Mutation	SNP	T	T	C	rs28572419	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	120	184	1	0.566038	0.00543478	T|0.968;C|0.032	0.032	strong	.	SIGLEC12	243	.	NM_053003	exon6	c.A1489G	p.I497V	AGATGATGCAGAA	.	PASS	Atlas-SNP
TBC1D15	64786	hgsc.bcm.edu	37	12	72307616	72307616	+	Silent	SNP	A	A	G	rs3759171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	48	66	0	0.96	0	A|0.446;G|0.554	0.554	strong	.	TBC1D15	99	.	NM_022771	exon13	c.A1362G	p.Q454Q	TGTTCAAGGAATG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101679569	101679569	+	Missense_Mutation	SNP	A	A	G	rs140064475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	25	69	0	0.568182	0	A|0.998;G|0.002	0.002	strong	.	UTP20	222	.	NM_014503	exon4	c.A236G	p.N79S	CATTCAATCAGTT	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112648125	112648125	+	Silent	SNP	G	G	T	rs71625219	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	313	320	0	1	0	GGT|0.500;TGG|0.500	.	alt	CD200R1_ENST00000440122,colon,carcinoma,0,2	CD200R1	91	2	NM_138806	exon4	c.C432A	p.T144T	GGCCACGGTACGA	.	PASS	Atlas-SNP
OTC	5009	hgsc.bcm.edu	37	X	38226603	38226603	+	Missense_Mutation	SNP	A	A	G	rs1800321	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	135	233	0	0.531496	0	A|0.721;0|0.027	.	strong	.	OTC	60	.	NM_000531	exon2	c.A137G	p.K46R	CTCTAAAAAACTT	.	PASS	Atlas-SNP
KEL	3792	hgsc.bcm.edu	37	7	142640004	142640004	+	Silent	SNP	T	T	C	rs8176039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	64	113	0	0.496124	0	A|0.102;C|0.060	0.060	strong	.	KEL	128	.	NM_000420	exon17	c.A1899G	p.L633L	ATTCTCTAAGAAT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46787697	46787697	+	Missense_Mutation	SNP	A	A	G	rs6008795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	82	0	0.466667	0	A|0.783;G|0.217	0.217	strong	.	CELSR1	242	.	NM_014246	exon15	c.T5981C	p.L1994P	GCTAGGAGCTTGT	.	PASS	Atlas-SNP
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	52	115	0	0.460177	0	C|0.861;T|0.139	0.139	strong	C14orf43,bladder,carcinoma,-1,1	.	.	1	NM_194278	exon2	c.G834A	p.P278P	TTGCTGCGGCATG	.	PASS	Atlas-SNP
OLFM3	118427	hgsc.bcm.edu	37	1	102296279	102296279	+	Silent	SNP	T	T	C	rs10493973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	80	183	0	0.490798	0	T|0.824;C|0.176	0.176	strong	.	OLFM3	178	.	NM_058170	exon3	c.A321G	p.K107K	CCGAAATTTTGCC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74290097	74290097	+	Silent	SNP	T	T	A	rs7225131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	49	1	0.506667	0.0204082	T|0.574;A|0.426	0.426	strong	QRICH2,NS,adenoma,0,1	QRICH2	143	1	NM_032134	exon4	c.A213T	p.S71S	TGTTTCTGAGCCC	.	scavenged	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	37	9	91978397	91978397	+	Missense_Mutation	SNP	C	C	T	rs13295305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	58	120	0	0.617021	0	C|0.880;T|0.120	0.120	strong	.	SEMA4D	81	.	NM_001142287	exon20	c.G2138A	p.R713K	ACAGCCCTCCAGG	.	PASS	Atlas-SNP
DARC	2532	hgsc.bcm.edu	37	1	159175354	159175354	+	Missense_Mutation	SNP	G	G	A	rs12075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	201	194	1	1	0.00515464	G|0.393;A|0.607	0.607	strong	.	DARC	76	.	NM_001122951	exon1	c.G131A	p.G44D	ACTATGGTGCCAA	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36583692	36583692	+	Missense_Mutation	SNP	A	A	G	rs61747277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	76	151	0	0.447059	0	A|0.982;G|0.018	0.018	strong	.	WDR62	102	.	NM_173636	exon19	c.A2312G	p.K771R	ATGACAAGAAGCG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152282899	152282899	+	Missense_Mutation	SNP	G	G	T	rs3120648	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	424	423	461	0	0.997642	0	G|0.915;T|0.085	0.085	strong	.	FLG	900	.	NM_002016	exon3	c.C4463A	p.T1488N	CGAATGGTGTCCT	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30772567	30772567	+	Missense_Mutation	SNP	T	T	C	rs202178544	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	15	109	0	0.12	0	.	.	weak	CCDC157_ENST00000405659,bladder,carcinoma,0,4	CCDC157	86	4	NM_001017437	exon12	c.T2092C	p.S698P	TCCCCATCTCGGC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305651	48305651	+	Missense_Mutation	SNP	G	G	A	rs62130758	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	45	98	0	0.523256	0	G|0.764;A|0.236	0.236	strong	.	TPRX1	46	.	NM_198479	exon2	c.C617T	p.P206L	GGGATCGGGCCTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228399628	228399628	+	Silent	SNP	G	G	A	rs114375717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	42	62	0	0.591549	0	G|0.992;A|0.008	0.008	strong	.	OBSCN	2142	.	NM_001271223	exon2	c.G144A	p.Q48Q	CCAGCAGCCGGTG	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443867	5443867	+	Missense_Mutation	SNP	C	C	T	rs10838092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	224	275	2	0.99115	0.00727273	C|0.602;T|0.398	0.398	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.C437T	p.T146I	GTAGAACTGGGTT	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145561594	145561594	+	Missense_Mutation	SNP	C	C	T	rs6670984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	58	113	0	0.464	0	C|0.526;T|0.474	0.474	strong	.	ANKRD35	96	.	NM_144698	exon10	c.C1282T	p.P428S	GGGCCACCCCAGA	.	PASS	Atlas-SNP
OR4C6	219432	hgsc.bcm.edu	37	11	55433040	55433040	+	Missense_Mutation	SNP	T	T	C	rs11230600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	63	147	0	0.431507	0	T|0.759;C|0.241	0.241	strong	.	OR4C6	114	.	NM_001004704	exon1	c.T398C	p.I133T	CGATCATCATGAG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33755787	33755787	+	Missense_Mutation	SNP	G	G	A	rs148857803	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	27	70	0	0.397059	0	G|0.998;A|0.002	0.002	strong	.	URB1	176	.	NM_014825	exon4	c.C511T	p.H171Y	CAAAATGGCTGCA	.	PASS	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	17	46	0	0.354167	0	A|0.934;G|0.066	0.066	strong	.	MCM8	125	.	NM_032485	exon18	c.A2354G	p.N785S	TCAACAACGTTGC	.	PASS	Atlas-SNP
FAM83C	128876	hgsc.bcm.edu	37	20	33874720	33874720	+	Missense_Mutation	SNP	C	C	T	rs2425049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	154	125	0	1	0	C|0.647;T|0.353	0.353	strong	.	FAM83C	80	.	NM_178468	exon4	c.G1862A	p.R621Q	GGTGCCCGTCTGG	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	37	2	86305404	86305404	+	Missense_Mutation	SNP	T	T	C	rs35239368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	64	111	0	0.5	0	T|0.930;C|0.070	0.070	strong	.	POLR1A	137	.	NM_015425	exon10	c.A1090G	p.K364E	AGTCTTTTTCCTG	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671209	31671209	+	Missense_Mutation	SNP	G	G	C	rs13036385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	54	95	0	0.446281	0	G|0.777;C|0.223	0.223	strong	.	.	.	.	NM_182519	exon3	c.G206C	p.R69P	ATGTCCGAGGACC	.	PASS	Atlas-SNP
ANKRD55	79722	hgsc.bcm.edu	37	5	55412471	55412471	+	Silent	SNP	C	C	T	rs60779428	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	135	228	0	0.490909	0	C|0.907;T|0.093	0.093	strong	ANKRD55,NS,malignant_melanoma,-2,2	ANKRD55	70	2	NM_024669	exon9	c.G936A	p.A312A	GACACACGCCGTG	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893745	123893745	+	Missense_Mutation	SNP	C	C	T	rs79715120	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	280	453	2	0.955631	0.00441501	C|0.925;T|0.075	0.075	strong	OR10G9,NS,carcinoma,-1,2	OR10G9	80	2	NM_001001953	exon1	c.C26T	p.A9V	TGACAGCGTTCAT	.	scavenged	Atlas-SNP
GNPDA1	10007	hgsc.bcm.edu	37	5	141381630	141381630	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	4	102	0	0.0305344	0	.	.	none	GNPDA1,colon,carcinoma,0,1	GNPDA1	16	1	NM_005471	exon7	c.G834A	p.E278E	GCTTTTCTCAGTT	.	scavenged	Atlas-SNP
OR5D14	219436	hgsc.bcm.edu	37	11	55563738	55563738	+	Missense_Mutation	SNP	G	G	A	rs67863827	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	112	204	0	0.429119	0	G|0.907;A|0.093	0.093	strong	OR5D14,rectum,carcinoma,+1,4	OR5D14	116	4	NM_001004735	exon1	c.G707A	p.R236H	GTGGGCGCCACAA	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5721049	5721049	+	Silent	SNP	A	A	G	rs35870680	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	72	155	0	0.510638	0	A|0.893;G|0.107	0.107	strong	.	EVC	90	.	NM_153717	exon2	c.A249G	p.S83S	CCCATCAAGGAGG	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552537	43552537	+	Silent	SNP	G	G	A	rs71238846	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	97	187	0	0.468599	0	G|0.865;A|0.135	0.135	strong	.	PLEKHM1	69	.	NM_014798	exon4	c.C852T	p.C284C	CTCCTCGCAATGG	.	PASS	Atlas-SNP
FTH1P18	441490	hgsc.bcm.edu	37	X	37061389	37061389	+	Missense_Mutation	SNP	C	C	T	rs28675922	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	25	18	0	1	0	C|0.736;T|0.264	0.264	strong	.	.	.	.	NM_001271682	exon1	c.G373A	p.G125R	GCTTCCCGACGTC	.	PASS	Atlas-SNP
RBM10	8241	hgsc.bcm.edu	37	X	47041414	47041414	+	Silent	SNP	C	C	T	rs112102343	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	73	111	0	0.506944	0	C|0.986;T|0.014	0.014	strong	.	RBM10	117	.	NM_001204468	exon16	c.C1953T	p.T651T	CCAGACCGGCCTC	.	PASS	Atlas-SNP
HS3ST3B1	9953	hgsc.bcm.edu	37	17	14248345	14248345	+	Silent	SNP	G	G	A	rs77608217	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	148	241	0	0.510345	0	G|0.995;A|0.005	0.005	strong	.	HS3ST3B1	19	.	NM_006041	exon2	c.G555A	p.R185R	TCTCAGGGACCTG	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241835110	241835110	+	Missense_Mutation	SNP	G	G	A	rs146162100	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	68	143	0	0.478873	0	G|0.990;A|0.010	0.010	strong	.	C2orf54	14	.	NM_001085437	exon1	c.C305T	p.P102L	TCCTCCGGCTGGG	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98165911	98165911	+	Missense_Mutation	SNP	T	T	C	rs1839230	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	8	5	0	0.571429	0	T|0.848;C|0.152	0.152	strong	.	.	.	.	NM_025190	exon20	c.A1448G	p.E483G	TTTTTTTCTCTGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677630	100677630	+	Missense_Mutation	SNP	C	C	T	rs78990442	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	124	138	0	0.478764	0	C|0.935;T|0.065	0.065	strong	.	MUC17	804	.	NM_001040105	exon3	c.C2933T	p.P978L	CGACTCCTAGTGA	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135358398	135358398	+	Silent	SNP	G	G	A	rs116294454	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	48	77	0	0.489796	0	G|0.978;A|0.022	0.022	strong	.	HBS1L	75	.	NM_001145207	exon5	c.C1197T	p.N399N	TGACTGGTTACAA	.	PASS	Atlas-SNP
OR52K2	119774	hgsc.bcm.edu	37	11	4471473	4471473	+	Missense_Mutation	SNP	C	C	T	rs7934336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	58	126	0	0.5	0	C|0.868;T|0.132	0.132	strong	.	OR52K2	61	.	NM_001005172	exon1	c.C904T	p.R302C	CAAATCCGTGAGA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124267703	124267703	+	Silent	SNP	T	T	C	rs11057355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	92	0	1	0	T|0.292;C|0.708	0.708	strong	.	DNAH10	888	.	NM_207437	exon7	c.T708C	p.S236S	GGTGTCTGACCTG	.	PASS	Atlas-SNP
REM1	28954	hgsc.bcm.edu	37	20	30070239	30070239	+	Silent	SNP	C	C	A	rs2233832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	41	76	0	0.427083	0	C|0.886;A|0.114	0.114	strong	.	REM1	54	.	NM_014012	exon4	c.C573A	p.I191I	CATCATCCTCGTG	.	PASS	Atlas-SNP
MTOR	2475	hgsc.bcm.edu	37	1	11190646	11190646	+	Silent	SNP	G	G	A	rs2275527	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	84	200	0	0.491228	0	G|0.716;A|0.284	0.284	strong	.	MTOR	327	.	NM_004958	exon39	c.C5553T	p.S1851S	GGCCTCGCTCTCA	.	PASS	Atlas-SNP
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	23	38	0	0.479167	0	C|0.604;A|0.396	0.396	strong	.	NCR1	60	.	NM_001145458	exon4	c.C553A	p.R185R	GCCCACCGAGGGA	.	PASS	Atlas-SNP
ZNF319	57567	hgsc.bcm.edu	37	16	58031996	58031996	+	Silent	SNP	G	G	A	rs115738968	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	18	49	0	0.529412	0	G|0.992;A|0.008	0.008	strong	.	ZNF319	42	.	NM_020807	exon2	c.C174T	p.P58P	CAGGCCGGGGTCT	.	PASS	Atlas-SNP
LZTS2	84445	hgsc.bcm.edu	37	10	102762439	102762439	+	Silent	SNP	C	C	T	rs142122181	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	70	108	0	0.57377	0	C|0.998;T|0.002	0.002	strong	.	LZTS2	57	.	NM_032429	exon2	c.C144T	p.H48H	CCACCACGGCCCT	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158532908	158532908	+	Missense_Mutation	SNP	T	T	C	rs114056876	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	49	92	0	0.544444	0	T|0.988;C|0.012	0.012	strong	.	OR6P1	47	.	NM_001160325	exon1	c.A487G	p.I163V	GGGAAATAAAAAG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	51	103	0	0.51	0	G|0.907;A|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon12	c.1290+2C>T	.	AGACGTGCTTTGG	.	PASS	Atlas-SNP
PCDHA5	56143	hgsc.bcm.edu	37	5	140201418	140201418	+	Missense_Mutation	SNP	C	C	T	rs56285019	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	50	95	0	0.543478	0	C|0.952;T|0.048	0.048	strong	.	PCDHA5	361	.	NM_018908	exon1	c.C58T	p.L20F	CTTCTCCTTGCCT	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31254820	31254820	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	4	243	0	0.0167364	0	.	.	none	DDX11,NS,carcinoma,+2,1	DDX11	188	1	NM_030653	exon21	c.G2106A	p.G702G	TGGAGGGGTGGTC	.	scavenged	Atlas-SNP
PDE10A	10846	hgsc.bcm.edu	37	6	165801790	165801790	+	Silent	SNP	G	G	A	rs1511746	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	38	77	0	0.436782	0	G|0.806;A|0.194	0.194	strong	.	PDE10A	154	.	NM_001130690	exon17	c.C1809T	p.L603L	CACCTGGAGGATG	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31477795	31477795	+	Missense_Mutation	SNP	G	G	C	rs115611533	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	26	35	0	0.52	0	G|0.992;C|0.008	0.008	strong	.	ARMC5	94	.	NM_001105247	exon6	c.G2393C	p.G798A	CGCCTGGTGCAGC	.	PASS	Atlas-SNP
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389793	2389793	+	Missense_Mutation	SNP	A	A	G	rs8100709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	41	61	0	0.539474	0	A|0.948;G|0.052	0.052	strong	.	TMPRSS9	79	.	NM_182973	exon1	c.A10G	p.T4A	GAGCCCACTGTGG	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73559453	73559453	+	Silent	SNP	C	C	T	rs139362844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	77	0	0.526882	0	C|0.996;T|0.004	0.004	strong	.	LLGL2	155	.	NM_001015002	exon8	c.C735T	p.L245L	CCTGCTCGTCAGC	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63884453	63884453	+	Silent	SNP	C	C	T	rs3751120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	99	0	0.517241	0	C|0.702;T|0.298	0.298	strong	.	FLRT1	46	.	NM_013280	exon2	c.C714T	p.R238R	CCAGCGCATCGCC	.	PASS	Atlas-SNP
NSUN5	55695	hgsc.bcm.edu	37	7	72717686	72717686	+	Silent	SNP	C	C	T	rs145622470	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	70	111	0	0.534351	0	C|0.993;T|0.007	0.007	strong	.	NSUN5	47	.	NM_148956	exon9	c.G1197A	p.P399P	GGCACCCGGGAAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105405942	105405942	+	Silent	SNP	G	G	A	rs28454709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	65	70	0	0.970149	0	G|0.467;A|0.533	0.533	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C15846T	p.L5282L	AGTGGAGAGGTGC	.	PASS	Atlas-SNP
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	46	94	0	0.429907	0	A|0.933;G|0.067	0.067	strong	.	ZNF320	67	.	NM_207333	exon4	c.T1182C	p.F394F	TGTACTAAAAACC	.	PASS	Atlas-SNP
PUS10	150962	hgsc.bcm.edu	37	2	61188643	61188643	+	Missense_Mutation	SNP	C	C	T	rs113622721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	112	211	0	0.476596	0	C|0.985;T|0.015	0.015	strong	.	PUS10	49	.	NM_144709	exon10	c.G829A	p.A277T	GAACAGCGCATAC	.	PASS	Atlas-SNP
CRNN	49860	hgsc.bcm.edu	37	1	152382436	152382436	+	Missense_Mutation	SNP	C	C	G	rs6695830	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	340	361	0	0.997067	0	C|0.939;G|0.061	0.061	strong	CRNN,NS,carcinoma,-2,1	CRNN	78	1	NM_016190	exon3	c.G1122C	p.Q374H	CTGTCCCTGTTCT	.	PASS	Atlas-SNP
EXTL1	2134	hgsc.bcm.edu	37	1	26357656	26357656	+	Missense_Mutation	SNP	C	C	A	rs2736831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	156	0	1	0	C|0.442;A|0.558	0.558	strong	.	EXTL1	61	.	NM_004455	exon5	c.C1135A	p.H379N	TCAGCTCACCCCT	.	PASS	Atlas-SNP
RPP38	10557	hgsc.bcm.edu	37	10	15145917	15145917	+	Missense_Mutation	SNP	A	A	C	rs12249258	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	44	92	0	0.505747	0	A|0.946;C|0.054	0.054	strong	.	RPP38	26	.	NM_001265601	exon2	c.A604C	p.S202R	GTCCCCAGTTTAA	.	PASS	Atlas-SNP
BPTF	2186	hgsc.bcm.edu	37	17	65919092	65919092	+	Silent	SNP	G	G	A	rs59088743	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	59	107	0	0.427536	0	G|0.981;A|0.019	0.019	strong	.	BPTF	415	.	NM_004459	exon16	c.G6072A	p.R2024R	GATCAGGGCATTT	.	PASS	Atlas-SNP
GHSR	2693	hgsc.bcm.edu	37	3	172165757	172165757	+	Silent	SNP	G	G	C	rs2232169	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	47	101	0	0.415929	0	G|0.963;C|0.037	0.037	strong	GHSR_ENST00000427970,NS,carcinoma,-2,1	GHSR	104	1	NM_198407	exon1	c.C447G	p.L149L	GGCCCGGAGTGGG	.	PASS	Atlas-SNP
CCL16	6360	hgsc.bcm.edu	37	17	34304680	34304680	+	Silent	SNP	C	C	T	rs74842203	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	137	258	0	0.511194	0	C|0.959;T|0.041	0.041	strong	.	CCL16	7	.	NM_004590	exon3	c.G285A	p.L95L	AGGCAGCAAAGGT	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103382	53103382	+	Silent	SNP	G	G	T	rs72598685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	42	55	0	0.575342	0	G|0.718;T|0.282	0.282	strong	.	POM121L12	146	.	NM_182595	exon1	c.G18T	p.P6P	AGCTCCGGCCGAG	.	PASS	Atlas-SNP
GRM5	2915	hgsc.bcm.edu	37	11	88337922	88337922	+	Missense_Mutation	SNP	G	G	A	rs61741175	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	28	49	0	0.518519	0	G|0.972;A|0.028	0.028	strong	GRM5_ENST00000418177,right_upper_lobe,carcinoma,+1,2	GRM5	414	2	NM_000842	exon5	c.C1358T	p.T453M	AGGATCGTATCTC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124354954	124354954	+	Missense_Mutation	SNP	C	C	T	rs7977449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	34	99	0	0.43038	0	C|0.971;T|0.029	0.029	strong	.	DNAH10	888	.	NM_207437	exon43	c.C7207T	p.R2403W	AACAAACGGAATC	.	PASS	Atlas-SNP
OR4A16	81327	hgsc.bcm.edu	37	11	55110989	55110989	+	Missense_Mutation	SNP	C	C	G	rs116541488	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	128	307	0	0.442907	0	C|0.988;G|0.012	0.012	strong	.	OR4A16	120	.	NM_001005274	exon1	c.C313G	p.L105V	CACTTACTTGGTG	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20423000	20423000	+	Missense_Mutation	SNP	G	G	A	rs9928053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	120	0	0.482517	0	G|0.922;A|0.078	0.078	strong	.	ACSM5	101	.	NM_017888	exon2	c.G194A	p.R65Q	GGAGTCGGCTGGA	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140051009	140051009	+	Silent	SNP	G	G	A	rs146252353	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	406	202	407	0	0.497537	0	G|0.994;A|0.006	0.006	strong	.	DND1	15	.	NM_194249	exon4	c.C931T	p.L311L	CATCTAGGGTCAG	.	PASS	Atlas-SNP
BBS5	129880	hgsc.bcm.edu	37	2	170336102	170336102	+	Silent	SNP	C	C	G	rs10188609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	33	104	0	0.407407	0	C|0.954;G|0.046	0.046	strong	.	BBS5	27	.	NM_152384	exon1	c.C39G	p.V13V	GGATGTCCGTTTC	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154478222	154478222	+	Silent	SNP	C	C	T	rs10001845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	53	152	0	0.348684	0	C|0.657;T|0.343	0.343	strong	.	KIAA0922	214	.	NM_001131007	exon6	c.C537T	p.V179V	TGGAGTCCTTTCC	.	PASS	Atlas-SNP
IMP3	55272	hgsc.bcm.edu	37	15	75932129	75932129	+	Silent	SNP	G	G	T	rs13737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	73	58	0	0.986486	0	G|0.628;T|0.372	0.372	strong	IMP3,colon,carcinoma,0,1	IMP3	10	1	NM_018285	exon1	c.C381A	p.A127A	GGCCACGGCAGCC	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31073244	31073244	+	Silent	SNP	C	C	A	rs34831291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	25	53	0	0.471698	0	C|0.990;A|0.010	0.010	strong	.	ZNF668	121	.	NM_001172669	exon4	c.G1074T	p.P358P	CTTGAACGGCCGG	.	PASS	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	37	3	9490272	9490272	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	5	241	0	0.0228311	0	.	.	none	SETD5_ENST00000402198,NS,carcinoma,+1,2	SETD5	210	2	NM_001080517	exon16	c.A2304G	p.R768R	ACGTCGAAGGCCC	.	scavenged	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53720436	53720436	+	Missense_Mutation	SNP	C	C	T	rs61747071	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	65	124	0	0.619048	0	C|0.953;T|0.047	0.047	strong	.	RPGRIP1L	118	.	NM_001127897	exon6	c.G685A	p.A229T	TCTCAGCCAAGTG	.	PASS	Atlas-SNP
SERPINA1	5265	hgsc.bcm.edu	37	14	94844975	94844975	+	Silent	SNP	G	G	A	rs9630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	82	154	0	0.488095	0	G|0.989;A|0.011	0.011	strong	.	SERPINA1	51	.	NM_001127701	exon7	c.C1068T	p.A356A	ATGCACGGCCTGG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444193	20444193	+	Silent	SNP	A	A	C	rs2318556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	220	225	0	0.995475	0	A|0.619;C|0.380;G|0.001	0.380	strong	.	OR4K15	82	.	NM_001005486	exon1	c.A516C	p.S172S	CATTTCATGGTTT	.	PASS	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	37	3	171338237	171338237	+	Silent	SNP	T	T	G	rs9881788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	96	0	1	0	T|0.504;G|0.496	0.496	strong	.	PLD1	134	.	NM_002662	exon24	c.A2667C	p.V889V	CTCAGTTACTAGG	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	37	17	61557200	61557200	+	Silent	SNP	C	C	T	rs4298	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	21	31	0	0.403846	0	C|0.850;T|0.150	0.150	strong	.	ACE	187	.	NM_000789	exon4	c.C582T	p.N194N	GCACAACGCTGCG	.	PASS	Atlas-SNP
PNMAL1	55228	hgsc.bcm.edu	37	19	46973693	46973693	+	Silent	SNP	C	C	T	rs73552938	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	64	61	1	0.984615	0.0163934	C|0.977;T|0.023	0.023	strong	PNMAL1_ENST00000438932,lower_third,carcinoma,-1,2	PNMAL1	87	2	NM_018215	exon2	c.G600A	p.P200P	AAGCCCCGGTTCT	.	scavenged	Atlas-SNP
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	150	1	1	0.00666667	A|0.595;G|0.405	0.405	strong	.	FCRLA	101	.	NM_001184866	exon5	c.A625G	p.S209G	GCAGGAAGCCCCA	.	PASS	Atlas-SNP
KIF23	9493	hgsc.bcm.edu	37	15	69709748	69709748	+	Silent	SNP	C	C	A	rs3759826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	68	0	0.470588	0	C|0.904;A|0.096	0.096	strong	.	KIF23	57	.	NM_138555	exon3	c.C108A	p.G36G	ACTGGGCTTTCCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513364	195513364	+	Missense_Mutation	SNP	C	C	T	rs79986529	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	443	129	552	0	0.291196	0	C|0.946;G|0.002;T|0.052	0.052	strong	.	MUC4	1505	.	NM_018406	exon2	c.G5087A	p.R1696H	GGAAGACGGGTGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179396159	179396159	+	Silent	SNP	C	C	T	rs371075036		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	3	74	0	0.03125	0	.	.	weak	TTN_ENST00000359218,caecum,carcinoma,-1,5	TTN	18412	5	NM_001267550	exon358	c.G105183A	p.A35061A	AGCATACGCCTCT	.	scavenged	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140237826	140237826	+	Silent	SNP	G	G	C	rs180990865	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	108	235	0	0.461538	0	G|0.989;C|0.011	0.011	strong	.	PCDHA10	358	.	NM_031859	exon1	c.G2193C	p.G731G	ATGTGGGCCGGTG	.	PASS	Atlas-SNP
TBL3	10607	hgsc.bcm.edu	37	16	2025206	2025206	+	Silent	SNP	A	A	C	rs8053843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	121	150	0	1	0	A|0.782;C|0.218	0.218	strong	.	TBL3	54	.	NM_006453	exon8	c.A654C	p.I218I	CAAGATATGTATC	.	PASS	Atlas-SNP
PODN	127435	hgsc.bcm.edu	37	1	53544271	53544271	+	Silent	SNP	G	G	C	rs62000444	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	61	97	0	0.508333	0	G|0.992;C|0.008	0.008	strong	.	PODN	86	.	NM_153703	exon8	c.G1233C	p.T411T	GCACACGGTGCAC	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641075	55641075	+	Missense_Mutation	SNP	A	A	G	rs7301705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	30	76	0	0.47619	0	A|0.753;G|0.247	0.247	strong	.	OR6C74	52	.	NM_001005490	exon1	c.A4G	p.R2G	ACTATGAGAAACC	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27763110	27763110	+	Silent	SNP	T	T	C	rs2289875	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	82	202	0	0.445652	0	T|0.904;C|0.096	0.096	strong	.	KIAA0556	348	.	NM_015202	exon17	c.T3417C	p.S1139S	CTATTCTGATGAG	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918112	51918112	+	Silent	SNP	A	A	G	rs3810099	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	60	118	0	0.521739	0	A|0.791;G|0.209	0.209	strong	SIGLEC12_ENST00000439889,NS,carcinoma,-1,4	SIGLEC10	112	4	NM_033130	exon8	c.T1581C	p.H527H	GGCCCCATGGACG	.	PASS	Atlas-SNP
SULT6B1	391365	hgsc.bcm.edu	37	2	37406645	37406645	+	Missense_Mutation	SNP	T	T	C	rs61737618	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	33	60	0	0.55	0	T|0.997;C|0.003	0.003	strong	.	SULT6B1	46	.	NM_001032377	exon4	c.A371G	p.Y124C	GAGCCATAGCTTG	.	PASS	Atlas-SNP
NAF1	92345	hgsc.bcm.edu	37	4	164087753	164087753	+	Missense_Mutation	SNP	G	G	A	rs12331663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	49	94	0	0.544444	0	G|0.963;A|0.037	0.037	strong	.	NAF1	69	.	NM_138386	exon1	c.C127T	p.P43S	GTAGCGGCGGCTG	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408275	29408275	+	Missense_Mutation	SNP	C	C	A	rs2074467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	55	122	0	0.454545	0	C|0.949;A|0.051	0.051	strong	.	OR10C1	58	.	NM_013941	exon1	c.C483A	p.F161L	CCCTTTCATCTTC	.	PASS	Atlas-SNP
PNMAL1	55228	hgsc.bcm.edu	37	19	46973315	46973315	+	Silent	SNP	G	G	A	rs61628326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	54	94	0	0.556701	0	G|0.982;A|0.018	0.018	strong	.	PNMAL1	87	.	NM_018215	exon2	c.C978T	p.A326A	GCTCTCGGCTTCT	.	PASS	Atlas-SNP
SYCE3	644186	hgsc.bcm.edu	37	22	50989824	50989824	+	Silent	SNP	C	C	T	rs6009990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	62	0	0.490909	0	C|0.935;T|0.065	0.065	strong	.	SYCE3	10	.	NM_001123225	exon3	c.G117A	p.A39A	CCAGGTCGCCTGC	.	PASS	Atlas-SNP
PRMT7	54496	hgsc.bcm.edu	37	16	68389772	68389772	+	Silent	SNP	C	C	T	rs1131933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	28	48	0	0.528302	0	C|0.488;T|0.512	0.512	strong	.	PRMT7	51	.	NM_019023	exon17	c.C1797T	p.T599T	GGGCACCGTGGAG	.	PASS	Atlas-SNP
COMMD10	51397	hgsc.bcm.edu	37	5	115428334	115428334	+	Silent	SNP	G	G	T	rs1129494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	36	87	0	0.367347	0	G|0.536;T|0.464	0.464	strong	COMMD10,NS,carcinoma,0,1	COMMD10	18	1	NM_016144	exon4	c.G336T	p.T112T	CAATACGTGGTCT	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383217	41383217	+	Missense_Mutation	SNP	T	T	C	rs78337605	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	96	362	0	0.351648	0	T|0.500;C|0.500	0.500	strong	.	CYP2A7	71	.	NM_000764	exon7	c.A1039G	p.T347A	TCTTGGTCCGGTC	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113739226	113739226	+	Silent	SNP	T	T	C	rs2281723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	51	68	0	0.607143	0	T|0.904;C|0.096	0.096	strong	.	MCF2L	182	.	NM_001112732	exon19	c.T2082C	p.Y694Y	GATCTATGAGAAG	.	PASS	Atlas-SNP
ISM2	145501	hgsc.bcm.edu	37	14	77950877	77950877	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	2	179	1	0.0111111	0.00558659	.	.	none	ISM2,NS,carcinoma,+1,1	ISM2	68	1	NM_199296	exon3	c.G416A	p.R139K	TCTTCCCTCAGAG	.	scavenged	Atlas-SNP
PPP6R3	55291	hgsc.bcm.edu	37	11	68377446	68377446	+	Missense_Mutation	SNP	C	C	T	rs34009811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	128	101	0	0.992248	0	C|0.950;T|0.050	0.050	strong	.	PPP6R3	159	.	NM_001164160	exon24	c.C2543T	p.A848V	CAGAGGCGAAGTG	.	PASS	Atlas-SNP
PHF10	55274	hgsc.bcm.edu	37	6	170105725	170105725	+	Silent	SNP	T	T	C	rs4286788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	63	166	0	0.45	0	T|0.995;C|0.005	0.005	strong	.	PHF10	76	.	NM_018288	exon10	c.A1209G	p.Q403Q	CTCACATTGGGAG	.	PASS	Atlas-SNP
DPPA4	55211	hgsc.bcm.edu	37	3	109056363	109056363	+	Missense_Mutation	SNP	A	A	G	rs16855561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	81	98	0	1	0	A|0.944;G|0.056	0.056	strong	.	DPPA4	56	.	NM_018189	exon1	c.T2C	p.M1T	CGCAACATGCTTC	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196509577	196509577	+	Missense_Mutation	SNP	C	C	G	rs76714248	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	9	207	2	0.0387931	0.00966184	C|0.991;G|0.009	0.009	strong	PAK2_ENST00000327134,colon,carcinoma,0,2	PAK2	113	2	NM_002577	exon2	c.C60G	p.S20R	GAGCAGCACCATC	.	scavenged	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161026103	161026103	+	Missense_Mutation	SNP	G	G	A	rs189364869	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	30	49	0	0.410959	0	G|0.999;A|0.001	0.001	strong	.	LPA	237	.	NM_005577	exon19	c.C2920T	p.R974W	GGGTCCGACTATG	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	150874033	150874033	+	Silent	SNP	T	T	C	rs61734152	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	27	66	0	0.36	0	T|0.983;C|0.017	0.017	strong	MED12L,NS,carcinoma,+2,1	MED12L	271	1	NM_053002	exon5	c.T642C	p.D214D	GGGCGATGGCCCT	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163137871	163137871	+	Silent	SNP	C	C	G	rs12479043	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	108	218	0	0.617143	0	C|0.879;G|0.121	0.121	strong	IFIH1,NS,carcinoma,0,1	IFIH1	102	1	NM_022168	exon7	c.G1491C	p.T497T	TTGCTTCGTGGCC	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192693	102192693	+	Silent	SNP	C	C	T	rs7066794	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	90	266	1	0.967742	0.0037594	C|0.500;T|0.500	0.500	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.C447T	p.G149G	CCTGGGCGTGACC	.	PASS	Atlas-SNP
KCNT2	343450	hgsc.bcm.edu	37	1	196303117	196303117	+	Silent	SNP	C	C	T	rs116401401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	72	122	0	0.489796	0	C|0.995;T|0.005	0.005	strong	.	KCNT2	243	.	NM_198503	exon17	c.G1857A	p.E619E	GCTTCCCTCTGTA	.	PASS	Atlas-SNP
NRDE2	55051	hgsc.bcm.edu	37	14	90767607	90767607	+	Silent	SNP	C	C	T	rs3825661	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	58	123	0	0.471545	0	C|0.328;T|0.672	0.672	strong	.	.	.	.	NM_017970	exon7	c.G1521A	p.V507V	ATCTTTCACGCTG	.	PASS	Atlas-SNP
CABYR	26256	hgsc.bcm.edu	37	18	21736486	21736486	+	Nonsense_Mutation	SNP	C	C	T	rs35554127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	35	62	0	0.5	0	C|0.986;T|0.014	0.014	strong	.	CABYR	51	.	NM_012189	exon4	c.C1021T	p.R341X	TCACCACGAGTTA	.	PASS	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078290	2078290	+	Silent	SNP	G	G	A	rs34483500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	86	152	0	0.521212	0	G|0.994;A|0.006	0.006	strong	MOBKL2A,colon,carcinoma,-2,1	.	.	1	NM_130807	exon3	c.C270T	p.V90V	CGACATGACGGGG	.	PASS	Atlas-SNP
GJA4	2701	hgsc.bcm.edu	37	1	35260769	35260769	+	Missense_Mutation	SNP	C	C	T	rs1764391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	49	39	0	0.98	0	C|0.634;T|0.366	0.366	strong	.	GJA4	25	.	NM_002060	exon2	c.C955T	p.P319S	CAAAAACCCCCAA	.	PASS	Atlas-SNP
HSD3B2	3284	hgsc.bcm.edu	37	1	119964625	119964625	+	Silent	SNP	G	G	A	rs6207	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	77	156	0	0.52027	0	G|0.996;A|0.004	0.004	strong	.	HSD3B2	48	.	NM_001166120	exon4	c.G501A	p.A167A	GCTGGCGGCTAAT	.	PASS	Atlas-SNP
MYRIP	25924	hgsc.bcm.edu	37	3	40223771	40223771	+	Missense_Mutation	SNP	G	G	A	rs59923220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	62	124	0	0.442857	0	G|0.927;A|0.073	0.073	strong	.	MYRIP	98	.	NM_015460	exon9	c.G934A	p.A312T	GTGGAGGCTCCAT	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28722103	28722103	+	Silent	SNP	T	T	C	rs2577074	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	101	203	0	0.485577	0	T|0.690;C|0.310	0.310	strong	.	DSC1	240	.	NM_004948	exon9	c.A1119G	p.L373L	CATTCGTAAAATC	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171176879	171176879	+	Silent	SNP	G	G	A	rs6671692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	86	206	0	0.438776	0	G|0.953;A|0.047	0.047	strong	.	FMO2	66	.	NM_001460	exon8	c.G1206A	p.E402E	CTCAGAGAGAACT	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58757683	58757683	+	Silent	SNP	A	A	G	rs257636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	92	300	0	0.440191	0	A|0.308;G|0.692	0.692	strong	.	GOT2	42	.	NM_002080	exon2	c.T213C	p.N71N	CTTTCCATTATCA	.	PASS	Atlas-SNP
POMZP3	22932	hgsc.bcm.edu	37	7	76240877	76240877	+	Missense_Mutation	SNP	A	A	T	rs73365247	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	110	226	0	0.387324	0	A|0.957;T|0.043	0.043	strong	.	POMZP3	19	.	NM_012230	exon6	c.T469A	p.C157S	ATTGACAGATGTC	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	3991479	3991479	+	Silent	SNP	A	A	G	rs6961589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	15	25	0	0.394737	0	A|0.926;G|0.074	0.074	strong	.	SDK1	361	.	NM_152744	exon7	c.A1077G	p.P359P	CGGGCCATACGTC	.	PASS	Atlas-SNP
FBXL17	64839	hgsc.bcm.edu	37	5	107197502	107197502	+	Silent	SNP	G	G	A	rs34990078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	47	81	0	0.5875	0	G|0.826;A|0.174	0.174	strong	FBXL17_ENST00000542267,colon,carcinoma,-2,2	FBXL17	60	2	NM_001163315	exon9	c.C2025T	p.T675T	CAGGACGGTGCTG	.	PASS	Atlas-SNP
KLHL1	57626	hgsc.bcm.edu	37	13	70413291	70413291	+	Silent	SNP	A	A	G	rs41283972	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	56	136	0	0.434109	0	A|0.919;G|0.081	0.081	strong	.	KLHL1	164	.	NM_020866	exon6	c.T1231C	p.L411L	CAGCCAATATCTG	.	PASS	Atlas-SNP
SBSN	374897	hgsc.bcm.edu	37	19	36018435	36018435	+	Missense_Mutation	SNP	G	G	A	rs147913080	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	5	6	0	1	0	G|0.977;A|0.023	0.023	strong	.	SBSN	58	.	NM_001166034	exon1	c.C749T	p.A250V	TGCCCCGCAGCAT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289705	74289705	+	Missense_Mutation	SNP	A	A	G	rs6501880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	425	201	410	0	0.472941	0	A|0.564;G|0.436	0.436	strong	.	QRICH2	143	.	NM_032134	exon4	c.T605C	p.L202S	CTGGCCAAGGGTA	.	PASS	Atlas-SNP
ISX	91464	hgsc.bcm.edu	37	22	35480467	35480467	+	Missense_Mutation	SNP	C	C	T	rs7291048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	101	0	0.490196	0	C|0.915;T|0.085	0.085	strong	.	ISX	62	.	NM_001008494	exon3	c.C473T	p.A158V	GTGTGGCCCTGCC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525330	248525330	+	Missense_Mutation	SNP	A	A	G	rs56721857	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	847	308	897	3	0.363636	0.00334448	A|0.878;G|0.122	0.122	strong	.	OR2T4	126	.	NM_001004696	exon1	c.A448G	p.M150V	GCCACCATGGCCT	.	PASS	Atlas-SNP
GSDMD	79792	hgsc.bcm.edu	37	8	144644405	144644405	+	Silent	SNP	G	G	A	rs11551198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	8	22	0	0.4	0	G|0.851;A|0.149	0.149	strong	.	GSDMD	28	.	NM_001166237	exon12	c.G1023A	p.P341P	TGGGCCGGTGGAG	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61959758	61959758	+	Missense_Mutation	SNP	C	C	T	rs115749294	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	75	88	0	0.572519	0	C|0.995;T|0.005	0.005	strong	.	COL20A1	137	.	NM_020882	exon34	c.C3689T	p.P1230L	TGGAGCCGGGCAC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14824799	14824799	+	Silent	SNP	G	G	A	rs12236053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	75	151	0	0.547445	0	G|0.831;A|0.169	0.169	strong	.	FREM1	261	.	NM_144966	exon12	c.C2073T	p.S691S	CCTGTGGCTGAAG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28923906	28923906	+	Missense_Mutation	SNP	A	A	G	rs116081362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	73	145	0	0.453416	0	A|0.967;G|0.033	0.033	strong	.	DSG1	176	.	NM_001942	exon13	c.A1839G	p.I613M	TGTCATACCACAA	.	PASS	Atlas-SNP
UNC13B	10497	hgsc.bcm.edu	37	9	35398900	35398900	+	Missense_Mutation	SNP	G	G	T	rs12339582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	88	186	0	0.44	0	G|0.960;T|0.040	0.040	strong	.	UNC13B	153	.	NM_006377	exon32	c.G3696T	p.E1232D	TGATGAGTGTGTT	.	PASS	Atlas-SNP
C10orf118	55088	hgsc.bcm.edu	37	10	115887340	115887340	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	3	149	0	0.0215827	0	.	.	none	C10orf118,NS,malignant_melanoma,0,1	C10orf118	70	1	NM_018017	exon14	c.A2273T	p.K758M	ATGGCCTTATCTA	.	scavenged	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205901000	205901000	+	Silent	SNP	G	G	A	rs33943971	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	72	163	0	0.431138	0	G|0.899;A|0.101	0.101	strong	.	SLC26A9	176	.	NM_134325	exon5	c.C540T	p.T180T	GATGGCGGTGAGG	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141274456	141274456	+	Splice_Site	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	12	80	0	0.181818	0	.	.	none	.	LRP1B	1315	.	NM_018557	exon51	c.8149+2T>C	.	TGTCTCACCACAG	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	33	57	0	0.52381	0	G|0.801;A|0.199	0.199	strong	.	ADAMTS17	127	.	NM_139057	exon15	c.C2112T	p.G704G	GAAGTCGCCCTTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093362	1093362	+	Silent	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	8	117	0	0.0606061	0	.	.	none	.	MUC2	614	.	NM_002457	exon30	c.C5181G	p.T1727T	CACCACCACTACG	.	PASS	Atlas-SNP
FRMPD2	143162	hgsc.bcm.edu	37	10	49420008	49420008	+	Missense_Mutation	SNP	T	T	C	rs1864345	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	80	0	0.43617	0	T|0.692;C|0.308	0.308	strong	.	FRMPD2	157	.	NM_001018071	exon13	c.A1600G	p.K534E	AGAACTTCAGCTC	.	PASS	Atlas-SNP
C14orf80	283643	hgsc.bcm.edu	37	14	105958010	105958010	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	77	147	0	0.5	0	.	.	none	.	C14orf80	19	.	NM_001134876	exon2	c.G199T	p.G67C	CCTGCGGGCAACG	.	PASS	Atlas-SNP
HIST1H3B	8358	hgsc.bcm.edu	37	6	26031962	26031962	+	Silent	SNP	G	G	A	rs34966100	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	59	113	0	0.41844	0	G|0.966;A|0.034	0.034	strong	.	HIST1H3B	59	.	NM_003537	exon1	c.C327T	p.N109N	GCAAAGGTTTGTG	.	PASS	Atlas-SNP
YTHDF1	54915	hgsc.bcm.edu	37	20	61834169	61834169	+	Missense_Mutation	SNP	G	G	A	rs34379989	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	66	140	0	0.445946	0	G|0.991;A|0.009	0.009	strong	.	YTHDF1	66	.	NM_017798	exon4	c.C1123T	p.H375Y	AGCTGTGAGCAGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73558952	73558952	+	Missense_Mutation	SNP	C	C	T	rs4747195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	80	0	0.509804	0	C|0.668;T|0.332	0.332	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon49	c.C7139T	p.P2380L	GGTCCCCGCCCCG	.	PASS	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100933576	100933576	+	Silent	SNP	T	T	C	rs17122597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	67	109	0	0.51938	0	T|0.931;C|0.069	0.069	strong	.	CDC14A	65	.	NM_033313	exon10	c.T903C	p.H301H	TACACATGCTGAA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103385309	103385309	+	Missense_Mutation	SNP	A	A	G	rs80279368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	141	208	0	0.54023	0	A|0.965;G|0.035	0.035	strong	.	.	.	.	NM_001146197	exon4	c.T17738C	p.V5913A	TCCAGAACACCTT	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143994279	143994279	+	Silent	SNP	A	A	G	rs61757295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	16	116	1	0.131148	0.00862069	A|0.988;G|0.012	0.012	strong	CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	NM_000498	exon7	c.T1144C	p.L382L	GCTCCAAAAACAG	.	scavenged	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	53997415	53997415	+	Missense_Mutation	SNP	G	G	T	rs142505794		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	23	34	0	0.605263	0	G|1.000;T|0.000	0.000	weak	.	WDR72	177	.	NM_182758	exon11	c.C1118A	p.A373D	CAGGTGGCAGTTA	.	PASS	Atlas-SNP
CSRNP1	64651	hgsc.bcm.edu	37	3	39184959	39184959	+	Missense_Mutation	SNP	C	C	T	rs1274958	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	181	0	1	0	T|0.767;G|0.005	0.767	strong	.	CSRNP1	59	.	NM_033027	exon5	c.G1357A	p.V453I	CCAGGACGCCTGA	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112513025	112513025	+	Silent	SNP	G	G	A	rs61742228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	51	97	0	0.51	0	G|0.985;A|0.015	0.015	strong	.	LAMA4	227	.	NM_001105206	exon6	c.C531T	p.P177P	GAGTAAGGGGTTT	.	PASS	Atlas-SNP
LCE2B	26239	hgsc.bcm.edu	37	1	152659392	152659392	+	Missense_Mutation	SNP	C	C	T	rs61730791	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	124	237	0	0.516667	0	C|0.986;T|0.014	0.014	strong	.	LCE2B	40	.	NM_014357	exon2	c.C73T	p.P25S	AAATGTCCACCTA	.	PASS	Atlas-SNP
MAP4	4134	hgsc.bcm.edu	37	3	47958037	47958037	+	Missense_Mutation	SNP	G	G	T	rs1060407	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	115	220	0	0.489362	0	G|0.754;T|0.246	0.246	strong	.	MAP4	176	.	NM_001134364	exon7	c.C1280A	p.S427Y	TCTGTGGATGATA	.	PASS	Atlas-SNP
PROP1	5626	hgsc.bcm.edu	37	5	177421275	177421275	+	Silent	SNP	C	C	T	rs2233784	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	68	107	0	0.519084	0	C|0.969;T|0.031	0.031	strong	PROP1,NS,carcinoma,-2,1	PROP1	28	1	NM_006261	exon2	c.G174A	p.P58P	TCCTTGCGGGGAG	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	37	19	12807066	12807066	+	Silent	SNP	G	G	C	rs6511832	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	38	0	0.42	0	G|0.902;C|0.098	0.098	strong	.	FBXW9	30	.	NM_032301	exon1	c.C330G	p.L110L	GTCGCGGAGCGCG	.	PASS	Atlas-SNP
PPFIA1	8500	hgsc.bcm.edu	37	11	70200516	70200516	+	Missense_Mutation	SNP	C	C	T	rs139448605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	26	51	0	0.412698	0	C|0.992;T|0.008	0.008	strong	.	PPFIA1	114	.	NM_177423	exon17	c.C2273T	p.A758V	AAGGGGCGCTGCA	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3189547	3189547	+	Missense_Mutation	SNP	C	C	A	rs363125	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	69	0	0.428571	0	C|0.812;A|0.188	0.188	strong	.	HTT	221	.	NM_002111	exon39	c.C5159A	p.T1720N	ACAGTACTTCAAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515448	195515448	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	587	10	235	0	0.0170358	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,12	MUC4	1505	12	NM_018406	exon2	c.A3003G	p.V1001V	TGTGGATACTGAG	.	scavenged	Atlas-SNP
PSKH2	85481	hgsc.bcm.edu	37	8	87076651	87076651	+	Missense_Mutation	SNP	T	T	C	rs16879427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	70	110	0	0.492958	0	T|0.874;C|0.126	0.126	strong	PSKH2,right_upper_lobe,carcinoma,-1,1	PSKH2	79	1	NM_033126	exon2	c.A395G	p.Q132R	TAAACTTGATCCT	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33666345	33666345	+	Missense_Mutation	SNP	C	C	A	rs77589178	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	103	257	1	0.459821	0.00389105	C|0.975;A|0.025	0.025	strong	.	WDR88	50	.	NM_173479	exon11	c.C1286A	p.T429N	GTGACACCTCTTC	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38956803	38956803	+	Silent	SNP	G	G	A	rs2228069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	89	0	0.527027	0	A|0.594;C|0.000;G|0.406	0.594	strong	.	RYR1	708	.	NM_001042723	exon24	c.G2943A	p.T981T	GCAGACGACACTG	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17264939	17264939	+	Silent	SNP	T	T	C	rs4558023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	428	142	275	1	0.331776	0.00363636	T|0.699;C|0.301	0.301	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon11	c.T1335C	p.D445D	AGAGGATGGAGAG	.	scavenged	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61908440	61908440	+	Missense_Mutation	SNP	T	T	C	rs2277283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	95	201	0	0.472637	0	T|0.764;C|0.236;A|0.000	0.236	strong	.	INCENP	122	.	NM_001040694	exon10	c.T1517C	p.M506T	TGCTCATGACCCC	.	PASS	Atlas-SNP
LGALS3	3958	hgsc.bcm.edu	37	14	55604935	55604935	+	Missense_Mutation	SNP	C	C	A	rs4644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	79	129	0	0.51634	0	C|0.700;A|0.300	0.300	strong	.	LGALS3	10	.	NM_002306	exon3	c.C191A	p.P64H	CCTACCCTGGAGC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418276	105418276	+	Missense_Mutation	SNP	G	G	A	rs35374867	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	140	285	0	0.462046	0	G|0.978;A|0.022	0.022	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C3512T	p.P1171L	AACGATGGCATCT	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	29972964	29972964	+	Silent	SNP	A	A	G	rs3786308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	124	0	1	0	A|0.855;G|0.145	0.145	strong	.	.	.	.	NM_022751	exon2	c.T156C	p.Y52Y	CAGCAGATAGTCA	.	PASS	Atlas-SNP
MLXIPL	51085	hgsc.bcm.edu	37	7	73020328	73020328	+	Missense_Mutation	SNP	G	G	T	rs34922362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	33	73	0	0.434211	0	G|0.978;T|0.022	0.022	strong	.	MLXIPL	54	.	NM_032954	exon6	c.C732A	p.D244E	ATTGAGGTCCAGG	.	PASS	Atlas-SNP
SNX7	51375	hgsc.bcm.edu	37	1	99150590	99150590	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	95	223	0	0.516304	0	.	.	none	.	SNX7	76	.	NM_015976	exon2	c.A330G	p.I110M	TACAATAGAAACT	.	PASS	Atlas-SNP
CTRC	11330	hgsc.bcm.edu	37	1	15767036	15767036	+	Silent	SNP	C	C	A	rs497078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	40	105	0	0.37037	0	A|0.000;C|0.887;T|0.113	0.000	strong	.	CTRC	28	.	NM_007272	exon3	c.C180A	p.G60G	GTGTGGCGGGACT	.	PASS	Atlas-SNP
FH	2271	hgsc.bcm.edu	37	1	241663825	241663825	+	Silent	SNP	G	G	A	rs2070080	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	68	149	0	0.478873	0	G|0.972;A|0.028	0.028	strong	FH,NS,carcinoma,0,1	FH	64	1	NM_000143	exon9	c.C1302T	p.C434C	CACCACGCAGTTT	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19166100	19166100	+	Missense_Mutation	SNP	C	C	T	rs9988418	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	83	134	0	0.446237	0	C|0.950;T|0.050	0.050	strong	.	TAS1R2	134	.	NM_152232	exon6	c.G2513A	p.R838K	TAGTCCCTCCTCA	.	PASS	Atlas-SNP
RFX8	731220	hgsc.bcm.edu	37	2	102031324	102031324	+	Missense_Mutation	SNP	T	T	G	rs6753088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	83	0	0.43617	0	T|0.991;G|0.009	0.009	strong	.	RFX8	16	.	NM_001145664	exon7	c.A553C	p.M185L	TAGCCATGTTGGA	.	PASS	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	106938740	106938740	+	Missense_Mutation	SNP	C	C	T	rs35258567	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	58	104	0	0.464	0	C|0.999;T|0.001	0.001	strong	COG5,colon,carcinoma,-1,1	COG5	78	1	NM_006348	exon12	c.G1253A	p.R418H	TAAAGACGTAATA	.	PASS	Atlas-SNP
POT1	25913	hgsc.bcm.edu	37	7	124464037	124464037	+	Silent	SNP	T	T	G	rs17147565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	102	200	0	0.525773	0	T|0.970;G|0.030	0.030	strong	POT1_ENST00000357628,NS,carcinoma,-2,2	POT1	186	2	NM_015450	exon19	c.A1884C	p.T628T	TGCAACTGTGGTG	.	PASS	Atlas-SNP
TGM3	7053	hgsc.bcm.edu	37	20	2291722	2291722	+	Missense_Mutation	SNP	A	A	C	rs6048066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	93	169	0	0.550296	0	A|0.871;C|0.129	0.129	strong	.	TGM3	105	.	NM_003245	exon4	c.A487C	p.I163L	GGCATCATCTTTG	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169606649	169606649	+	Missense_Mutation	SNP	C	C	A	rs62333891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	52	130	0	0.419355	0	C|0.887;A|0.113	0.113	strong	.	PALLD	179	.	NM_001166108	exon6	c.C1274A	p.T425N	GTCCAACTTCATA	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79031372	79031372	+	Missense_Mutation	SNP	G	G	C	rs6859595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	121	105	1	0.991803	0.00952381	G|0.737;C|0.263	0.263	strong	.	CMYA5	643	.	NM_153610	exon2	c.G6784C	p.V2262L	CAAAACGTTAAAG	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12943200	12943200	+	Missense_Mutation	SNP	A	A	G	rs3121079	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	123	320	1	0.991935	0.003125	.	.	weak	.	PRAMEF4	62	.	NM_001009611	exon2	c.T16C	p.W6R	GAGTCCAGATGCT	.	PASS	Atlas-SNP
C3orf22	152065	hgsc.bcm.edu	37	3	126270923	126270923	+	Silent	SNP	G	G	C	rs34760151	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	50	83	0	0.471698	0	G|0.912;C|0.088	0.088	strong	.	C3orf22	17	.	NM_152533	exon3	c.C132G	p.P44P	CTCCCAGGGCTGC	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43420290	43420290	+	Silent	SNP	A	A	G	rs76022539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	89	207	0	0.505682	0	A|0.961;G|0.039	0.039	strong	.	PSG6	89	.	NM_001031850	exon2	c.T414C	p.T138T	GGTGACAGTGAAA	.	PASS	Atlas-SNP
KCTD7	154881	hgsc.bcm.edu	37	7	66094184	66094184	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	5	2	0	0.625	0	.	.	none	KCTD7,brain,glioma,-2,1	KCTD7	26	1	NM_001167961	exon1	c.C133T	p.L45L	CCCCTGCTGCCAC	.	scavenged	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G	rs200585722	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	37	328	0	0.158798	0	.	.	weak	.	KRTAP5-8	28	.	NM_021046	exon1	c.C20G	p.S7C	GCTGCTCTGGAGG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78319136	78319136	+	Missense_Mutation	SNP	G	G	A	rs9674961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	139	1	1	0.00719424	G|0.368;A|0.632	0.632	strong	RNF213_ENST00000411702,colon,carcinoma,0,6	RNF213	766	6	NM_001256071	exon29	c.G7001A	p.S2334N	CCATCAGTCACTT	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14389469	14389469	+	Silent	SNP	C	C	T	rs7715916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	71	0	1	0	C|0.891;T|0.109	0.109	strong	.	TRIO	305	.	NM_007118	exon25	c.C4020T	p.I1340I	CATCATCTTCGGA	.	PASS	Atlas-SNP
SLCO2A1	6578	hgsc.bcm.edu	37	3	133653566	133653566	+	Silent	SNP	G	G	A	rs72978391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	32	49	0	0.432432	0	G|0.970;A|0.030	0.030	strong	.	SLCO2A1	72	.	NM_005630	exon14	c.C1923T	p.G641G	GATGAGGCCTGCC	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27752135	27752135	+	Silent	SNP	C	C	T	rs12447120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	136	1	1	0.00735294	C|0.837;T|0.163	0.163	strong	.	KIAA0556	348	.	NM_015202	exon15	c.C2517T	p.D839D	CTCAGACATCTTT	.	PASS	Atlas-SNP
TAT	6898	hgsc.bcm.edu	37	16	71602665	71602665	+	Silent	SNP	C	C	T	rs16973331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	63	118	0	0.470149	0	C|0.958;T|0.042	0.042	strong	.	TAT	80	.	NM_000353	exon11	c.G1173A	p.E391E	CGTGAACTCCACA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107746313	107746313	+	Silent	SNP	T	T	C	rs35265257	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	80	169	0	0.496894	0	T|0.982;C|0.018	0.018	strong	LAMB4,right_upper_lobe,carcinoma,-1,1	LAMB4	253	1	NM_007356	exon8	c.A819G	p.E273E	GCGACATTCGCTA	.	PASS	Atlas-SNP
SERPINB7	8710	hgsc.bcm.edu	37	18	61471593	61471593	+	Silent	SNP	A	A	G	rs11873045	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	35	44	0	0.583333	0	A|0.943;G|0.057	0.057	strong	.	SERPINB7	66	.	NM_001261830	exon8	c.A867G	p.Q289Q	GAAACAATATTTG	.	PASS	Atlas-SNP
OR2J3	442186	hgsc.bcm.edu	37	6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	rs79293918	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	370	177	386	0	0.478378	0	T|0.981;C|0.019	0.019	strong	.	OR2J3	53	.	NM_001005216	exon1	c.T719C	p.V240A	AGAAAGTGTTTGG	.	PASS	Atlas-SNP
KREMEN2	79412	hgsc.bcm.edu	37	16	3016716	3016716	+	Missense_Mutation	SNP	C	C	G	rs111311295	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	60	120	0	0.483871	0	C|0.999;G|0.001	0.001	strong	.	KREMEN2	13	.	NM_024507	exon5	c.C560G	p.P187R	TGGCCCCCGCCAC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062065	64062065	+	Missense_Mutation	SNP	T	T	C	rs10878075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	60	145	0	0.38961	0	T|0.711;C|0.289	0.289	strong	.	DPY19L2	97	.	NM_173812	exon1	c.A109G	p.M37V	TTTCCATCTCCTC	.	PASS	Atlas-SNP
SCFD2	152579	hgsc.bcm.edu	37	4	53740161	53740161	+	Missense_Mutation	SNP	C	C	T	rs149034746		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	3	132	0	0.0198676	0	C|1.000;T|0.000	0.000	weak	SCFD2,caecum,carcinoma,0,1	SCFD2	78	1	NM_152540	exon9	c.G2030A	p.R677Q	TGCAGTCGGTCAG	.	scavenged	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3760056	3760056	+	Silent	SNP	G	G	A	rs61729800	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	42	115	0	0.42	0	G|0.973;A|0.027	0.027	strong	APBA3,colon,carcinoma,0,1	APBA3	28	1	NM_004886	exon2	c.C207T	p.G69G	CAGATCGCCTGGC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	20	31	0	0.645161	0	T|0.653;C|0.347	0.347	strong	.	.	.	.	NM_014811	exon4	c.T1301C	p.M434T	AGACCATGGACCC	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13040858	13040858	+	Silent	SNP	A	A	G	rs145309087	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	90	169	0	0.526316	0	A|0.987;G|0.013	0.013	strong	.	CEP192	340	.	NM_032142	exon14	c.A1839G	p.P613P	ATCACCAGAGAAG	.	PASS	Atlas-SNP
PSMF1	9491	hgsc.bcm.edu	37	20	1099523	1099523	+	Missense_Mutation	SNP	T	T	G	rs1803415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	82	0	1	0	G|0.777;N|0.000	0.777	strong	.	PSMF1	27	.	NM_006814	exon1	c.T107G	p.F36C	GTTACTTCGGCTT	.	PASS	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	32	91	0	0.390244	0	A|0.776;C|0.001	.	strong	AP3B1,NS,carcinoma,0,1	AP3B1	94	1	NM_003664	exon18	c.T2016C	p.A672A	CTTCTTAGCAGAA	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25374636	25374636	+	Silent	SNP	A	A	G	rs35957316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	46	80	0	0.528736	0	A|0.952;G|0.048	0.048	strong	.	RNF17	259	.	NM_001184993	exon13	c.A1722G	p.Q574Q	AGCACAACCATGC	.	PASS	Atlas-SNP
LYZL6	57151	hgsc.bcm.edu	37	17	34264859	34264859	+	Silent	SNP	A	A	G	rs2280783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	161	1	1	0.00621118	A|0.847;G|0.153	0.153	strong	LYZL6,NS,carcinoma,0,1	LYZL6	18	1	NM_020426	exon2	c.T201C	p.D67D	GCTTCCATCTGCA	.	PASS	Atlas-SNP
FBL	2091	hgsc.bcm.edu	37	19	40329747	40329747	+	Silent	SNP	C	C	T	rs150137200	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	81	180	0	0.442623	0	C|0.996;T|0.004	0.004	strong	.	FBL	37	.	NM_001436	exon5	c.G477A	p.P159P	AGCCCCCGGTTTG	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42171483	42171483	+	Missense_Mutation	SNP	G	G	A	rs1197682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	29	55	0	0.557692	0	G|0.866;A|0.134	0.134	strong	.	SPTBN5	171	.	NM_016642	exon16	c.C3052T	p.H1018Y	GGAAGTGGACCCT	.	PASS	Atlas-SNP
CDX1	1044	hgsc.bcm.edu	37	5	149562398	149562398	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	71	124	0	0.44375	0	.	.	none	.	CDX1	11	.	NM_001804	exon2	c.G513T	p.K171N	GGAGAAGGAGTTT	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31294714	31294714	+	Nonsense_Mutation	SNP	C	C	A	rs3784589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	70	134	0	0.546875	0	C|0.940;A|0.060	0.060	strong	.	TRPM1	183	.	NM_001252020	exon27	c.G4240T	p.E1414X	TAGTTTCTTCTTT	.	PASS	Atlas-SNP
MRGPRE	116534	hgsc.bcm.edu	37	11	3249552	3249552	+	Missense_Mutation	SNP	C	C	T	rs4391795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	21	30	0	0.552632	0	C|0.673;T|0.327	0.327	strong	.	MRGPRE	35	.	NM_001039165	exon2	c.G478A	p.G160S	AGGCGCCGCTGAG	.	PASS	Atlas-SNP
DIAPH2	1730	hgsc.bcm.edu	37	X	96354707	96354707	+	Silent	SNP	T	T	C	rs20387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	75	124	0	0.528169	0	T|0.993;C|0.007	0.007	strong	.	DIAPH2	148	.	NM_007309	exon20	c.T2262C	p.H754H	GAAACATCTTCCT	.	PASS	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55277553	55277553	+	Silent	SNP	C	C	T	rs61691036	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	112	142	0	0.523364	0	C|0.979;T|0.021	0.021	strong	.	C1orf177	36	.	NM_001110533	exon5	c.C567T	p.S189S	TCATTCCGAGGGC	.	PASS	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	37	1	237620034	237620034	+	Silent	SNP	G	G	A	rs78281932	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	54	105	0	0.504673	0	G|0.960;A|0.040	0.040	strong	.	RYR2	1273	.	NM_001035	exon16	c.G1611A	p.L537L	GTTGCTGGGTAAG	.	PASS	Atlas-SNP
OR10J3	441911	hgsc.bcm.edu	37	1	159283746	159283746	+	Missense_Mutation	SNP	T	T	C	rs11265165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	66	114	0	0.507692	0	T|0.843;C|0.157	0.157	strong	OR10J3,NS,carcinoma,+1,1	OR10J3	86	1	NM_001004467	exon1	c.A704G	p.Q235R	TTCTTCTGACCTT	.	PASS	Atlas-SNP
SARS2	54938	hgsc.bcm.edu	37	19	39410465	39410465	+	Silent	SNP	G	G	A	rs35389151	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	80	124	0	0.522876	0	G|0.997;A|0.003	0.003	strong	.	SARS2	33	.	NM_001145901	exon8	c.C702T	p.R234R	AGCCCCGCGCAGG	.	PASS	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89933362	89933362	+	Silent	SNP	G	G	A	rs17867249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	42	115	0	0.4	0	G|0.865;A|0.135	0.135	strong	.	C7orf63	158	.	NM_001039706	exon18	c.G2130A	p.A710A	TATTGCGGTTATG	.	PASS	Atlas-SNP
SGSM1	129049	hgsc.bcm.edu	37	22	25294155	25294155	+	Missense_Mutation	SNP	A	A	C	rs6004350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	66	104	0	0.559322	0	A|0.872;C|0.128	0.128	strong	SGSM1_ENST00000400359,NS,carcinoma,-1,2	SGSM1	150	2	NM_001039948	exon20	c.A2404C	p.T802P	ACCCCCACGGTGC	.	PASS	Atlas-SNP
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	75	121	0	0.531915	0	A|0.785;G|0.215	0.215	strong	.	CABLES2	30	.	NM_031215	exon6	c.T780C	p.H260H	CAGGCCATGGCTG	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77921013	77921013	+	Silent	SNP	A	A	G	rs78142936	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	41	50	0	0.532468	0	A|0.935;G|0.065	0.065	strong	.	USP35	179	.	NM_020798	exon10	c.A2112G	p.G704G	GGAAGGAGAGAGG	.	PASS	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39581395	39581395	+	Missense_Mutation	SNP	T	T	A	rs79109719	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	79	0	1	0	T|0.968;A|0.032	0.032	strong	.	ADAM18	169	.	NM_014237	exon19	c.T2146A	p.S716T	AGTAAATCATGTA	.	PASS	Atlas-SNP
CDH12	1010	hgsc.bcm.edu	37	5	22078584	22078584	+	Missense_Mutation	SNP	C	C	T	rs4371716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	94	192	0	0.484536	0	C|0.643;T|0.357	0.357	strong	CDH12,NS,carcinoma,+2,1	CDH12	238	1	NM_004061	exon5	c.G202A	p.V68M	AGCCCACGTATTC	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52325767	52325767	+	Missense_Mutation	SNP	T	T	G	rs16916207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	24	59	0	0.45283	0	T|0.846;G|0.154	0.154	strong	.	PXDNL	414	.	NM_144651	exon15	c.A1847C	p.D616A	ACAGCATCAAGAA	.	PASS	Atlas-SNP
ATP6V1E2	90423	hgsc.bcm.edu	37	2	46739683	46739683	+	Silent	SNP	A	A	G	rs17035245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	120	211	0	0.528634	0	A|0.964;G|0.036	0.036	strong	.	ATP6V1E2	25	.	NM_080653	exon2	c.T168C	p.Y56Y	CTCATAATACTCC	.	PASS	Atlas-SNP
DEGS2	123099	hgsc.bcm.edu	37	14	100615707	100615707	+	Silent	SNP	G	G	A	rs113575369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	67	73	0	0.563025	0	G|0.991;A|0.009	0.009	strong	.	DEGS2	25	.	NM_206918	exon2	c.C423T	p.D141D	GTCCACGTCCAGC	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204966428	204966428	+	Missense_Mutation	SNP	C	C	G	rs2802808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	123	223	0	0.480469	0	C|0.678;G|0.322	0.322	strong	NFASC_ENST00000339876,caecum,carcinoma,0,2	NFASC	396	2	NM_001005388	exon25	c.C2913G	p.I971M	CACCATCGCCACC	.	PASS	Atlas-SNP
OPRD1	4985	hgsc.bcm.edu	37	1	29189597	29189597	+	Silent	SNP	C	C	T	rs2234918	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	33	64	1	0.445946	0.015625	C|0.504;T|0.496	0.496	strong	OPRD1,rectum,carcinoma,0,1	OPRD1	36	1	NM_000911	exon3	c.C921T	p.G307G	GCTGGGCTACGCC	.	scavenged	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49071964	49071964	+	Silent	SNP	A	A	G	rs2075866	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	150	156	0	1	0	0|0.014;T|0.004	.	strong	.	CACNA1F	218	.	NM_005183	exon28	c.T3309C	p.H1103H	GGGGCCATGGTCC	.	PASS	Atlas-SNP
SYDE2	84144	hgsc.bcm.edu	37	1	85666156	85666156	+	Missense_Mutation	SNP	T	T	G	rs12121540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	52	100	0	0.514852	0	T|0.705;G|0.295	0.295	strong	.	SYDE2	135	.	NM_032184	exon1	c.A524C	p.Q175P	CCTTCCTGGCGGT	.	PASS	Atlas-SNP
DSCR6	53820	hgsc.bcm.edu	37	21	38390419	38390419	+	Missense_Mutation	SNP	G	G	A	rs61735126	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	26	35	0	0.472727	0	G|0.989;A|0.011	0.011	strong	.	DSCR6	16	.	NM_018962	exon4	c.G485A	p.R162Q	GGCAGCGATCCTC	.	PASS	Atlas-SNP
MROH6	642475	hgsc.bcm.edu	37	8	144654693	144654693	+	Silent	SNP	G	G	C	rs4873804	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	77	0	0.471429	0	G|0.624;C|0.376	0.376	strong	C8orf73_ENST00000398882,NS,carcinoma,0,2	.	.	2	NM_001100878	exon1	c.C192G	p.P64P	CTCAGAGGGGGCG	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122351055	122351055	+	Missense_Mutation	SNP	G	G	A	rs34383355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	15	47	0	0.652174	0	G|0.981;A|0.019	0.019	strong	PARP15_ENST00000464300,NS,carcinoma,0,2	PARP15	115	2	NM_001113523	exon10	c.G1561A	p.A521T	TCCTACGCAATAG	.	PASS	Atlas-SNP
KIF21A	55605	hgsc.bcm.edu	37	12	39734066	39734066	+	Silent	SNP	T	T	G	rs150241656	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	136	270	0	0.505576	0	T|0.998;G|0.002	0.002	strong	.	KIF21A	238	.	NM_001173464	exon16	c.A2211C	p.A737A	TTGAGCTGCTTGA	.	PASS	Atlas-SNP
CCT8	10694	hgsc.bcm.edu	37	21	30433876	30433876	+	Missense_Mutation	SNP	C	C	T	rs8129954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	67	0	0.460526	0	C|0.973;T|0.027	0.027	strong	.	CCT8	38	.	NM_006585	exon12	c.G1225A	p.V409I	CGGGTACAAGACG	.	PASS	Atlas-SNP
FBXL4	26235	hgsc.bcm.edu	37	6	99374436	99374436	+	Silent	SNP	T	T	C	rs17058965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	78	152	0	0.496815	0	T|0.996;C|0.004	0.004	strong	.	FBXL4	54	.	NM_012160	exon3	c.A429G	p.L143L	GGTTTCTAGAACA	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27765155	27765155	+	Silent	SNP	T	T	C	rs34130136	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	36	83	0	0.428571	0	T|0.993;C|0.007	0.007	strong	.	GABRG3	115	.	NM_033223	exon7	c.T750C	p.S250S	ATTGAGTAGAAGA	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119052826	119052826	+	Missense_Mutation	SNP	C	C	A	rs4245191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	90	0	1	0	C|0.378;A|0.622	0.622	strong	.	NLRX1	128	.	NM_024618	exon9	c.C2378A	p.A793E	TGACGGCGGCAGG	.	PASS	Atlas-SNP
LCE3C	353144	hgsc.bcm.edu	37	1	152573464	152573464	+	Missense_Mutation	SNP	G	G	A	rs148755167	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	79	62	0	0.490683	0	G|0.988;A|0.012	0.012	strong	.	LCE3C	3	.	NM_178434	exon1	c.G257A	p.R86H	CCTGCCGTGGCCA	.	PASS	Atlas-SNP
OR4X1	390113	hgsc.bcm.edu	37	11	48285424	48285424	+	Silent	SNP	A	A	G	rs713323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	82	160	0	0.491018	0	A|0.982;G|0.018	0.018	strong	.	OR4X1	75	.	NM_001004726	exon1	c.A12G	p.T4T	TGCTACAAACAAT	.	PASS	Atlas-SNP
STX1A	6804	hgsc.bcm.edu	37	7	73122923	73122923	+	Silent	SNP	A	A	G	rs2228607	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	41	127	0	0.372727	0	A|0.473;G|0.527	0.527	strong	.	STX1A	16	.	NM_004603	exon3	c.T204C	p.D68D	ACTCTCATCGGGG	.	PASS	Atlas-SNP
KCND1	3750	hgsc.bcm.edu	37	X	48820064	48820064	+	Silent	SNP	G	G	A	rs3027483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	135	270	0	0.482143	0	G|0.884;A|0.116	0.116	strong	.	KCND1	63	.	NM_004979	exon6	c.C1722T	p.R574R	GCTGGAGCGGCTG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170063471	170063471	+	Silent	SNP	A	A	G	rs35114151	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	36	98	0	0.371134	0	A|0.954;G|0.046	0.046	strong	.	LRP2	751	.	NM_004525	exon39	c.T6759C	p.D2253D	TAAAGAATCATCA	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38776303	38776303	+	Silent	SNP	T	T	C	rs11466652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	110	0	0.992308	0	T|0.814;C|0.186	0.186	strong	TLR10,NS,carcinoma,-2,1	TLR10	87	1	NM_001017388	exon2	c.A909G	p.K303K	CTCCAATTTTATA	.	PASS	Atlas-SNP
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201822	32201822	+	Silent	SNP	G	G	T	rs9982910	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	95	216	0	0.454545	0	G|0.504;T|0.496	0.496	strong	.	.	.	.	NM_181606	exon2	c.C195A	p.G65G	GCAGCCGCCCAGG	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62455982	62455982	+	Silent	SNP	G	G	A	rs6681983	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	34	94	0	0.465753	0	G|0.985;A|0.015	0.015	strong	.	INADL	179	.	NM_176877	exon28	c.G3813A	p.P1271P	TAACCCGGAAGGA	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17083839	17083839	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	500	151	420	0	0.302	0	.	.	none	Q13209_HUMAN,NS,carcinoma,+1,1	.	.	1	NM_001271733	exon15	c.T1958A	p.L653Q	CCTTTCAGGACCC	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	30	68	0	0.517241	0	C|0.612;T|0.388	0.388	strong	.	.	.	.	NM_001080826	exon2	c.G1205A	p.R402Q	GCCTCCCGGGGGT	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180218820	180218820	+	Silent	SNP	C	C	A	rs2070925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	44	72	0	0.556962	0	C|0.928;A|0.072	0.072	strong	.	MGAT1	48	.	NM_001114617	exon3	c.G1152T	p.V384V	CACCCGCACCTCC	.	PASS	Atlas-SNP
ARID3C	138715	hgsc.bcm.edu	37	9	34622389	34622389	+	Missense_Mutation	SNP	A	A	C	rs3808869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	120	94	0	0.991736	0	A|0.428;C|0.572	0.572	strong	.	ARID3C	33	.	NM_001017363	exon5	c.T1003G	p.C335G	GCATGCAAGGTCG	.	PASS	Atlas-SNP
EID3	493861	hgsc.bcm.edu	37	12	104698265	104698265	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	2	72	0	0.0294118	0	.	.	none	EID3,rectum,carcinoma,-1,2	EID3	28	2	NM_001008394	exon1	c.C553T	p.R185X	AAGCCCCGACTTG	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677645	100677645	+	Missense_Mutation	SNP	C	C	A	rs114262718	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	53	124	0	0.196296	0	C|0.936;A|0.064	0.064	strong	.	MUC17	804	.	NM_001040105	exon3	c.C2948A	p.T983N	GAACGACTCCATT	.	PASS	Atlas-SNP
RPA1	6117	hgsc.bcm.edu	37	17	1782957	1782957	+	Silent	SNP	C	C	T	rs2230930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	43	89	0	0.5	0	C|0.802;N|0.000	.	strong	.	RPA1	48	.	NM_002945	exon11	c.C1056T	p.S352S	CACATCCGGGAAG	.	PASS	Atlas-SNP
STRIP2	57464	hgsc.bcm.edu	37	7	129098602	129098602	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	45	141	0	0.401786	0	.	.	none	FAM40B,lymph_node,lymphoid_neoplasm,0,1	.	.	1	NM_020704	exon11	c.G1324A	p.G442R	TTCATCGGATTCA	.	PASS	Atlas-SNP
ANKRD53	79998	hgsc.bcm.edu	37	2	71212380	71212380	+	Silent	SNP	C	C	A	rs61732288	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	56	134	0	0.414815	0	C|0.968;A|0.032	0.032	strong	.	ANKRD53	55	.	NM_001115116	exon6	c.C1543A	p.R515R	GCTGTGCGATCTC	.	PASS	Atlas-SNP
TCF12	6938	hgsc.bcm.edu	37	15	57384061	57384061	+	Silent	SNP	A	A	G	rs34560099	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	33	90	0	0.362637	0	A|0.959;G|0.041	0.041	strong	.	TCF12	242	.	NM_207036	exon5	c.A297G	p.P99P	GTCCCCAACACCT	.	PASS	Atlas-SNP
P2RY1	5028	hgsc.bcm.edu	37	3	152554357	152554357	+	Silent	SNP	A	A	G	rs701265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	187	191	0	1	0	A|0.653;G|0.347	0.347	strong	.	P2RY1	49	.	NM_002563	exon1	c.A786G	p.V262V	CCTGGTAATCATT	.	PASS	Atlas-SNP
PEX1	5189	hgsc.bcm.edu	37	7	92118654	92118654	+	Silent	SNP	G	G	A	rs34825053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	61	122	0	0.435714	0	G|0.992;A|0.008	0.008	strong	.	PEX1	102	.	NM_000466	exon23	c.C3720T	p.H1240H	TCTTGTGTGACCA	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909168	123909168	+	Missense_Mutation	SNP	G	G	A	rs41528551	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	433	14	504	0	0.0323326	0	G|0.907;A|0.093	0.093	strong	OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	NM_001004463	exon1	c.C541T	p.P181S	TGGGCGGTGCGTC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280864	152280864	+	Silent	SNP	A	A	G	rs75034106		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	676	674	428	0	0.997041	0	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.T6498C	p.S2166S	GTGATGAGACCCT	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70225504	70225504	+	Silent	SNP	G	G	T	rs3758626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	34	77	0	0.435897	0	G|0.672;T|0.328	0.328	strong	.	DNA2	76	.	NM_001080449	exon4	c.C507A	p.A169A	ATTTATGGCTTTT	.	PASS	Atlas-SNP
CBLC	23624	hgsc.bcm.edu	37	19	45284495	45284495	+	Missense_Mutation	SNP	C	C	T	rs114569424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	48	91	0	0.494845	0	C|0.994;T|0.006	0.006	strong	.	CBLC	41	.	NM_001130852	exon3	c.C532T	p.L178F	GAGTCCCTCCTGG	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	29	56	0	0.460317	0	G|0.402;A|0.598	0.598	strong	.	ESPL1	158	.	NM_012291	exon20	c.G4551A	p.G1517G	AGGTGGGAAGACT	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604419	140604419	+	Missense_Mutation	SNP	G	G	A	rs61731253	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	108	161	0	0.54	0	G|0.979;A|0.021	0.021	strong	.	PCDHB14	132	.	NM_018934	exon1	c.G1342A	p.A448T	GACAACGCCCCCA	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27490194	27490194	+	Silent	SNP	T	T	C	rs13096477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	86	211	0	0.464865	0	T|0.851;C|0.149	0.149	strong	.	SLC4A7	119	.	NM_001258379	exon3	c.A225G	p.R75R	TTTTCTTCTCCGG	.	PASS	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	37	1	153745128	153745128	+	Silent	SNP	G	G	C	rs6663011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	115	173	4	0.552885	0.0231214	C|0.159;G|0.841;T|0.000	0.159	strong	INTS3,NS,carcinoma,0,1	INTS3	83	1	NM_023015	exon28	c.G2835C	p.T945T	CCAGACGCCAATT	.	scavenged	Atlas-SNP
ALG11	440138	hgsc.bcm.edu	37	13	52598668	52598668	+	Missense_Mutation	SNP	C	C	A	rs148434423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	100	223	0	0.462963	0	C|0.999;A|0.001	0.001	strong	.	ALG11	39	.	NM_001004127	exon3	c.C802A	p.L268I	CTCTCACTATGGA	.	PASS	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124663895	124663895	+	Silent	SNP	G	G	A	rs16898689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	47	51	0	0.546512	0	G|0.857;A|0.143	0.143	strong	.	KLHL38	81	.	NM_001081675	exon1	c.C1272T	p.P424P	GACTGCGGGGTGG	.	PASS	Atlas-SNP
MRPS21	54460	hgsc.bcm.edu	37	1	150280550	150280550	+	Missense_Mutation	SNP	G	G	A	rs4845	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	112	188	0	0.538462	0	G|0.888;A|0.112	0.112	strong	.	MRPS21	8	.	NM_018997	exon2	c.G152A	p.R51Q	GCCGCCGGCGACA	.	PASS	Atlas-SNP
DDX3X	1654	hgsc.bcm.edu	37	X	41204446	41204446	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	25	129	0	0.19084	0	.	.	none	.	DDX3X	138	.	NM_001193416	exon11	c.G1039C	p.D347H	GTGTTAGATGAAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388819	1388819	+	Missense_Mutation	SNP	T	T	C	rs144797159		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	20	67	0	0.125	0	.	.	weak	CRIPAK,NS,carcinoma,0,4	CRIPAK	185	4	NM_175918	exon1	c.T520C	p.C174R	TGCCCATGTGGAG	.	PASS	Atlas-SNP
ITLN1	55600	hgsc.bcm.edu	37	1	160853312	160853312	+	Silent	SNP	C	C	T	rs79969862	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	61	154	0	0.409396	0	C|0.984;T|0.016	0.016	strong	.	ITLN1	45	.	NM_017625	exon3	c.G63A	p.E21E	ATTAGCCTCATCT	.	PASS	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88902725	88902725	+	Silent	SNP	G	G	A	rs6812524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	128	197	0	0.475836	0	G|0.921;A|0.079	0.079	strong	.	SPP1	35	.	NM_001251830	exon7	c.G354A	p.S118S	TGACTCGAACGAC	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181019253	181019253	+	Silent	SNP	T	T	C	rs61731103	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	150	273	0	0.506757	0	T|0.967;C|0.033	0.033	strong	.	MR1	46	.	NM_001195035	exon4	c.T435C	p.N145N	CTTCAATAAAGAC	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22575481	22575481	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	309	4	292	0	0.012945	0	.	.	none	ZNF98_ENST00000357774,caecum,carcinoma,0,2	ZNF98	230	2	NM_001098626	exon4	c.G556A	p.E186K	CACATTCTTTACA	.	scavenged	Atlas-SNP
F10	2159	hgsc.bcm.edu	37	13	113798236	113798236	+	Missense_Mutation	SNP	G	G	A	rs3211783	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	29	47	0	0.491525	0	G|0.973;A|0.027	0.027	strong	.	F10	53	.	NM_000504	exon6	c.G574A	p.G192R	AGCAGCGGGGAGG	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27668587	27668587	+	Missense_Mutation	SNP	C	C	G	rs17057901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	67	176	0	0.482014	0	C|0.978;G|0.022	0.022	strong	.	PBK	29	.	NM_018492	exon7	c.G660C	p.E220D	ACCATTCTCCTCC	.	PASS	Atlas-SNP
DGKB	1607	hgsc.bcm.edu	37	7	14758273	14758273	+	Silent	SNP	C	C	T	rs1997040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	67	143	0	0.440789	0	C|0.500;T|0.500	0.500	strong	.	DGKB	166	.	NM_145695	exon5	c.G360A	p.R120R	AGTAGTCCGGGGA	.	PASS	Atlas-SNP
NTSR2	23620	hgsc.bcm.edu	37	2	11800180	11800180	+	Silent	SNP	G	G	A	rs35653499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	55	93	0	0.52381	0	G|0.982;A|0.018	0.018	strong	.	NTSR2	36	.	NM_012344	exon3	c.C978T	p.D326D	CCACGCGTCATCA	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7887499	7887499	+	Missense_Mutation	SNP	T	T	G	rs35899625	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	116	144	0	0.560386	0	T|0.995;G|0.005	0.005	strong	.	PER3	95	.	NM_016831	exon17	c.T2486G	p.L829W	TGCCCTTGTCCGA	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73789332	73789332	+	Silent	SNP	C	C	T	rs75137555	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	431	230	397	0	0.533643	0	C|0.979;T|0.021	0.021	strong	.	C2CD3	288	.	NM_015531	exon23	c.G4431A	p.R1477R	TGGGCCCCTGGTG	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	46	187	0	0.373984	0	G|0.882;A|0.118	0.118	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon1	c.C64T	p.R22W	TCATCCGGACTAA	.	PASS	Atlas-SNP
SLC26A8	116369	hgsc.bcm.edu	37	6	35923246	35923246	+	Missense_Mutation	SNP	T	T	C	rs2295852	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	83	181	0	0.477012	0	T|0.572;C|0.428	0.428	strong	SLC26A8,rectum,carcinoma,0,1	SLC26A8	95	1	NM_052961	exon17	c.A1915G	p.I639V	GGTTAATGGAGGA	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7576569	7576569	+	Silent	SNP	T	T	C	rs146407262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	38	89	0	0.447059	0	T|0.991;C|0.009	0.009	strong	.	DSP	306	.	NM_004415	exon19	c.T2673C	p.Y891Y	GAATTATCGTGAT	.	PASS	Atlas-SNP
DHTKD1	55526	hgsc.bcm.edu	37	10	12160868	12160868	+	Silent	SNP	C	C	T	rs12769375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	83	0	0.448718	0	C|0.985;T|0.015	0.015	strong	.	DHTKD1	104	.	NM_018706	exon15	c.C2523T	p.F841F	CCCCTTCCCGTTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281304	152281304	+	Missense_Mutation	SNP	A	A	C	rs7512857	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	512	230	248	1	0.449219	0.00403226	A|0.968;C|0.032	0.032	strong	.	FLG	900	.	NM_002016	exon3	c.T6058G	p.S2020A	TGCCTGAGTGTCT	.	PASS	Atlas-SNP
ZP4	57829	hgsc.bcm.edu	37	1	238053226	238053226	+	Missense_Mutation	SNP	G	G	A	rs34370253	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	84	210	1	0.488372	0.0047619	G|0.972;A|0.028	0.028	strong	ZP4,caecum,carcinoma,0,1	ZP4	161	1	NM_021186	exon3	c.C341T	p.A114V	TCAGCCGCGCCTG	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106814086	106814086	+	Silent	SNP	T	T	C	rs16873732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	80	187	0	0.522876	0	T|0.939;C|0.061	0.061	strong	.	ZFPM2	219	.	NM_012082	exon8	c.T1776C	p.P592P	GATGCCTGAAGCT	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43268242	43268242	+	Missense_Mutation	SNP	C	C	T	rs76352186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	98	247	1	0.420601	0.00404858	C|0.936;T|0.064	0.064	strong	.	PSG8	101	.	NM_001130167	exon2	c.G256A	p.G86S	TTTGACCGTCTAC	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163831	73163831	+	Silent	SNP	C	C	T	rs2931423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	59	121	0	0.453846	0	C|0.759;T|0.241	0.241	strong	.	.	.	.	NM_001080479	exon19	c.C2283T	p.G761G	TCCAGGCACCACC	.	PASS	Atlas-SNP
KCNA7	3743	hgsc.bcm.edu	37	19	49575304	49575304	+	Missense_Mutation	SNP	G	G	A	rs77059600	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	13	4	0	0.65	0	G|0.847;A|0.153	0.153	strong	KCNA7,rectum,carcinoma,0,1	KCNA7	30	1	NM_031886	exon1	c.C539T	p.A180V	GCGGCTGCAGCAG	.	scavenged	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579102	55579102	+	Missense_Mutation	SNP	C	C	T	rs34961497	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	131	261	0	0.474638	0	C|0.907;T|0.093	0.093	strong	OR5L1,NS,carcinoma,-1,1	OR5L1	145	1	NM_001004738	exon1	c.C160T	p.R54W	AGCTCTCGGCTCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418938	105418938	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	5	276	0	0.0174216	0	.	.	none	AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.G2850A	p.A950A	CACTTCCGCCTTG	.	scavenged	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55119289	55119289	+	Silent	SNP	G	G	C	rs9332417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	64	130	0	0.444444	0	G|0.547;C|0.453	0.453	strong	.	.	.	.	NM_001039464	exon3	c.G690C	p.L230L	GAACCTGAATGTA	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122649481	122649481	+	Missense_Mutation	SNP	C	C	T	rs150399543	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	26	65	0	0.448276	0	C|0.997;T|0.003	0.003	strong	WDR11,NS,carcinoma,-1,1	WDR11	95	1	NM_018117	exon18	c.C2303T	p.A768V	TAATAGCAATGTA	.	PASS	Atlas-SNP
UPK3A	7380	hgsc.bcm.edu	37	22	45685002	45685002	+	Silent	SNP	A	A	G	rs1135360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	56	0	1	0	A|0.413;G|0.587	0.587	strong	.	UPK3A	14	.	NM_006953	exon4	c.A549G	p.S183S	GTGGTCAGACCCC	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160287443	160287443	+	Missense_Mutation	SNP	A	A	C	rs200904019	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	70	172	0	0.432099	0	A|0.998;C|0.002	0.002	strong	.	BAZ2B	196	.	NM_013450	exon10	c.T2125G	p.C709G	CAGAACATAAGGC	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065509	79065509	+	Missense_Mutation	SNP	T	T	C	rs146076001		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	783	340	461	1	0.434227	0.0021692	T|1.000;C|0.000	0.000	weak	.	ADAMTS7	142	.	NM_014272	exon14	c.A2047G	p.M683V	CCTCCATAGCACC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49933974	49933974	+	Missense_Mutation	SNP	T	T	C	rs7072606	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	68	0	1	0	T|0.865;C|0.135	0.135	strong	.	WDFY4	205	.	NM_020945	exon6	c.T640C	p.S214P	CTCCTCTCAGGAA	.	PASS	Atlas-SNP
KMO	8564	hgsc.bcm.edu	37	1	241712134	241712134	+	Silent	SNP	C	C	T	rs11556464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	5	16	0	0.333333	0	C|0.616;T|0.384	0.384	strong	.	KMO	69	.	NM_003679	exon2	c.C60T	p.G20G	GGTTGGCTCATTA	.	PASS	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	37	22	31492781	31492781	+	Missense_Mutation	SNP	C	C	T	rs34292278	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	53	75	0	0.546392	0	C|0.929;T|0.071	0.071	strong	.	SMTN	219	.	NM_001207017	exon15	c.C2179T	p.R727C	GAGGGGCGCGGCA	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197614	39197614	+	Silent	SNP	G	G	A	rs141856614	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	54	245	0	0.274112	0	G|0.935;A|0.065	0.065	strong	.	KRTAP1-1	23	.	NM_030967	exon1	c.C36T	p.P12P	GCAGCTGGGAAAT	.	PASS	Atlas-SNP
EPS8L3	79574	hgsc.bcm.edu	37	1	110301260	110301260	+	Missense_Mutation	SNP	C	C	T	rs6693815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	38	72	0	0.469136	0	C|0.668;T|0.332	0.332	strong	.	EPS8L3	73	.	NM_139053	exon7	c.G490A	p.G164S	CCTGGCCTGGCTG	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153418535	153418535	+	Missense_Mutation	SNP	A	A	G	rs5742604		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	912	287	430	1	0.314693	0.00232558	.	.	weak	.	OPN1LW	87	.	NM_020061	exon3	c.A532G	p.I178V	TCCTGGATCTGGT	.	PASS	Atlas-SNP
ACSS1	84532	hgsc.bcm.edu	37	20	25038484	25038484	+	Silent	SNP	G	G	A	rs66817095	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	66	141	0	0.488889	0	G|0.845;T|0.155	.	alt	.	ACSS1	46	.	NM_001252677	exon1	c.C255T	p.T85T	GTAGGGGGTGTCC	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7690872	7690872	+	Silent	SNP	G	G	A	rs10079813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	53	107	0	0.445378	0	G|0.976;A|0.024	0.024	strong	.	ADCY2	337	.	NM_020546	exon5	c.G789A	p.R263R	CCAGAGGCTGCAG	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	104897606	104897606	+	Missense_Mutation	SNP	C	C	G	rs146399863	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	45	75	0	0.535714	0	C|0.999;G|0.001	0.001	strong	.	RIMS2	1357	.	NM_001100117	exon4	c.C779G	p.A260G	AGTATGCTACTTC	.	PASS	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	37	7	154672646	154672646	+	Silent	SNP	T	T	C	rs3817522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	55	102	0	0.458333	0	T|0.742;C|0.258	0.258	strong	.	DPP6	383	.	NM_130797	exon21	c.T2127C	p.F709F	CGTGTTTGGGAAG	.	PASS	Atlas-SNP
TANK	10010	hgsc.bcm.edu	37	2	162088034	162088034	+	Missense_Mutation	SNP	C	C	T	rs2229759	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	12	39	0	0.5	0	C|0.977;T|0.023	0.023	strong	TANK,NS,carcinoma,-1,1	TANK	35	1	NM_004180	exon7	c.C1073T	p.P358L	ATTCCCCGGGAAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512117	195512117	+	Missense_Mutation	SNP	C	C	G	rs200655750	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	85	685	5	0.256798	0.00729927	C|0.939;G|0.061	0.061	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G6334C	p.A2112P	GAAGAGCGGTGGC	.	scavenged	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235949920	235949920	+	Silent	SNP	A	A	G	rs3731645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	52	0	0.520548	0	A|0.760;G|0.240	0.240	strong	SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	NM_014521	exon4	c.A507G	p.P169P	CAATCCATTTCTG	.	PASS	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	37	19	7684502	7684502	+	Silent	SNP	G	G	A	rs4134869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	78	142	0	0.484472	0	G|0.944;A|0.056	0.056	strong	.	XAB2	69	.	NM_020196	exon19	c.C2538T	p.A846A	CACTGCGGCTGGC	.	PASS	Atlas-SNP
BMPER	168667	hgsc.bcm.edu	37	7	33946464	33946464	+	Silent	SNP	C	C	T	rs112068976	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	51	107	0	0.536842	0	C|0.999;T|0.001	0.001	strong	BMPER,NS,carcinoma,+1,1	BMPER	131	1	NM_133468	exon3	c.C168T	p.V56V	TGAAGTCCTCCAG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Silent	SNP	T	T	C	rs12731746	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	155	141	0	0.99359	0	T|0.545;C|0.455	0.455	strong	.	ARID4B	142	.	NM_016374	exon11	c.A897G	p.E299E	ACTTACTTCTTCT	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	37	5	98199204	98199204	+	Silent	SNP	C	C	T	rs161941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	136	1	1	0.00735294	C|0.658;T|0.342	0.342	strong	.	CHD1	137	.	NM_001270	exon31	c.G4335A	p.E1445E	AGTATGCTCTAGT	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145742879	145742879	+	Silent	SNP	T	T	C	rs2306386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	10	13	0	0.5	0	T|0.468;C|0.532	0.532	strong	.	RECQL4	75	.	NM_004260	exon3	c.A132G	p.E44E	GCGGTATTCCCGG	.	PASS	Atlas-SNP
FCRL6	343413	hgsc.bcm.edu	37	1	159785425	159785425	+	Missense_Mutation	SNP	A	A	G	rs4443889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	91	0	1	0	A|0.725;G|0.275	0.275	strong	FCRL6,NS,carcinoma,0,1	FCRL6	61	1	NM_001004310	exon10	c.A1279G	p.S427G	CCCCTTAGCGACT	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95906023	95906023	+	Silent	SNP	G	G	A	rs17828632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	29	90	0	0.367089	0	G|0.883;A|0.117	0.117	strong	.	SYNE3	130	.	NM_152592	exon12	c.C2172T	p.A724A	CACCACGGCAGCA	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	86	224	0	0.411483	0	C|0.681;T|0.319	0.319	strong	C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	NM_001163560	exon10	c.G831A	p.T277T	AACATTCGTTTCT	.	PASS	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32196647	32196647	+	Silent	SNP	C	C	G	rs909001	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	30	66	0	0.526316	0	C|0.675;G|0.325	0.325	strong	.	BAI2	128	.	NM_001703	exon29	c.G4134C	p.P1378P	CCCCTCCGGCCGG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39264690	39264690	+	Missense_Mutation	SNP	T	T	C	rs2496425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	43	80	0	0.413462	0	T|0.546;C|0.454	0.454	strong	FREM2,colon,carcinoma,0,1	FREM2	385	1	NM_207361	exon1	c.T3209C	p.F1070S	AAATCTTTGTAGG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40364397	40364397	+	Missense_Mutation	SNP	C	C	T	rs148917660	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	41	60	0	0.532468	0	C|0.997;T|0.003	0.003	strong	.	FCGBP	416	.	NM_003890	exon31	c.G14245A	p.G4749S	AGTCACCGCAGAG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157959794	157959794	+	Missense_Mutation	SNP	T	T	C	rs73745196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	35	87	0	0.546875	0	T|0.974;C|0.026	0.026	strong	.	PTPRN2	243	.	NM_130843	exon6	c.A739G	p.S247G	AGGCACTGAGGGC	.	PASS	Atlas-SNP
DEPDC7	91614	hgsc.bcm.edu	37	11	33053107	33053107	+	Silent	SNP	C	C	T	rs966191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	57	76	0	0.513514	0	C|0.588;T|0.412	0.412	strong	.	DEPDC7	94	.	NM_001077242	exon5	c.C966T	p.D322D	ATCTGACGTTCAT	.	PASS	Atlas-SNP
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	60	105	0	0.47619	0	G|0.346;N|0.000	0.346	strong	.	ACO1	149	.	NM_002197	exon11	c.A1263G	p.E421E	CACTGAATTCACC	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	67	138	0	0.290043	0	G|0.750;A|0.250	0.250	strong	.	PSPH	23	.	NM_004577	exon4	c.C117T	p.G39G	CTCAACGCCACAG	.	PASS	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152082320	152082320	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	12	219	1	0.0410959	0.00456621	.	.	none	TCHH,NS,carcinoma,0,5	TCHH	275	5	NM_007113	exon3	c.A3373G	p.R1125G	CCTCTCTCAGCAG	.	scavenged	Atlas-SNP
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843708	16843708	+	Missense_Mutation	SNP	T	T	A	rs74811083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	58	74	0	0.617021	0	T|0.985;A|0.015	0.015	strong	.	TNFRSF13B	34	.	NM_012452	exon4	c.A563T	p.K188M	CCCCTCTTCTTGA	.	PASS	Atlas-SNP
BPIFA3	128861	hgsc.bcm.edu	37	20	31812206	31812206	+	Missense_Mutation	SNP	A	A	G	rs112731808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	94	168	0	0.494737	0	A|0.983;G|0.017	0.017	strong	.	.	.	.	NM_178466	exon3	c.A324G	p.I108M	CCAGATATCATTC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037419	33037419	+	Silent	SNP	G	G	A	rs1126543	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	164	0	1	0	G|0.700;A|0.300	0.300	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.C345T	p.N115N	CGTACCGTTGGTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678932	100678932	+	Missense_Mutation	SNP	A	A	G	rs114941002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	10	119	0	0.0680272	0	.	.	weak	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.A4235G	p.E1412G	GTTCTGAGGCTAG	.	scavenged	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	32	51	0	0.542373	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C2327T	p.S776L	AGAAGTCGGAGAT	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671609	238671609	+	Missense_Mutation	SNP	A	A	G	rs2001301	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	144	258	0	0.527473	0	A|0.873;G|0.127	0.127	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.A1253G	p.N418S	GTGGGAACCACAC	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62173561	62173561	+	Missense_Mutation	SNP	C	C	G	rs310657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	192	204	0	0.994819	0	C|0.889;G|0.111	0.111	strong	SRMS,NS,carcinoma,+2,1	SRMS	48	1	NM_080823	exon5	c.G901C	p.V301L	CCGTGACGATGTA	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39306004	39306004	+	Missense_Mutation	SNP	A	A	G	rs238829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	153	307	0	0.442197	0	A|0.962;G|0.038	0.038	strong	.	KRTAP4-5	34	.	NM_033188	exon1	c.T16C	p.C6R	AGCCACAACAGGA	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52652174	52652174	+	Silent	SNP	T	T	C	rs13329278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	104	182	0	0.5	0	T|0.887;C|0.113	0.113	strong	.	MYO5A	145	.	NM_000259	exon25	c.A3414G	p.S1138S	TGTCCTTGATGGA	.	PASS	Atlas-SNP
OR1L1	26737	hgsc.bcm.edu	37	9	125424277	125424277	+	Missense_Mutation	SNP	A	A	G	rs70157	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	114	169	0	0.633333	0	A|0.860;G|0.140	0.140	strong	.	OR1L1	54	.	NM_001005236	exon1	c.A283G	p.S95G	TCTTACAGTGAGT	.	PASS	Atlas-SNP
PRSS1	5644	hgsc.bcm.edu	37	7	142460752	142460752	+	Missense_Mutation	SNP	C	C	G	rs140793689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	424	10	383	2	0.0235849	0.00522193	.	.	weak	PRSS1,NS,carcinoma,-2,2	PRSS1	68	2	NM_002769	exon5	c.C625G	p.Q209E	AATGGACAGCTCC	.	scavenged	Atlas-SNP
SEMA6C	10500	hgsc.bcm.edu	37	1	151112483	151112483	+	Missense_Mutation	SNP	T	T	C	rs75185260	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	39	98	0	0.367925	0	T|0.953;C|0.047	0.047	strong	.	SEMA6C	70	.	NM_001178061	exon4	c.A202G	p.T68A	TCAAGGTCAGGAA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151932990	151932990	+	Missense_Mutation	SNP	C	C	T	rs76844681	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	9	206	0	0.0494506	0	C|0.999;T|0.001	0.001	weak	MLL3_ENST00000355193,NS,malignant_melanoma,+1,4	MLL3	1564	4	NM_170606	exon16	c.G2681A	p.R894Q	GGTCTCCGCTTTC	.	scavenged	Atlas-SNP
NTN4	59277	hgsc.bcm.edu	37	12	96077312	96077312	+	Silent	SNP	C	C	T	rs17851048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	47	95	0	0.474747	0	C|0.819;T|0.181	0.181	strong	.	NTN4	67	.	NM_021229	exon6	c.G1356A	p.A452A	GCTCCCCGCACAG	.	PASS	Atlas-SNP
LHX3	8022	hgsc.bcm.edu	37	9	139096782	139096782	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	12	39	0	0.333333	0	.	.	none	.	LHX3	23	.	NM_178138	exon1	c.G77A	p.R26Q	TTACCCCGAGTCC	.	PASS	Atlas-SNP
FSHB	2488	hgsc.bcm.edu	37	11	30255185	30255185	+	Silent	SNP	C	C	T	rs6169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	70	0	1	0	C|0.436;T|0.564	0.564	strong	.	FSHB	28	.	NM_000510	exon3	c.C228T	p.Y76Y	GGTATACGAAACA	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	123	214	1	0.457249	0.0046729	G|0.579;A|0.421	0.421	strong	RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	NM_015085	exon20	c.G1842A	p.P614P	CTCTCCGGAAATC	.	scavenged	Atlas-SNP
TMEM89	440955	hgsc.bcm.edu	37	3	48659009	48659009	+	Missense_Mutation	SNP	G	G	T	rs9834639	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	80	174	0	0.449438	0	G|0.878;T|0.122	0.122	strong	.	TMEM89	10	.	NM_001008269	exon1	c.C181A	p.P61T	CTCCAGGGCCCAG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27277716	27277716	+	Missense_Mutation	SNP	A	A	T	rs61736082	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	79	173	0	0.490683	0	A|0.952;T|0.048	0.048	strong	.	POM121L2	61	.	NM_033482	exon1	c.T2234A	p.I745N	TTGGAGATGCTGG	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66397521	66397521	+	Silent	SNP	C	C	T	rs62638719	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	105	124	0	0.606936	0	C|0.996;T|0.004	0.004	strong	ARSG,NS,carcinoma,+1,1	ARSG	55	1	NM_001267727	exon11	c.C1233T	p.S411S	CAACAGCGGGGCA	.	PASS	Atlas-SNP
ITGBL1	9358	hgsc.bcm.edu	37	13	102227872	102227872	+	Silent	SNP	C	C	T	rs3916912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	76	174	0	0.520548	0	C|0.831;T|0.169	0.169	strong	.	ITGBL1	83	.	NM_004791	exon4	c.C561T	p.D187D	CATAGACGATGAA	.	PASS	Atlas-SNP
ABCC2	1244	hgsc.bcm.edu	37	10	101611294	101611294	+	Missense_Mutation	SNP	G	G	A	rs8187710	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	35	78	1	0.454545	0.0128205	G|0.752;A|0.248	0.248	strong	ABCC2,NS,carcinoma,-1,1	ABCC2	160	1	NM_000392	exon32	c.G4544A	p.C1515Y	TAGAGTGCGGCAG	.	scavenged	Atlas-SNP
PLBD1	79887	hgsc.bcm.edu	37	12	14656768	14656768	+	Missense_Mutation	SNP	G	G	C	rs1600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	185	159	0	0.994624	0	G|0.490;C|0.510	0.510	strong	.	PLBD1	36	.	NM_024829	exon11	c.C1600G	p.P534A	CCTCTGGCATGCC	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160448324	160448324	+	Missense_Mutation	SNP	C	C	G	rs8191754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	125	227	1	0.553097	0.00440529	C|0.862;G|0.138	0.138	strong	.	IGF2R	251	.	NM_000876	exon6	c.C754G	p.L252V	GACGGACTGAAGC	.	PASS	Atlas-SNP
NOVA1	4857	hgsc.bcm.edu	37	14	26917826	26917826	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	2	117	0	0.013986	0	.	.	none	NOVA1,NS,carcinoma,-1,1	NOVA1	146	1	NM_002515	exon5	c.T863C	p.L288P	CCTAATAGCCCTG	.	scavenged	Atlas-SNP
NR5A1	2516	hgsc.bcm.edu	37	9	127262864	127262864	+	Silent	SNP	C	C	T	rs1110062	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	53	36	0	1	0	C|0.948;T|0.052	0.052	strong	.	NR5A1	32	.	NM_004959	exon4	c.G375A	p.P125P	CCCCATCGGGGGC	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	rs1661715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	23	54	0	0.489362	0	C|0.622;T|0.378	0.378	strong	LLGL2_ENST00000167462,rectum,carcinoma,0,6	LLGL2	155	6	NM_004524	exon18	c.C2275T	p.P759S	GATGAGCCTGTGC	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47611598	47611598	+	Missense_Mutation	SNP	T	T	C	rs2405599	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	140	265	0	0.507246	0	T|0.740;C|0.260	0.260	strong	.	CYP4A22	60	.	NM_001010969	exon10	c.T1283C	p.L428P	CCAACCTAGAGGT	.	PASS	Atlas-SNP
SFXN2	118980	hgsc.bcm.edu	37	10	104486489	104486489	+	Silent	SNP	C	C	T	rs35153373	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	77	139	0	0.49359	0	C|0.980;T|0.020	0.020	strong	.	SFXN2	40	.	NM_178858	exon2	c.C96T	p.D32D	CACGGACCCCCGC	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839081	15839081	+	Silent	SNP	C	C	T	rs2067083	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	168	437	1	0.394366	0.00228833	C|0.708;T|0.292	0.292	strong	.	OR10H2	59	.	NM_013939	exon1	c.C228T	p.A76A	CGTGGCCATCATC	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86385812	86385812	+	Silent	SNP	T	T	C	rs2228352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	50	109	0	0.42735	0	T|0.968;C|0.032	0.032	strong	.	IMMT	65	.	NM_006839	exon10	c.A1065G	p.V355V	CTGAGATACAACC	.	PASS	Atlas-SNP
ASPG	374569	hgsc.bcm.edu	37	14	104559852	104559852	+	Silent	SNP	T	T	C	rs941953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	128	0	1	0	T|0.625;C|0.375	0.375	strong	.	ASPG	34	.	NM_001080464	exon3	c.T216C	p.I72I	GAGGATTCTCTAC	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18656225	18656225	+	Silent	SNP	G	G	A	rs11044142	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	57	117	0	0.435115	0	G|0.842;A|0.158	0.158	strong	.	PIK3C2G	315	.	NM_004570	exon22	c.G2904A	p.Q968Q	GGTGCAGATGGTA	.	PASS	Atlas-SNP
MIIP	60672	hgsc.bcm.edu	37	1	12082334	12082334	+	Missense_Mutation	SNP	A	A	T	rs11553925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	70	156	0	0.503597	0	A|0.799;T|0.201	0.201	strong	MIIP,brain,glioma,0,1	MIIP	34	1	NM_021933	exon3	c.A297T	p.K99N	TGCCAAATGCCAG	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29779847	29779847	+	Missense_Mutation	SNP	A	A	C	rs61737900	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	50	183	0	0.208333	0	A|0.783;C|0.217	0.217	strong	SVIL,NS,carcinoma,0,4	SVIL	226	4	NM_021738	exon22	c.T4121G	p.L1374R	TGAAGGAGATCTT	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7545691	7545691	+	Missense_Mutation	SNP	G	G	C	rs10486176	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	58	95	0	0.423358	0	G|0.869;C|0.131	0.131	strong	.	COL28A1	113	.	NM_001037763	exon11	c.C980G	p.T327S	GGTCCAGTAATTC	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183184650	183184650	+	Missense_Mutation	SNP	G	G	C	rs12065473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	77	150	0	0.445087	0	G|0.963;C|0.037	0.037	strong	.	LAMC2	113	.	NM_005562	exon3	c.G331C	p.A111P	ACAGGAGCCAGAT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17086976	17086976	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	491	53	396	0	0.107943	0	.	.	none	Q13209_HUMAN,NS,carcinoma,-2,2	.	.	2	NM_001271733	exon4	c.C348T	p.P116P	GAGCGTGGGCATG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656479	46656479	+	Missense_Mutation	SNP	A	A	G	rs6519993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	40	91	0	0.547945	0	A|0.724;G|0.276	0.276	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T2741C	p.L914P	GGAAAGAGGTCAT	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642827	1642827	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	9	184	1	0.0436893	0.00543478	.	.	none	KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.C497G	p.S166C	GAGGAGGAGCAGC	.	scavenged	Atlas-SNP
PADI4	23569	hgsc.bcm.edu	37	1	17668508	17668508	+	Silent	SNP	C	C	T	rs16825565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	54	143	0	0.442623	0	C|0.984;T|0.016	0.016	strong	.	PADI4	70	.	NM_012387	exon7	c.C723T	p.P241P	GGTCCCCGGTGGA	.	PASS	Atlas-SNP
LAIR1	3903	hgsc.bcm.edu	37	19	54871664	54871664	+	Missense_Mutation	SNP	G	G	C	rs74463408	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	78	92	0	0.304688	0	G|0.886;C|0.114	0.114	strong	LAIR1,colon,carcinoma,+1,2	LAIR1	44	2	NM_002287	exon4	c.C380G	p.P127R	GAGTCCGGGCCTC	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30496382	30496382	+	Silent	SNP	G	G	C	rs2075818	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	97	154	0	0.554286	0	G|0.683;C|0.317	0.317	strong	.	NOD1	79	.	NM_006092	exon4	c.C156G	p.A52A	ATCTTCGGCCGAG	.	PASS	Atlas-SNP
SHANK1	50944	hgsc.bcm.edu	37	19	51172526	51172526	+	Missense_Mutation	SNP	G	G	C	rs41275782	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	43	109	0	0.43	0	G|0.936;C|0.064	0.064	strong	.	SHANK1	210	.	NM_016148	exon22	c.C2691G	p.D897E	AGGTCTGTCATCT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	544	115	491	0	0.211397	0	C|0.931;T|0.069	0.069	strong	.	LILRB3	67	.	NM_006864	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3686676	3686676	+	Missense_Mutation	SNP	C	C	G	rs35953127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	45	0	1	0	C|0.957;G|0.043	0.043	strong	.	SIGLEC1	210	.	NM_023068	exon3	c.G421C	p.V141L	TGGGCACCCTGGG	.	PASS	Atlas-SNP
ADH1B	125	hgsc.bcm.edu	37	4	100237169	100237169	+	Silent	SNP	C	C	T	rs139645116	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	137	317	1	0.479021	0.00315457	C|0.998;T|0.002	0.002	strong	.	ADH1B	68	.	NM_000668	exon5	c.G453A	p.T151T	CACCACCGTGTAC	.	PASS	Atlas-SNP
LRP11	84918	hgsc.bcm.edu	37	6	150158486	150158486	+	Missense_Mutation	SNP	A	A	G	rs375299752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	41	120	0	0.383178	0	.	.	weak	.	LRP11	27	.	NM_032832	exon4	c.T1027C	p.F343L	GGCAGAAGTCTTC	.	PASS	Atlas-SNP
BET3L	100128327	hgsc.bcm.edu	37	6	116818225	116818225	+	Silent	SNP	C	C	T	rs114678052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	87	0	1	0	C|0.968;T|0.032	0.032	strong	.	BET3L	18	.	NM_001139444	exon5	c.G438A	p.A146A	ATCAGCCGCCAAA	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207890892	207890892	+	Missense_Mutation	SNP	G	G	A	rs116455739	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	137	325	1	0.447712	0.00307692	G|0.972;A|0.028	0.028	strong	.	CR1L	97	.	NM_175710	exon11	c.G1498A	p.V500I	AAAGAAGTATCTT	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76950686	76950686	+	Missense_Mutation	SNP	C	C	A	rs17151689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	103	160	0	0.528205	0	C|0.925;A|0.075	0.075	strong	PION,NS,carcinoma,-1,1	PION	74	1	NM_017439	exon25	c.G1958T	p.W653L	TTCCTCCAATTGG	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16291983	16291983	+	Silent	SNP	A	A	G	rs9930886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	68	126	0	0.472222	0	A|0.707;G|0.293	0.293	strong	.	ABCC6	110	.	NM_001171	exon10	c.T1233C	p.N411N	CACCAGATTGACC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511757	4511757	+	Missense_Mutation	SNP	C	C	T	rs74627313	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	455	108	293	0	0.237363	0	C|0.967;T|0.033	0.033	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G2173A	p.G725S	CAGCACCGGTCAC	.	PASS	Atlas-SNP
WDR59	79726	hgsc.bcm.edu	37	16	74943471	74943471	+	Missense_Mutation	SNP	T	T	C	rs61734551	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	21	43	0	0.477273	0	T|0.988;C|0.012	0.012	strong	.	WDR59	66	.	NM_030581	exon16	c.A1570G	p.T524A	AAGCCGTGGTCAC	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158532605	158532605	+	Missense_Mutation	SNP	C	C	A	rs115786820	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	87	140	0	0.497143	0	C|0.987;A|0.013	0.013	strong	.	OR6P1	47	.	NM_001160325	exon1	c.G790T	p.A264S	ACATGGCCCGGGG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795657	29795657	+	Silent	SNP	G	G	A	rs1630185	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	80	161	0	0.434783	0	G|0.518;A|0.482	0.482	strong	.	HLA-G	90	.	NM_002127	exon2	c.G36A	p.L12L	CCTGCTGCTCTCG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15794425	15794425	+	Missense_Mutation	SNP	A	A	G	rs116788636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	49	124	0	0.266304	0	A|0.990;G|0.010	0.010	strong	.	CYP4F12	89	.	NM_023944	exon7	c.A770G	p.H257R	GCTTCCACAGGGC	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15668319	15668319	+	Missense_Mutation	SNP	G	G	A	rs12126178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	90	202	1	0.494505	0.00495049	G|0.930;A|0.070	0.070	strong	FHAD1_ENST00000375999,NS,carcinoma,0,2	FHAD1	78	2	NM_052929	exon15	c.G1994A	p.R665Q	CTGAACGAGGAGA	.	scavenged	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110778128	110778128	+	Missense_Mutation	SNP	T	T	C	rs714368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	38	86	0	0.404255	0	T|0.701;C|0.299	0.299	strong	.	SLC22A16	81	.	NM_033125	exon2	c.A146G	p.H49R	ACATGATGAGGGG	.	PASS	Atlas-SNP
FAM129C	199786	hgsc.bcm.edu	37	19	17638141	17638141	+	Missense_Mutation	SNP	G	G	A	rs73504235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	221	238	0	1	0	G|0.990;A|0.010	0.010	strong	.	FAM129C	110	.	NM_001098524	exon2	c.G85A	p.D29N	GGAGACGACAGCA	.	PASS	Atlas-SNP
FOXC1	2296	hgsc.bcm.edu	37	6	1611085	1611085	+	Silent	SNP	C	C	T	rs2230096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	295	130	270	0	0.440678	0	C|0.970;T|0.030	0.030	strong	.	FOXC1	19	.	NM_001453	exon1	c.C405T	p.C135C	CGAGTGCTTCGTC	.	PASS	Atlas-SNP
SLC22A14	9389	hgsc.bcm.edu	37	3	38347851	38347851	+	Missense_Mutation	SNP	A	A	G	rs2073714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	100	167	0	0.598802	0	A|0.927;G|0.073	0.073	strong	SLC22A14,NS,carcinoma,0,1	SLC22A14	64	1	NM_004803	exon1	c.A334G	p.K112E	CTGTCCAAAGCTG	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39603498	39603498	+	Silent	SNP	G	G	A	rs61737582	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	83	72	0	0.697479	0	G|0.921;A|0.079	0.079	strong	C13orf23,NS,carcinoma,-2,1	.	.	1	NM_025138	exon4	c.C195T	p.V65V	TGGCTGGACAGCC	.	PASS	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122413196	122413196	+	Missense_Mutation	SNP	T	T	C	rs77422261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	99	145	0	0.592814	0	T|0.928;C|0.072	0.072	strong	.	WDR66	143	.	NM_144668	exon18	c.T2818C	p.F940L	ACCCCATTCTATG	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818517	55818517	+	Missense_Mutation	SNP	T	T	A	rs1045002	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	126	201	0	0.565022	0	A|0.366;N|0.000	0.366	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T1409A	p.I470N	CTTCCATTTTAAA	.	PASS	Atlas-SNP
LCE2B	26239	hgsc.bcm.edu	37	1	152659471	152659471	+	Missense_Mutation	SNP	T	T	G	rs3737859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	141	250	0	0.524164	0	T|0.841;G|0.159	0.159	strong	LCE2B,NS,carcinoma,0,1	LCE2B	40	1	NM_014357	exon2	c.T152G	p.I51S	GTCCCATCTCTGG	.	PASS	Atlas-SNP
TMCC1	23023	hgsc.bcm.edu	37	3	129546664	129546664	+	Silent	SNP	C	C	T	rs72987361	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	38	75	0	0.481013	0	C|0.897;T|0.103	0.103	strong	.	TMCC1	105	.	NM_001017395	exon3	c.G558A	p.E186E	TCCCTCCTCTCCT	.	PASS	Atlas-SNP
DAB2	1601	hgsc.bcm.edu	37	5	39377132	39377132	+	Missense_Mutation	SNP	G	G	A	rs700241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	65	162	0	0.422078	0	G|0.945;A|0.055	0.055	strong	.	DAB2	124	.	NM_001343	exon12	c.C1757T	p.T586I	CTTGTTGTTGACC	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29788107	29788107	+	Silent	SNP	G	G	A	rs4799640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	77	213	0	0.442529	0	G|0.778;A|0.222	0.222	strong	.	MEP1B	54	.	NM_005925	exon9	c.G792A	p.S264S	GGACTCGTGCAGT	.	PASS	Atlas-SNP
COL10A1	1300	hgsc.bcm.edu	37	6	116441646	116441646	+	Missense_Mutation	SNP	C	C	G	rs2228547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	29	43	0	0.453125	0	C|0.838;G|0.162	0.162	strong	.	COL10A1	51	.	NM_000493	exon3	c.G1633C	p.G545R	TTACCCCCTGGTT	.	PASS	Atlas-SNP
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	27	45	0	0.428571	0	T|0.701;C|0.299	0.299	strong	.	COQ3	19	.	NM_017421	exon4	c.A400G	p.K134E	TTGTTTTCAGAAG	.	PASS	Atlas-SNP
ZNF107	51427	hgsc.bcm.edu	37	7	64168641	64168641	+	Silent	SNP	A	A	G	rs73363327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	9	44	0	0.36	0	A|0.985;G|0.015	0.015	strong	.	ZNF107	107	.	NM_016220	exon7	c.A1959G	p.R653R	TAATAGACATAAG	.	PASS	Atlas-SNP
KSR2	283455	hgsc.bcm.edu	37	12	117993064	117993064	+	Silent	SNP	C	C	T	rs7955803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	159	294	1	0.486239	0.00340136	C|0.758;T|0.242	0.242	strong	.	KSR2	208	.	NM_173598	exon9	c.G1341A	p.P447P	GTCACACGGAACG	.	PASS	Atlas-SNP
TRIM16L	147166	hgsc.bcm.edu	37	17	18634541	18634541	+	Silent	SNP	C	C	T	rs8073459	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	110	253	0	0.468085	0	C|0.920;T|0.080	0.080	strong	.	TRIM16L	15	.	NM_001037330	exon3	c.C360T	p.S120S	GTTTTCCAAGGAA	.	PASS	Atlas-SNP
SLC47A2	146802	hgsc.bcm.edu	37	17	19608773	19608773	+	Silent	SNP	G	G	A	rs4925042	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	48	0	0.439394	0	G|0.622;A|0.378	0.378	strong	.	SLC47A2	61	.	NM_152908	exon10	c.C993T	p.Y331Y	CACCTCGTAGATG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62200929	62200929	+	Silent	SNP	G	G	A	rs6089925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	43	50	0	0.589041	0	G|0.847;A|0.153	0.153	strong	.	.	.	.	NM_001037335	exon5	c.C660T	p.Y220Y	CCGTGCGTAGAGC	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519442	43519442	+	Missense_Mutation	SNP	T	T	C	rs10414166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	127	0	1	0	T|0.203;C|0.797	0.797	strong	.	PSG11	57	.	NM_002785	exon4	c.A790G	p.N264D	TAGAGTTTGCGAA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124274474	124274474	+	Missense_Mutation	SNP	A	A	G	rs10846559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	100	0	1	0	A|0.235;G|0.765	0.765	strong	.	DNAH10	888	.	NM_207437	exon11	c.A1438G	p.I480V	GGACAGATTTTGG	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673029	7673029	+	Missense_Mutation	SNP	T	T	C	rs77873429	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	17	67	0	0.288136	0	T|0.914;C|0.086	0.086	strong	.	PPFIBP2	87	.	NM_003621	exon23	c.T2390C	p.M797T	AGAAAATGGCCTC	.	PASS	Atlas-SNP
VWA5A	4013	hgsc.bcm.edu	37	11	123989383	123989383	+	Missense_Mutation	SNP	G	G	A	rs35215239	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	28	91	0	0.358974	0	G|0.978;A|0.022	0.022	strong	VWA5A,larynx,carcinoma,0,1	VWA5A	102	1	NM_014622	exon5	c.G613A	p.E205K	CCTACCGAGTACC	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011526	46011526	+	Silent	SNP	T	T	A	rs371768583		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	34	245	2	0.113333	0.00816326	.	.	weak	KRTAP10-6,NS,carcinoma,0,2	KRTAP10-6	57	2	NM_198688	exon1	c.A840T	p.T280T	GCATGATGTGGAA	.	scavenged	Atlas-SNP
GLCE	26035	hgsc.bcm.edu	37	15	69561181	69561181	+	Silent	SNP	T	T	C	rs56045514	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	35	60	0	0.564516	0	T|0.951;C|0.049	0.049	strong	.	GLCE	48	.	NM_015554	exon5	c.T1452C	p.H484H	GCAGCATGGAGTT	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	237	227	0	0.991632	0	C|0.770;T|0.230	0.230	strong	PCDHB15,NS,carcinoma,-2,1	PCDHB15	138	1	NM_018935	exon1	c.C1621T	p.L541L	CCGGCGCTGAGCA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101718932	101718932	+	Missense_Mutation	SNP	C	C	G	rs62513920	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	72	183	0	0.27907	0	C|0.811;G|0.188	0.188	strong	.	PABPC1	76	.	NM_002568	exon11	c.G1549C	p.V517L	TGCGAACTCCTGC	.	PASS	Atlas-SNP
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628992	1628992	+	Silent	SNP	G	G	A	rs60210378	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	186	119	0	0.973822	0	G|0.561;A|0.439	0.439	strong	KRTAP5-3,NS,carcinoma,0,1	KRTAP5-3	33	1	NM_001012708	exon1	c.C624T	p.G208G	CCCACAGCCTGAG	.	PASS	Atlas-SNP
SUFU	51684	hgsc.bcm.edu	37	10	104386934	104386934	+	Silent	SNP	T	T	C	rs17114803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	40	0	0.483871	0	T|0.814;C|0.186	0.186	strong	.	SUFU	44	.	NM_016169	exon11	c.T1299C	p.I433I	ACAGATTCTGTTG	.	PASS	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18180451	18180451	+	Missense_Mutation	SNP	A	A	G	rs375947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	80	0	0.417582	0	A|0.701;G|0.299	0.299	strong	.	IL12RB1	92	.	NM_005535	exon10	c.T1094C	p.M365T	TACGTCATGCTCT	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43690506	43690506	+	Missense_Mutation	SNP	G	G	C	rs8107936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	30	1	1	0.0333333	G|0.373;C|0.627	0.627	strong	PSG5,rectum,carcinoma,0,1	PSG5	58	1	NM_002781	exon1	c.C52G	p.L18V	GCAGGAGCCCCTT	.	scavenged	Atlas-SNP
KIAA1737	85457	hgsc.bcm.edu	37	14	77580068	77580068	+	Missense_Mutation	SNP	A	A	G	rs759593	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	44	89	0	0.407407	0	A|0.953;G|0.047	0.047	strong	.	KIAA1737	26	.	NM_033426	exon4	c.A607G	p.T203A	GAGCCAACCAAGG	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103124265	103124265	+	Missense_Mutation	SNP	A	A	G	rs150638029	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	50	91	0	0.543478	0	A|1.000;G|0.000	0.000	strong	.	RELN	593	.	NM_173054	exon62	c.T10016C	p.M3339T	TGCGACATGCTCC	.	PASS	Atlas-SNP
SLC28A1	9154	hgsc.bcm.edu	37	15	85448796	85448796	+	Silent	SNP	A	A	T	rs8187755	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	74	182	1	0.373737	0.00549451	A|0.973;T|0.027	0.027	strong	SLC28A1_ENST00000537624,NS,carcinoma,+1,2	SLC28A1	118	2	NM_004213	exon8	c.A630T	p.G210G	TTGGGGACTTGGA	.	scavenged	Atlas-SNP
TTC32	130502	hgsc.bcm.edu	37	2	20101487	20101487	+	Silent	SNP	G	G	A	rs2304589	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	38	0	0.530612	0	G|0.740;A|0.260	0.260	strong	.	TTC32	13	.	NM_001008237	exon1	c.C129T	p.S43S	GTCGCTGGAGGCC	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57552088	57552088	+	Silent	SNP	T	T	C	rs28756858	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	30	73	0	0.612245	0	A|0.000;C|0.268;T|0.732	0.268	strong	.	CCDC102A	22	.	NM_033212	exon6	c.A1140G	p.A380A	GACCTGTGCCCGC	.	PASS	Atlas-SNP
HIST1H2AB	8335	hgsc.bcm.edu	37	6	26033641	26033641	+	Silent	SNP	G	G	A	rs2230654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	125	176	0	0.553097	0	G|0.810;A|0.190	0.190	strong	.	HIST1H2AB	18	.	NM_003513	exon1	c.C156T	p.L52L	CGCCGCGAGATAC	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184290348	184290348	+	Silent	SNP	G	G	A	rs9862375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	72	127	0	0.483221	0	G|0.918;A|0.082	0.082	strong	.	EPHB3	114	.	NM_004443	exon3	c.G240A	p.V80V	CCAGGTGTGTAAT	.	PASS	Atlas-SNP
SGCA	6442	hgsc.bcm.edu	37	17	48247689	48247689	+	Silent	SNP	C	C	T	rs1801191	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	74	179	0	0.480519	0	C|0.911;T|0.089	0.089	strong	.	SGCA	35	.	NM_000023	exon7	c.C933T	p.V311V	CTATGTCATGTGC	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129291499	129291499	+	Silent	SNP	G	G	A	rs2285368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	116	170	0	0.565854	0	G|0.865;A|0.135	0.135	strong	.	PLXND1	149	.	NM_015103	exon15	c.C3030T	p.S1010S	GAGCTCGGAGCCT	.	PASS	Atlas-SNP
SLC28A1	9154	hgsc.bcm.edu	37	15	85478573	85478573	+	Silent	SNP	C	C	A	rs8187779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	77	174	1	0.542253	0.00574713	C|0.995;A|0.005	0.005	strong	SLC28A1,colon,carcinoma,-1,1	SLC28A1	118	1	NM_004213	exon15	c.C1405A	p.R469R	ATCCTGCGGCCTG	.	scavenged	Atlas-SNP
SCO1	6341	hgsc.bcm.edu	37	17	10600653	10600653	+	Missense_Mutation	SNP	G	G	A	rs1802083	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	21	29	0	0.488372	0	G|0.948;A|0.052	0.052	strong	.	SCO1	24	.	NM_004589	exon1	c.C172T	p.P58S	AGCCAGGGCGCCC	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	159	273	0	0.489231	0	G|0.693;C|0.307	0.307	strong	TDRD5,NS,neuroblastoma,+1,1	TDRD5	149	1	NM_173533	exon3	c.G378C	p.R126S	AGGAAGGGTTGCC	.	PASS	Atlas-SNP
LCE1C	353133	hgsc.bcm.edu	37	1	152777877	152777877	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	409	29	279	0	0.0709046	0	.	.	none	.	LCE1C	40	.	NM_178351	exon2	c.C78T	p.T26T	CTTTGGGGTGGGG	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68605169	68605169	+	Missense_Mutation	SNP	G	G	A	rs4777035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	45	118	0	0.343511	0	G|0.313;A|0.686	0.686	strong	.	ITGA11	110	.	NM_001004439	exon24	c.C2915T	p.P972L	CTGTTGGGCTTGA	.	PASS	Atlas-SNP
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839746	27839746	+	Silent	SNP	T	T	C	rs200956	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	85	145	0	0.53125	0	A|0.004;C|0.245	0.245	strong	.	HIST1H3I	28	.	NM_003533	exon1	c.A348G	p.K116K	GACGCGTTTGGCG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20852267	20852267	+	Missense_Mutation	SNP	C	C	T	rs2228041	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	50	77	0	0.617284	0	C|0.957;T|0.043	0.043	strong	.	TEP1	224	.	NM_007110	exon24	c.G3464A	p.R1155Q	ATCAGCCGTTGCA	.	PASS	Atlas-SNP
ZFP69	339559	hgsc.bcm.edu	37	1	40960619	40960619	+	Missense_Mutation	SNP	G	G	A	rs41301076	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	60	105	0	0.517241	0	G|0.946;A|0.054	0.054	strong	.	.	.	.	NM_198494	exon6	c.G469A	p.E157K	ACCATTGAGTCAA	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	9	28	0	0.36	0	T|0.000;G|0.000;C|0.278;A|0.721	0.278	strong	.	TTLL6	113	.	NM_001130918	exon1	c.T58G	p.W20G	TAGTCCAGCTTGC	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3613690	3613690	+	Silent	SNP	G	G	A	rs144685315	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	46	91	0	0.494624	0	G|0.999;A|0.001	0.001	strong	.	NLRC3	103	.	NM_178844	exon5	c.C1248T	p.Y416Y	TTGCTCGTAAAAC	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48602933	48602933	+	Missense_Mutation	SNP	T	T	C	rs2307282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	113	0	0.452381	0	T|0.956;C|0.044	0.044	strong	PLA2G4C,middle_lobe,carcinoma,+1,1	PLA2G4C	76	1	NM_001159322	exon5	c.A472G	p.R158G	CTTCTCTGGTTTG	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32673884	32673884	+	Silent	SNP	A	A	G	rs150651833	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	57	155	0	0.419118	0	A|0.998;G|0.002	0.002	strong	.	BIRC6	838	.	NM_016252	exon22	c.A4506G	p.P1502P	CTCACCATTTGAT	.	PASS	Atlas-SNP
PTGES	9536	hgsc.bcm.edu	37	9	132510960	132510960	+	Silent	SNP	G	G	A	rs3205181	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	48	49	0	0.676056	0	G|0.969;A|0.031	0.031	strong	.	PTGES	7	.	NM_004878	exon2	c.C183T	p.S61S	GGGGTCGCTCCTG	.	PASS	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	37	22	35713931	35713931	+	Silent	SNP	C	C	T	rs57755951	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	94	181	0	0.477157	0	C|0.982;T|0.018	0.018	strong	.	TOM1	43	.	NM_001135732	exon2	c.C114T	p.D38D	CTGCGACATCATC	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883608	152883608	+	Silent	SNP	G	G	A	rs7545413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	186	185	0	0.978947	0	G|0.664;A|0.336	0.336	strong	.	IVL	100	.	NM_005547	exon2	c.G1335A	p.Q445Q	GGAGCAGCAGCAG	.	PASS	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147907	93147907	+	Silent	SNP	A	A	T	rs9669519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	144	0	1	0	A|0.440;T|0.560	0.560	strong	.	PLEKHG7	38	.	NM_001004330	exon6	c.A357T	p.P119P	CGTGCCAGAGCTG	.	PASS	Atlas-SNP
PDGFRL	5157	hgsc.bcm.edu	37	8	17434813	17434813	+	Missense_Mutation	SNP	G	G	A	rs114432448	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	68	152	0	0.485714	0	G|0.987;A|0.013	0.013	strong	.	PDGFRL	27	.	NM_006207	exon2	c.G52A	p.D18N	CTGGAGGATGGTG	.	PASS	Atlas-SNP
HKDC1	80201	hgsc.bcm.edu	37	10	70980243	70980243	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	54	0	0.528571	0	.	.	none	.	HKDC1	98	.	NM_025130	exon1	c.C52A	p.Q18K	GAGGACCAGATCA	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13717508	13717508	+	Silent	SNP	G	G	A	rs1806201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	52	114	0	0.374101	0	G|0.746;A|0.254	0.254	strong	GRIN2B,NS,carcinoma,0,2	GRIN2B	303	2	NM_000834	exon13	c.C2664T	p.T888T	GGTTGCGGTGGGG	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56387142	56387142	+	Silent	SNP	G	G	A	rs34361729	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	56	78	0	0.571429	0	G|0.879;A|0.121	0.121	strong	RFX7_ENST00000423270,NS,carcinoma,-1,2	RFX7	170	2	NM_022841	exon9	c.C2784T	p.H928H	GGAAGTGTGAGAT	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103292224	103292224	+	Silent	SNP	T	T	C	rs2072403	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	85	1	0.493151	0.0117647	T|0.899;C|0.101	0.101	strong	RELN,NS,malignant_melanoma,-2,1	RELN	593	1	NM_173054	exon15	c.A1776G	p.E592E	AGAAAATTCCAAG	.	scavenged	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79029383	79029383	+	Missense_Mutation	SNP	T	T	G	rs1428224	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	85	0	1	0	T|0.702;G|0.298	0.298	strong	.	CMYA5	643	.	NM_153610	exon2	c.T4795G	p.S1599A	GAGGTATCTTCTA	.	PASS	Atlas-SNP
PODNL1	79883	hgsc.bcm.edu	37	19	14043843	14043843	+	Missense_Mutation	SNP	C	C	T	rs80103045	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	4	0	1	0	C|0.980;T|0.020	0.020	strong	.	PODNL1	27	.	NM_024825	exon8	c.G1214A	p.R405H	AACCGGCGGAAGG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54726237	54726237	+	Missense_Mutation	SNP	C	C	G	rs16985555	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	427	14	1123	0	0.0327869	0	C|0.333;G|0.667	0.667	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_006864	exon3	c.G268C	p.E90Q	GGTGCTCTGTCAT	.	scavenged	Atlas-SNP
WFDC8	90199	hgsc.bcm.edu	37	20	44184375	44184375	+	Missense_Mutation	SNP	T	T	C	rs2250860	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	188	183	1	1	0.00546448	T|0.663;C|0.337	0.337	strong	.	WFDC8	28	.	NM_181510	exon4	c.A410G	p.N137S	TCCTCATTTAAGA	.	PASS	Atlas-SNP
CSF2	1437	hgsc.bcm.edu	37	5	131411460	131411460	+	Missense_Mutation	SNP	T	T	C	rs25882	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	5	15	0	0.625	0	C|0.319;N|0.000	0.319	strong	.	CSF2	2	.	NM_000758	exon4	c.T350C	p.I117T	CCCAGATTATCAC	.	PASS	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107460162	107460162	+	Missense_Mutation	SNP	G	G	A	rs80079355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	29	64	0	0.426471	0	G|0.962;A|0.038	0.038	strong	ST6GAL2,rectum,carcinoma,0,1	ST6GAL2	159	1	NM_032528	exon2	c.C272T	p.A91V	GGCCCCGCATGAA	.	PASS	Atlas-SNP
SLC5A5	6528	hgsc.bcm.edu	37	19	17988794	17988794	+	Silent	SNP	C	C	T	rs35209536	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	41	65	0	0.488095	0	C|0.982;T|0.018	0.018	strong	.	SLC5A5	67	.	NM_000453	exon7	c.C861T	p.V287V	CCAGGTCGGCCTG	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	139	30	0	0.803468	0	T|0.599;C|0.401	0.401	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.A635G	p.H212R	TTACCATGGAGCT	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226026406	226026406	+	Missense_Mutation	SNP	A	A	G	rs2234922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	65	103	0	0.570175	0	A|0.779;G|0.221	0.221	strong	.	EPHX1	57	.	NM_001136018	exon4	c.A416G	p.H139R	CAGGCCATACCCC	.	PASS	Atlas-SNP
ACOX2	8309	hgsc.bcm.edu	37	3	58512285	58512285	+	Silent	SNP	T	T	C	rs13097249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	76	168	0	0.408602	0	T|0.932;C|0.068	0.068	strong	.	ACOX2	53	.	NM_003500	exon10	c.A1254G	p.S418S	CAGCTTTGAGTAG	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2203462	2203462	+	Silent	SNP	T	T	C	rs140746531	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	49	73	0	0.505155	0	T|1.000;C|0.000	0.000	strong	.	SMG6	97	.	NM_017575	exon2	c.A585G	p.P195P	CCTGTCTGGTTTA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549464	32549464	+	Silent	SNP	T	T	C	rs78767604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	340	92	181	0	0.270588	0	T|0.855;C|0.145	0.145	strong	.	HLA-DRB1	41	.	NM_002124	exon3	c.A522G	p.T174T	CAGGCCTGTGGAC	.	PASS	Atlas-SNP
POU5F1B	5462	hgsc.bcm.edu	37	8	128428592	128428592	+	Missense_Mutation	SNP	G	G	A	rs140000439	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	81	155	0	0.503106	0	G|0.985;A|0.015	0.015	strong	.	POU5F1B	32	.	NM_001159542	exon1	c.G481A	p.G161R	ACCCTGGGATATA	.	PASS	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	110011230	110011230	+	Missense_Mutation	SNP	C	C	T	rs10774775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	49	49	0	0.636364	0	C|0.693;T|0.307	0.307	strong	.	MMAB	16	.	NM_052845	exon1	c.G56A	p.R19H	CACCCGCGCAGGC	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	158	161	0	0.993711	0	G|0.836;A|0.164	0.164	strong	.	SLITRK2	221	.	NM_001144005	exon5	c.G309A	p.T103T	CCGAACGGGGGCA	.	PASS	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	46	105	0	0.5	0	C|0.781;T|0.219	0.219	strong	.	C10orf90	121	.	NM_001004298	exon3	c.G401A	p.R134H	CCTCTGCGGGGGC	.	PASS	Atlas-SNP
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407887	75407887	+	Missense_Mutation	SNP	G	G	T	rs57006992	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	32	30	0	0.551724	0	G|0.933;T|0.067	0.067	strong	.	SYNPO2L	118	.	NM_001114133	exon4	c.C1523A	p.P508H	AAGAAGGGGGGTG	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141625346	141625346	+	Silent	SNP	T	T	C	rs79054985	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	87	206	0	0.497143	0	T|0.965;C|0.035	0.035	strong	.	LRP1B	1315	.	NM_018557	exon27	c.A4392G	p.R1464R	ATGACCTCGGATG	.	PASS	Atlas-SNP
SYCP2	10388	hgsc.bcm.edu	37	20	58441612	58441612	+	Silent	SNP	C	C	T	rs58905758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	29	63	0	0.617021	0	C|0.983;T|0.017	0.017	strong	.	SYCP2	204	.	NM_014258	exon39	c.G4158A	p.T1386T	AGACTGCGTAGTA	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057952	46057952	+	Silent	SNP	C	C	A	rs74701761	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	473	113	294	0	0.238901	0	C|0.982;A|0.018	0.018	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C618A	p.V206V	GCCCGTCCCCTCC	.	PASS	Atlas-SNP
SNX29	92017	hgsc.bcm.edu	37	16	12162969	12162969	+	Silent	SNP	A	A	G	rs1641843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	98	0	1	0	A|0.468;G|0.532	0.532	strong	SNX29_ENST00000306030,NS,carcinoma,0,1	SNX29	60	1	NM_032167	exon10	c.A1299G	p.P433P	TCTCCCAGATCCT	.	PASS	Atlas-SNP
RAD21L1	642636	hgsc.bcm.edu	37	20	1224774	1224774	+	Missense_Mutation	SNP	A	A	C	rs17717241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	40	65	0	0.5	0	A|0.928;C|0.072	0.072	strong	.	RAD21L1	51	.	NM_001136566	exon11	c.A1268C	p.H423P	CTCAGCATAGCTC	.	PASS	Atlas-SNP
CIDEC	63924	hgsc.bcm.edu	37	3	9918861	9918861	+	Silent	SNP	C	C	A	rs456168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	39	78	0	0.393939	0	C|0.678;A|0.322	0.322	strong	CIDEC,NS,carcinoma,0,1	CIDEC	22	1	NM_001199623	exon3	c.G135T	p.L45L	CTCCGACAGCAGC	.	PASS	Atlas-SNP
IRF3	3661	hgsc.bcm.edu	37	19	50162909	50162909	+	Missense_Mutation	SNP	C	C	G	rs7251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	102	0	1	0	C|0.546;G|0.454	0.454	strong	IRF3,NS,carcinoma,0,1	IRF3	27	1	NM_001197122	exon8	c.G1296C	p.E432D	GCTCAGCTCTCCC	.	PASS	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150666843	150666843	+	Silent	SNP	A	A	G	rs6579846	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	96	128	0	0.52459	0	A|0.800;C|0.190;G|0.010	0.010	strong	SLC36A3,NS,carcinoma,0,1	SLC36A3	54	1	NM_001145017	exon7	c.T795C	p.L265L	GCTCCCAAGGGTG	.	PASS	Atlas-SNP
DNMT3A	1788	hgsc.bcm.edu	37	2	25469502	25469502	+	Silent	SNP	C	C	T	rs2276598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	36	91	0	0.439024	0	C|0.792;T|0.208	0.208	strong	.	DNMT3A	1807	.	NM_175629	exon10	c.G1266A	p.L422L	TGGCTCCAGGCCC	.	PASS	Atlas-SNP
COLEC12	81035	hgsc.bcm.edu	37	18	334994	334994	+	Missense_Mutation	SNP	A	A	G	rs2305025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	16	40	0	0.5	0	A|0.363;G|0.637	0.637	strong	COLEC12,NS,carcinoma,0,1	COLEC12	121	1	NM_130386	exon6	c.T1564C	p.S522P	CACTGGAGCCCTG	.	PASS	Atlas-SNP
NKX2-5	1482	hgsc.bcm.edu	37	5	172662014	172662014	+	Missense_Mutation	SNP	G	G	A	rs28936670	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	77	181	0	0.490446	0	G|0.993;A|0.007	0.007	strong	.	NKX2-5	42	.	NM_004387	exon1	c.C73T	p.R25C	GGCTGCGCTGCTG	.	PASS	Atlas-SNP
AGMO	392636	hgsc.bcm.edu	37	7	15458186	15458186	+	Silent	SNP	T	T	C	rs28635514	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	76	134	0	0.503311	0	T|0.943;C|0.057	0.057	strong	.	AGMO	98	.	NM_001004320	exon5	c.A606G	p.T202T	TACCTCTGTATGG	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53994178	53994178	+	Missense_Mutation	SNP	G	G	A	rs10421308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	75	164	0	0.477707	0	G|0.911;A|0.089	0.089	strong	ZNF813_ENST00000396403,NS,carcinoma,0,1	ZNF813	81	1	NM_001004301	exon4	c.G692A	p.R231K	TCTTAAGGAAACA	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634672	178634672	+	Missense_Mutation	SNP	C	C	T	rs398829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	61	0	1	0	C|0.635;T|0.365	0.365	strong	.	ADAMTS2	190	.	NM_021599	exon4	c.G733A	p.V245I	CTAGGACGCCCAG	.	PASS	Atlas-SNP
MKKS	8195	hgsc.bcm.edu	37	20	10394046	10394046	+	Silent	SNP	G	G	A	rs16991547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	52	98	0	0.477064	0	G|0.800;A|0.200	0.200	strong	MKKS,NS,carcinoma,0,1	MKKS	35	1	NM_170784	exon3	c.C117T	p.P39P	ACCTGAGGGGCCA	.	PASS	Atlas-SNP
DDX26B	203522	hgsc.bcm.edu	37	X	134713861	134713861	+	Silent	SNP	C	C	T	rs2298302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	503	499	427	1	0.992048	0.00234192	C|0.893;0|0.003	.	strong	.	DDX26B	130	.	NM_182540	exon15	c.C2157T	p.D719D	GTCTGACGACTTC	.	PASS	Atlas-SNP
ATAD3A	55210	hgsc.bcm.edu	37	1	1458915	1458915	+	Missense_Mutation	SNP	C	C	T	rs113107431	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	102	131	0	0.563536	0	C|0.972;T|0.028	0.028	strong	.	ATAD3A	35	.	NM_018188	exon9	c.C1075T	p.P359S	AGTCGACCCCAGG	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101719201	101719201	+	Missense_Mutation	SNP	A	A	G	rs72681439	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	19	115	1	0.213483	0.00869565	A|0.500;G|0.500	0.500	strong	PABPC1,bladder,carcinoma,+1,1	PABPC1	76	1	NM_002568	exon10	c.T1361C	p.I454T	GGGCGGATAGCAC	.	scavenged	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	37	19	1077985	1077985	+	Missense_Mutation	SNP	A	A	G	rs7251797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	172	171	0	0.988506	0	A|0.534;G|0.466	0.466	strong	.	HMHA1	78	.	NM_001258328	exon11	c.A1363G	p.S455G	GCAGGCAGCACGG	.	PASS	Atlas-SNP
PCNXL2	80003	hgsc.bcm.edu	37	1	233388242	233388242	+	Silent	SNP	A	A	G	rs6682865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	80	136	0	0.5	0	A|0.968;G|0.032	0.032	strong	.	PCNXL2	204	.	NM_014801	exon7	c.T1986C	p.F662F	GCCCTGAAAACTT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	127	244	0	0.473881	0	T|0.826;C|0.174	0.174	strong	LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	NM_006864	exon11	c.A1573G	p.R525G	CCACCCTGTCCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509113	195509113	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	60	177	0	0.191693	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C9338T	p.A3113V	GTGGATGCTGAGG	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3322139	3322139	+	Silent	SNP	C	C	T	rs61745281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	56	0	0.545455	0	C|0.984;T|0.016	0.016	strong	.	PRDM16	147	.	NM_022114	exon8	c.C1113T	p.C371C	CGACTGCGGGAAG	.	PASS	Atlas-SNP
NDUFS1	4719	hgsc.bcm.edu	37	2	207012483	207012483	+	Silent	SNP	A	A	G	rs11548670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	60	174	0	0.405405	0	A|0.946;G|0.054	0.054	strong	.	NDUFS1	82	.	NM_001199984	exon6	c.T456C	p.D152D	CTGCAGATCACAT	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112546	248112546	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	32	255	0	0.0946746	0	.	.	none	OR2L8,NS,carcinoma,0,1	OR2L8	92	1	NM_001001963	exon1	c.C387T	p.L129L	TCCTCTCCACTAT	.	scavenged	Atlas-SNP
PROKR2	128674	hgsc.bcm.edu	37	20	5283316	5283316	+	Silent	SNP	G	G	C	rs3746683	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	48	90	0	0.461538	0	G|0.887;C|0.113	0.113	strong	PROKR2,caecum,carcinoma,-2,3	PROKR2	90	3	NM_144773	exon2	c.C525G	p.A175A	GACCAAGGCGATC	.	PASS	Atlas-SNP
SPATA9	83890	hgsc.bcm.edu	37	5	95011166	95011166	+	Missense_Mutation	SNP	G	G	A	rs140676515	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	63	120	1	0.459854	0.00833333	G|0.998;A|0.002	0.002	strong	SPATA9,NS,carcinoma,+1,1	SPATA9	17	1	NM_031952	exon3	c.C328T	p.R110C	GCAGACGACCAGA	.	scavenged	Atlas-SNP
OR8K5	219453	hgsc.bcm.edu	37	11	55927591	55927591	+	Missense_Mutation	SNP	A	A	G	rs2512938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	68	126	0	0.492754	0	A|0.974;G|0.026	0.026	strong	.	OR8K5	82	.	NM_001004058	exon1	c.T203C	p.F68S	TCAACAAAAGCCA	.	PASS	Atlas-SNP
WDR73	84942	hgsc.bcm.edu	37	15	85188839	85188839	+	Missense_Mutation	SNP	C	C	T	rs11073619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	30	77	0	0.422535	0	C|0.903;T|0.097	0.097	strong	.	WDR73	15	.	NM_032856	exon7	c.G746A	p.R249H	CAAAGACGCCCAT	.	PASS	Atlas-SNP
GSTO2	119391	hgsc.bcm.edu	37	10	106058940	106058940	+	Silent	SNP	C	C	T	rs157078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	61	126	0	0.469231	0	C|0.952;T|0.048	0.048	strong	.	GSTO2	23	.	NM_183239	exon7	c.C630T	p.D210D	GTGGGACCCCACA	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982200	240982200	+	Missense_Mutation	SNP	C	C	T	rs114958540	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	10	147	2	0.0588235	0.0136054	C|0.980;T|0.019	0.019	strong	PRR21,NS,carcinoma,+1,2	PRR21	53	2	NM_001080835	exon1	c.G200A	p.C67Y	AAGGGACATGGGT	.	scavenged	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106960447	106960447	+	Silent	SNP	G	G	A	rs11152999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	38	76	0	0.413043	0	G|0.804;A|0.196	0.196	strong	.	AIM1	161	.	NM_001624	exon1	c.G231A	p.E77E	CCCAGAGTCCAAG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15794470	15794470	+	Missense_Mutation	SNP	G	G	A	rs150943202	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	36	101	0	0.232258	0	G|0.989;A|0.011	0.011	strong	CYP4F12,NS,haematopoietic_neoplasm,+1,1	CYP4F12	89	1	NM_023944	exon7	c.G815A	p.R272Q	TCATCCGGGAGCG	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	129986338	129986338	+	Silent	SNP	C	C	T	rs6973851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	35	44	0	1	0	C|0.418;T|0.582	0.582	strong	.	CPA5	61	.	NM_080385	exon3	c.C12T	p.T4T	GGGCACCCCTGGA	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5926507	5926507	+	Silent	SNP	T	T	C	rs555164	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	49	165	0	0.352518	0	T|0.698;C|0.302	0.302	strong	NPHP4,NS,carcinoma,0,1	NPHP4	119	1	NM_015102	exon26	c.A3570G	p.E1190E	CCGTGGTTCCCCG	.	PASS	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773388	140773388	+	Silent	SNP	G	G	T	rs2240700	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	95	283	0	0.386179	0	G|0.805;T|0.195	0.195	strong	PCDHGA8,caecum,carcinoma,+1,3	PCDHGA8	146	3	NM_014004	exon1	c.G1008T	p.S336S	CATTTCGGTGGAA	.	PASS	Atlas-SNP
ENTPD5	957	hgsc.bcm.edu	37	14	74454675	74454675	+	Missense_Mutation	SNP	C	C	G	rs60372237	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	47	104	0	0.494737	0	C|0.997;G|0.003	0.003	strong	.	ENTPD5	26	.	NM_001249	exon4	c.G131C	p.S44T	CTGGCGCTGACAT	.	PASS	Atlas-SNP
RARS2	57038	hgsc.bcm.edu	37	6	88224164	88224164	+	Silent	SNP	T	T	C	rs8802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	94	154	0	0.522222	0	T|0.871;C|0.129	0.129	strong	.	RARS2	61	.	NM_020320	exon20	c.A1704G	p.K568K	AAGAAGTTTCATT	.	PASS	Atlas-SNP
SSH2	85464	hgsc.bcm.edu	37	17	27959903	27959903	+	Missense_Mutation	SNP	G	G	A	rs2289629	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	41	91	0	0.427083	0	G|0.775;A|0.225	0.225	strong	.	SSH2	107	.	NM_033389	exon15	c.C2228T	p.S743L	TTTTCCGAGTGAG	.	PASS	Atlas-SNP
PARP12	64761	hgsc.bcm.edu	37	7	139746793	139746793	+	Missense_Mutation	SNP	C	C	T	rs34111764	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	53	130	0	0.477477	0	C|0.893;T|0.107	0.107	strong	.	PARP12	59	.	NM_022750	exon5	c.G877A	p.V293I	AATGAACTCTATG	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361451	+	Silent	SNP	G	G	A	rs80227456		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	713	296	757	0	0.415147	0	.	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.C244T	p.L82L	TCACTAGCGTGGA	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721606	49721606	+	Missense_Mutation	SNP	G	G	A	rs138238101		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	587	55	547	23	0.0936968	0.0420475	.	.	weak	MST1,caecum,carcinoma,0,1	MST1	84	1	NM_020998	exon18	c.C2033T	p.P678L	GCAAGTGGGCCCC	.	scavenged	Atlas-SNP
FAM83B	222584	hgsc.bcm.edu	37	6	54806379	54806379	+	Silent	SNP	A	A	G	rs17678648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	51	112	0	0.435897	0	A|0.956;G|0.044	0.044	strong	.	FAM83B	186	.	NM_001010872	exon5	c.A2610G	p.P870P	TTCTCCAGGTCCA	.	PASS	Atlas-SNP
EEFSEC	60678	hgsc.bcm.edu	37	3	127872506	127872506	+	Silent	SNP	C	C	T	rs11711710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	16	23	0	0.571429	0	C|0.866;T|0.134	0.134	strong	.	EEFSEC	53	.	NM_021937	exon1	c.C156T	p.G52G	TCTGGGCTTCTCG	.	PASS	Atlas-SNP
DLG1	1739	hgsc.bcm.edu	37	3	196842831	196842831	+	Silent	SNP	A	A	G	rs79212676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	88	170	0	0.451282	0	A|0.990;G|0.010	0.010	strong	.	DLG1	120	.	NM_001098424	exon14	c.T1509C	p.S503S	CTCTCCACTTAGA	.	PASS	Atlas-SNP
SMARCAL1	50485	hgsc.bcm.edu	37	2	217315787	217315787	+	Silent	SNP	T	T	C	rs2066527	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	62	119	0	0.525424	0	T|0.912;C|0.088	0.088	strong	SMARCAL1,NS,carcinoma,0,1	SMARCAL1	93	1	NM_014140	exon12	c.T2070C	p.T690T	CAAAACTGTGAGT	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7951149	7951149	+	Silent	SNP	C	C	T	rs9904554	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	64	123	0	0.474074	0	C|0.899;T|0.101	0.101	strong	ALOX15B,NS,carcinoma,0,1	ALOX15B	66	1	NM_001141	exon13	c.C1767T	p.G589G	CGAGGGCTTCATA	.	PASS	Atlas-SNP
SLC18A1	6570	hgsc.bcm.edu	37	8	20036827	20036827	+	Missense_Mutation	SNP	C	C	G	rs2270637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	93	190	0	0.476923	0	C|0.796;G|0.204	0.204	strong	SLC18A1,colon,carcinoma,0,1	SLC18A1	68	1	NM_001142324	exon4	c.G293C	p.S98T	ATTCCACTAGGTA	.	PASS	Atlas-SNP
MRPS11	64963	hgsc.bcm.edu	37	15	89010976	89010976	+	Missense_Mutation	SNP	C	C	T	rs16941904	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	69	81	0	0.584746	0	C|0.929;T|0.071	0.071	strong	.	MRPS11	14	.	NM_176805	exon1	c.C28T	p.R10W	GGGTCGCGGTTCC	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671759	25671759	+	Missense_Mutation	SNP	C	C	T	rs115121649	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	5	91	0	0.0431034	0	C|0.879;T|0.122	0.122	strong	PABPC3,NS,carcinoma,-1,1	PABPC3	129	1	NM_030979	exon1	c.C1423T	p.R475C	ACGCAGCGTGTTG	.	scavenged	Atlas-SNP
PDZD8	118987	hgsc.bcm.edu	37	10	119133968	119133968	+	Silent	SNP	G	G	C	rs3814230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	34	96	0	0.515152	0	G|0.766;C|0.234	0.234	strong	.	PDZD8	85	.	NM_173791	exon1	c.C771G	p.S257S	AAACTGGGAGCGC	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	138	3	1	0.0217391	T|0.521;C|0.479	0.479	strong	FAM83E,NS,carcinoma,0,2	FAM83E	34	2	NM_017708	exon1	c.A271G	p.T91A	CATCGGTGGTGGT	.	scavenged	Atlas-SNP
C1orf95	375057	hgsc.bcm.edu	37	1	226785102	226785102	+	Splice_Site	SNP	A	A	G	rs73098850	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	101	171	0	0.492683	0	A|0.961;G|0.039	0.039	strong	.	C1orf95	16	.	NM_001003665	exon3	c.383-2A>G	.	CCCTGTATTTTCC	.	PASS	Atlas-SNP
AGPAT1	10554	hgsc.bcm.edu	37	6	32139186	32139186	+	Missense_Mutation	SNP	G	G	A	rs11964847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	65	136	0	0.488722	0	G|0.995;A|0.005	0.005	strong	AGPAT1,NS,carcinoma,+1,1	AGPAT1	22	1	NM_006411	exon2	c.C88T	p.P30S	CACTGGGGCTGCA	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141759274	141759274	+	Silent	SNP	T	T	C	rs77338861		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	338	1	1	0.00295858	C|1.000;|0.000	1.000	weak	.	MGAM	767	.	NM_004668	exon32	c.T3822C	p.D1274D	GCAGGATGTGCAG	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Missense_Mutation	SNP	G	G	A	rs62070401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	98	239	0	0.385827	0	G|0.754;A|0.246	0.246	strong	.	CDRT1	83	.	NM_006382	exon6	c.C1232T	p.T411M	ACCTACGTGTCAG	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79929004	79929004	+	Missense_Mutation	SNP	C	C	T	rs140993797	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	62	77	0	0.659574	0	C|1.000;T|0.000	0.000	strong	.	VPS13A	735	.	NM_001018038	exon36	c.C4211T	p.T1404I	ATCTCACCATGGT	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7963949	7963949	+	Missense_Mutation	SNP	A	A	G	rs2042919	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	33	64	0	0.464789	0	A|0.759;G|0.241	0.241	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.A542G	p.E181G	CCACCGAACGGGC	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26247456	26247456	+	Silent	SNP	G	G	A	rs5996988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	22	72	0	0.37931	0	G|0.748;A|0.252	0.252	strong	MYO18B,NS,carcinoma,0,1	MYO18B	322	1	NM_032608	exon21	c.G3795A	p.G1265G	CATGGGGCTCACT	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31598339	31598339	+	Silent	SNP	G	G	C	rs45612839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	55	130	0	0.466102	0	G|0.936;C|0.064	0.064	strong	.	XDH	191	.	NM_000379	exon15	c.C1509G	p.G503G	CACCATGCCACCA	.	PASS	Atlas-SNP
PTGFRN	5738	hgsc.bcm.edu	37	1	117527444	117527444	+	Silent	SNP	C	C	T	rs17036676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	94	149	0	0.487047	0	C|0.994;T|0.006	0.006	strong	PTGFRN,NS,chondrosarcoma,+1,1	PTGFRN	91	1	NM_020440	exon8	c.C2310T	p.R770R	GGAGCGCGTGAGT	.	PASS	Atlas-SNP
NRG2	9542	hgsc.bcm.edu	37	5	139422232	139422232	+	Silent	SNP	G	G	A	rs144634106	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	30	66	0	0.625	0	G|0.965;A|0.035	0.035	strong	.	NRG2	69	.	NM_013982	exon1	c.C423T	p.A141A	GCCGCCGGCTGGG	.	PASS	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	110011229	110011229	+	Silent	SNP	G	G	T	rs36013132	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	49	48	0	0.628205	0	.	.	alt	.	MMAB	16	.	NM_052845	exon1	c.C57A	p.R19R	GCACCCGCGCAGG	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149755845	149755845	+	Silent	SNP	A	A	G	rs34796297	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	23	42	0	0.425926	0	A|0.984;G|0.016	0.016	strong	.	TCOF1	154	.	NM_001135243	exon13	c.A2094G	p.E698E	TGAGGAATCAGAT	.	PASS	Atlas-SNP
PKDCC	91461	hgsc.bcm.edu	37	2	42275819	42275819	+	Silent	SNP	T	T	C	rs11897440	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	33	41	0	1	0	T|0.448;C|0.552	0.552	strong	.	PKDCC	21	.	NM_138370	exon1	c.T480C	p.G160G	CGGCGGTGCCGCG	.	PASS	Atlas-SNP
LCE3D	84648	hgsc.bcm.edu	37	1	152552311	152552311	+	Silent	SNP	G	G	A	rs149516289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	137	271	0	0.520913	0	G|0.992;A|0.008	0.008	strong	.	LCE3D	28	.	NM_032563	exon2	c.C102T	p.S34S	GCCAGAGGAAGCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277575	152277575	+	Missense_Mutation	SNP	C	C	T	rs79771385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	570	281	509	3	0.492982	0.00589391	C|0.959;T|0.041	0.041	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.G9787A	p.G3263S	CGTGACCGGCTCT	.	scavenged	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	37	16	2136866	2136866	+	Silent	SNP	C	C	T	rs35534817	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	34	59	0	0.507463	0	C|0.975;T|0.025	0.025	strong	.	TSC2	364	.	NM_000548	exon38	c.C4983T	p.T1661T	TGGCACCATCAAG	.	PASS	Atlas-SNP
MICALL1	85377	hgsc.bcm.edu	37	22	38323700	38323700	+	Missense_Mutation	SNP	C	C	T	rs2272829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	50	88	0	0.49505	0	C|0.949;T|0.051	0.051	strong	.	MICALL1	53	.	NM_033386	exon9	c.C1748T	p.P583L	TTGCCCCCAGGAC	.	PASS	Atlas-SNP
SAG	6295	hgsc.bcm.edu	37	2	234229320	234229320	+	Missense_Mutation	SNP	A	A	G	rs7565275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	45	79	0	0.523256	0	A|0.937;G|0.063	0.063	strong	.	SAG	77	.	NM_000541	exon5	c.A226G	p.I76V	GAGGACATTGACG	.	PASS	Atlas-SNP
COG4	25839	hgsc.bcm.edu	37	16	70546234	70546234	+	Silent	SNP	G	G	A	rs3762171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	201	185	0	0.995049	0	G|0.578;A|0.422	0.422	strong	.	COG4	64	.	NM_015386	exon5	c.C646T	p.L216L	GGGGCAGATCACC	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	67	178	0	0.385057	0	T|0.915;C|0.085	0.085	strong	.	LY75	151	.	NM_002349	exon29	c.A4040G	p.K1347R	AAAAACTTCTCAT	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123800218	123800218	+	Missense_Mutation	SNP	C	C	T	rs17216529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	48	210	0	0.315789	0	C|0.880;T|0.120	0.120	strong	.	C5	124	.	NM_001735	exon4	c.G433A	p.V145I	AATAAACTCTAAC	.	PASS	Atlas-SNP
MSMP	692094	hgsc.bcm.edu	37	9	35754052	35754052	+	Missense_Mutation	SNP	C	C	T	rs189235807	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	63	161	0	0.453237	0	C|1.000;T|0.000	0.000	strong	.	MSMP	15	.	NM_001044264	exon1	c.G75A	p.M25I	TAGAGACATCACC	.	PASS	Atlas-SNP
KRT39	390792	hgsc.bcm.edu	37	17	39114962	39114962	+	Missense_Mutation	SNP	C	C	T	rs7213256	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	55	140	0	0.37931	0	C|0.741;T|0.259	0.259	strong	KRT39,colon,carcinoma,0,1	KRT39	53	1	NM_213656	exon7	c.G1367A	p.R456Q	AGTATCCGGGACA	.	PASS	Atlas-SNP
KCNAB1	7881	hgsc.bcm.edu	37	3	155838488	155838488	+	Missense_Mutation	SNP	G	G	C	rs67167156	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	61	110	0	0.616162	0	G|0.981;C|0.019	0.019	strong	.	KCNAB1	176	.	NM_172160	exon1	c.G88C	p.G30R	GTAGCAGGGAAAG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170092395	170092395	+	Silent	SNP	A	A	G	rs2229267	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	64	68	0	1	0	T|0.095;G|0.314	0.314	strong	.	LRP2	751	.	NM_004525	exon29	c.T4875C	p.C1625C	ATAATCACAAAAG	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65216120	65216120	+	Silent	SNP	C	C	T	rs57421986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	40	76	0	0.571429	0	A|0.000;C|0.891;T|0.108	0.108	strong	.	SPTB	378	.	NM_001024858	exon35	c.G6891A	p.A2297A	GCTCTGCGCCTTG	.	PASS	Atlas-SNP
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	97	0	1	0	A|0.466;G|0.534	0.534	strong	.	RSBN1L	74	.	NM_198467	exon2	c.A630G	p.E210E	AAAAGAAAGAGAA	.	PASS	Atlas-SNP
PRODH2	58510	hgsc.bcm.edu	37	19	36298022	36298022	+	Missense_Mutation	SNP	T	T	C	rs73594420	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	101	1	0.417582	0.00990099	T|0.889;C|0.111	0.111	strong	PRODH2,NS,carcinoma,0,1	PRODH2	68	1	NM_021232	exon6	c.A827G	p.N276S	TGGAGGTTCTAGG	.	scavenged	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	77	121	0	0.578947	0	G|0.341;A|0.659	0.659	strong	.	NOTCH1	1980	.	NM_017617	exon34	c.C6555T	p.D2185D	CTTGCCGTCCTGG	.	PASS	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097183	1097183	+	Missense_Mutation	SNP	G	G	A	rs11761941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	79	129	0	0.526667	0	G|0.903;A|0.097	0.097	strong	.	GPR146	20	.	NM_138445	exon1	c.G32A	p.G11E	GCACAGGGCTGGT	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13223570	13223570	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	5	173	0	0.0219298	0	.	.	none	MPDZ_ENST00000541718,NS,carcinoma,0,2	MPDZ	324	2	NM_003829	exon5	c.G533A	p.R178K	TCTCACCTATGGG	.	scavenged	Atlas-SNP
HECW2	57520	hgsc.bcm.edu	37	2	197087061	197087061	+	Silent	SNP	T	T	C	rs16847486	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	55	79	0	0.591398	0	T|0.965;C|0.035	0.035	strong	.	HECW2	239	.	NM_020760	exon24	c.A4020G	p.L1340L	GTCACATAGACTA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38964275	38964275	+	Missense_Mutation	SNP	A	A	G	rs34694816	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	10	11	0	0.416667	0	A|0.949;G|0.051	0.051	strong	.	RYR1	708	.	NM_001042723	exon28	c.A4024G	p.S1342G	GGCTGGAGCGAGG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26422993	26422993	+	Silent	SNP	C	C	T	rs7290069	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	19	45	0	0.463415	0	C|0.968;T|0.032	0.032	strong	MYO18B,NS,carcinoma,+2,1	MYO18B	322	1	NM_032608	exon43	c.C7053T	p.C2351C	TTCCTGCGAGTCC	.	PASS	Atlas-SNP
S100A2	6273	hgsc.bcm.edu	37	1	153534027	153534027	+	Missense_Mutation	SNP	C	C	T	rs1047325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	248	253	0	0.992	0	C|0.841;T|0.159	0.159	strong	.	S100A2	14	.	NM_005978	exon3	c.G182A	p.S61N	TCCAGGCTGCCCA	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50716068	50716068	+	Silent	SNP	C	C	T	rs11547732	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	95	153	0	0.505319	0	T|0.048;G|0.000;C|0.952;A|0.000	0.048	strong	.	PLXNB2	172	.	NM_012401	exon33	c.G5148A	p.A1716A	GGTCTGCGCGATG	.	PASS	Atlas-SNP
EPPIN-WFDC6	100526773	hgsc.bcm.edu	37	20	44174306	44174306	+	Silent	SNP	G	G	A	rs374858005		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	278	132	256	1	0.47482	0.00390625	.	.	weak	.	.	.	.	NM_001198986	exon2	c.C195T	p.C65C	TTTTCCGCAGCTG	.	PASS	Atlas-SNP
HDLBP	3069	hgsc.bcm.edu	37	2	242173247	242173247	+	Silent	SNP	G	G	A	rs2230359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	135	137	0	0.985401	0	T|0.032;G|0.738;C|0.133;A|0.097	0.097	strong	.	HDLBP	118	.	NM_005336	exon24	c.C3276T	p.D1092D	CCCATCGTCCTTA	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	51254901	51254901	+	Silent	SNP	G	G	A	rs1045874	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	73	131	0	0.51049	0	G|0.853;A|0.147	0.147	strong	NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	3	NM_004801	exon2	c.C511T	p.L171L	AGGCCAGGGTGAG	.	PASS	Atlas-SNP
AP3D1	8943	hgsc.bcm.edu	37	19	2116616	2116616	+	Silent	SNP	T	T	C	rs73512353	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	27	67	0	0.457627	0	T|0.992;C|0.008	0.008	strong	.	AP3D1	81	.	NM_001261826	exon17	c.A1989G	p.E663E	CAGCTCTTCCTCG	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1630992	1630992	+	Silent	SNP	G	G	A	rs9912287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	62	112	0	0.462687	0	G|0.790;A|0.208	0.208	strong	.	WDR81	180	.	NM_001163809	exon1	c.G2739A	p.L913L	GGTGCTGAAGGAC	.	PASS	Atlas-SNP
LGALS9	3965	hgsc.bcm.edu	37	17	25970633	25970633	+	Missense_Mutation	SNP	G	G	A	rs61732238	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	558	250	535	1	0.448029	0.00186916	G|0.833;A|0.167	0.167	strong	.	LGALS9	29	.	NM_009587	exon5	c.G527A	p.G176E	CCAGGGGGCGCAG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79447763	79447763	+	Missense_Mutation	SNP	T	T	C	rs34670941	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	132	238	0	0.456747	0	T|0.854;C|0.146	0.146	strong	.	FRAS1	779	.	NM_025074	exon70	c.T10877C	p.V3626A	CATGGGTTGACCC	.	PASS	Atlas-SNP
TEKT1	83659	hgsc.bcm.edu	37	17	6733672	6733672	+	Silent	SNP	T	T	C	rs8078571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	220	284	0	1	0	T|0.415;C|0.585	0.585	strong	TEKT1,NS,carcinoma,0,1	TEKT1	49	1	NM_053285	exon2	c.A24G	p.P8P	CTTGGGTGGAGGT	.	PASS	Atlas-SNP
MRPS2	51116	hgsc.bcm.edu	37	9	138395969	138395969	+	Missense_Mutation	SNP	A	A	G	rs3748199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	32	0	1	0	A|0.868;G|0.132	0.132	strong	.	MRPS2	17	.	NM_016034	exon4	c.A881G	p.H294R	TGAGCCATTCCCT	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179364	55179364	+	Missense_Mutation	SNP	A	A	G	rs1048801	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	390	371	349	1	0.951282	0.00286533	A|0.608;G|0.392	0.392	strong	LILRB4,NS,carcinoma,-1,1	LILRB4	86	1	NM_006847	exon12	c.A1241G	p.Q414R	ACGCCCAGCTGCA	.	PASS	Atlas-SNP
EEF1D	1936	hgsc.bcm.edu	37	8	144671489	144671489	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	25	59	0	0.390625	0	.	.	none	.	EEF1D	48	.	NM_001130053	exon3	c.C763G	p.P255A	CTGGGGGATGGCC	.	PASS	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95537501	95537501	+	Silent	SNP	C	C	T	rs11889464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	69	43	0	0.985714	0	C|0.897;T|0.103	0.103	strong	.	TEKT4	72	.	NM_144705	exon1	c.C177T	p.R59R	CGACCGCGACCAG	.	PASS	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	37	2	210558162	210558162	+	Missense_Mutation	SNP	G	G	A	rs741006	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	110	171	0	0.52381	0	G|0.850;A|0.150	0.150	strong	.	MAP2	372	.	NM_002374	exon7	c.G1268A	p.R423K	AGCAAAGGGATAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515122	195515122	+	Missense_Mutation	SNP	G	G	C	rs202171964	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	101	165	0	0.286119	0	G|0.949;C|0.052	0.052	strong	.	MUC4	1505	.	NM_018406	exon2	c.C3329G	p.T1110S	GAGGAAGTGTCGG	.	PASS	Atlas-SNP
PIBF1	10464	hgsc.bcm.edu	37	13	73369642	73369642	+	Missense_Mutation	SNP	A	A	G	rs1372000	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	144	80	0	0.993103	0	G|0.329;N|0.000	0.329	strong	.	PIBF1	65	.	NM_006346	exon4	c.A499G	p.I167V	CAATATATTAAAT	.	PASS	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	93	267	0	0.32069	0	G|0.831;A|0.169	0.169	strong	GABBR2,NS,malignant_melanoma,-1,1	GABBR2	126	1	NM_005458	exon15	c.C2052T	p.P684P	GAGTGCGGGGATG	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	5	27	0	0.217391	0	G|0.500;A|0.500	0.500	weak	CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	4	NM_001114091	exon14	c.C1788T	p.F596F	TCTCTGGAAGAAT	.	scavenged	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238289842	238289842	+	Missense_Mutation	SNP	G	G	A	rs34741387	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	33	50	0	0.568965	0	G|0.991;A|0.009	0.009	strong	.	COL6A3	608	.	NM_004369	exon5	c.C1613T	p.T538M	GAACTCGTGAATA	.	PASS	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	126	262	0	0.5	0	A|0.574;G|0.426	0.426	strong	PAPOLB,NS,carcinoma,0,1	PAPOLB	93	1	NM_020144	exon1	c.T1347C	p.N449N	TTCAGAATTATCT	.	PASS	Atlas-SNP
ELF4	2000	hgsc.bcm.edu	37	X	129201179	129201179	+	Silent	SNP	C	C	T	rs2181440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	72	134	0	0.666667	0	C|0.813;T|0.187	0.187	strong	.	ELF4	67	.	NM_001421	exon9	c.G1509A	p.T503T	TGTGACCGTGGGT	.	PASS	Atlas-SNP
TEX14	56155	hgsc.bcm.edu	37	17	56690848	56690848	+	Silent	SNP	T	T	C	rs8077548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	68	159	1	0.456376	0.00628931	T|0.835;C|0.165	0.165	strong	TEX14_ENST00000240361,NS,carcinoma,0,2	TEX14	343	2	NM_001201457	exon9	c.A957G	p.L319L	TTTCTCTAGGTCC	.	scavenged	Atlas-SNP
MRM1	79922	hgsc.bcm.edu	37	17	34958531	34958531	+	Missense_Mutation	SNP	C	C	T	rs60978234	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	8	21	0	0.380952	0	C|0.993;T|0.007	0.007	strong	MRM1,NS,haematopoietic_neoplasm,-2,1	MRM1	19	1	NM_024864	exon1	c.C292T	p.P98S	GACATTCCAGTTC	.	PASS	Atlas-SNP
ZSCAN18	65982	hgsc.bcm.edu	37	19	58597611	58597611	+	Missense_Mutation	SNP	G	G	C	rs147947490	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	48	90	0	0.45283	0	G|0.993;C|0.007	0.007	strong	.	ZSCAN18	104	.	NM_001145542	exon6	c.C936G	p.D312E	GGCAGCGTCAGGC	.	PASS	Atlas-SNP
YARS2	51067	hgsc.bcm.edu	37	12	32908518	32908518	+	Silent	SNP	G	G	A	rs11539444	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	39	79	0	0.513158	0	G|0.854;A|0.146	0.146	strong	.	YARS2	33	.	NM_001040436	exon1	c.C291T	p.G97G	AAACAGGCCCAGC	.	PASS	Atlas-SNP
CDC5L	988	hgsc.bcm.edu	37	6	44413463	44413463	+	Silent	SNP	T	T	A	rs2273666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	58	147	0	0.504348	0	T|0.878;A|0.122	0.122	strong	.	CDC5L	86	.	NM_001253	exon15	c.T2163A	p.L721L	TTTGCTTGGGGGT	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231118041	231118041	+	Missense_Mutation	SNP	A	A	C	rs3820975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	80	183	0	0.446927	0	A|0.867;C|0.133	0.133	strong	.	SP140	121	.	NM_007237	exon11	c.A1068C	p.L356F	TTGTTTATCTGCA	.	PASS	Atlas-SNP
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	83	116	0	0.546053	0	C|0.800;T|0.200	0.200	strong	GATA2,colon,carcinoma,0,2	GATA2	122	2	NM_001145662	exon3	c.G490A	p.A164T	AGTGGGCTGCTGT	.	PASS	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26596080	26596080	+	Missense_Mutation	SNP	G	G	A	rs7550997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	24	56	0	0.352941	0	G|0.849;A|0.151	0.151	strong	.	CEP85	61	.	NM_022778	exon9	c.G1624A	p.A542T	AGAGAAGCAGAAT	.	PASS	Atlas-SNP
LGALS3	3958	hgsc.bcm.edu	37	14	55611839	55611839	+	Missense_Mutation	SNP	A	A	T	rs11125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	59	78	0	0.551402	0	A|0.943;T|0.057	0.057	strong	.	LGALS3	10	.	NM_002306	exon6	c.A603T	p.Q201H	GATACAAGTACTG	.	PASS	Atlas-SNP
ATRAID	51374	hgsc.bcm.edu	37	2	27439751	27439751	+	Missense_Mutation	SNP	G	G	T	rs7437	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	127	257	1	0.473881	0.00389105	G|0.940;T|0.060	0.060	strong	.	.	.	.	NM_080592	exon7	c.G790T	p.A264S	CTGGGAGCCACCA	.	PASS	Atlas-SNP
RRS1	23212	hgsc.bcm.edu	37	8	67341378	67341378	+	Silent	SNP	G	G	A	rs3739334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	89	142	0	0.589404	0	G|0.919;A|0.081	0.081	strong	.	RRS1	13	.	NM_015169	exon1	c.G12A	p.Q4Q	GGGCCAGAGCGTG	.	PASS	Atlas-SNP
GEN1	348654	hgsc.bcm.edu	37	2	17962117	17962117	+	Silent	SNP	T	T	A	rs61762986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	109	0	0.491379	0	T|0.987;A|0.013	0.013	strong	.	GEN1	79	.	NM_182625	exon14	c.T1638A	p.S546S	CATGTCTTCTCTA	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062052	64062052	+	Missense_Mutation	SNP	G	G	A	rs10878074	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	68	160	0	0.409639	0	G|0.718;A|0.282	0.282	strong	.	DPY19L2	97	.	NM_173812	exon1	c.C122T	p.A41V	CCTAGGGCCGACT	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46654323	46654323	+	Silent	SNP	G	G	A	rs6007740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	49	93	0	0.415254	0	G|0.736;A|0.264	0.264	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C4897T	p.L1633L	CTGACAGGAGTAT	.	PASS	Atlas-SNP
SCG3	29106	hgsc.bcm.edu	37	15	51984362	51984362	+	Missense_Mutation	SNP	A	A	G	rs35664837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	16	44	0	0.285714	0	A|0.935;G|0.065	0.065	strong	.	SCG3	50	.	NM_013243	exon7	c.A697G	p.M233V	ACTCCAATGGCAG	.	PASS	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	37	15	94945719	94945719	+	Missense_Mutation	SNP	G	G	T	rs7178698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	68	141	0	0.43871	0	G|0.358;T|0.642	0.642	strong	.	MCTP2	122	.	NM_001159644	exon10	c.G854T	p.R285L	AGCACCGCAAAGA	.	PASS	Atlas-SNP
SYCE3	644186	hgsc.bcm.edu	37	22	50989678	50989678	+	Missense_Mutation	SNP	A	A	G	rs6009989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	76	162	0	0.513514	0	A|0.933;G|0.067	0.067	strong	.	SYCE3	10	.	NM_001123225	exon3	c.T263C	p.L88P	GCCTACAGCCTTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506462	195506462	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	39	113	0	0.458824	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+2,2	MUC4	1505	2	NM_018406	exon2	c.C11989G	p.H3997D	TGGCGTGACCTGT	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4116697	4116697	+	Silent	SNP	G	G	A	rs61735695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	56	134	0	0.434109	0	G|0.990;A|0.010	0.010	strong	SDK1,NS,carcinoma,+1,2	SDK1	361	2	NM_152744	exon21	c.G3078A	p.T1026T	CAGCACGACGCAC	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59821936	59821936	+	Silent	SNP	C	C	T	rs61755340	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	126	275	0	0.45	0	C|0.993;T|0.007	0.007	strong	.	DAAM1	95	.	NM_014992	exon20	c.C2440T	p.L814L	CAGTTGCTGGAGG	.	PASS	Atlas-SNP
PPAT	5471	hgsc.bcm.edu	37	4	57268328	57268328	+	Silent	SNP	T	T	C	rs2271924	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	51	83	0	0.579545	0	T|0.907;C|0.093	0.093	strong	.	PPAT	41	.	NM_002703	exon6	c.A681G	p.T227T	TCCTTCTGTTTCT	.	PASS	Atlas-SNP
RPRD1B	58490	hgsc.bcm.edu	37	20	36668874	36668874	+	Silent	SNP	G	G	A	rs2273353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	62	129	1	0.529915	0.00775194	G|0.747;A|0.253	0.253	strong	RPRD1B,NS,carcinoma,+1,2	RPRD1B	25	2	NM_021215	exon2	c.G189A	p.A63A	TTTAGCGAATGAT	.	scavenged	Atlas-SNP
EBF1	1879	hgsc.bcm.edu	37	5	158204425	158204425	+	Silent	SNP	A	A	G	rs1368298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	203	175	0	0.995098	0	A|0.408;G|0.592	0.592	strong	EBF1,NS,carcinoma,0,1	EBF1	110	1	NM_024007	exon10	c.T1032C	p.Y344Y	ACCTGTATAAATG	.	PASS	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37028127	37028127	+	Silent	SNP	A	A	G	rs73631164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	199	208	1	0.961353	0.00480769	A|0.644;G|0.356	0.356	strong	.	FAM47C	267	.	NM_001013736	exon1	c.A1644G	p.P548P	CCGCCCAGAGCCT	.	PASS	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	37	5	180043439	180043439	+	Silent	SNP	G	G	A	rs56127961	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	94	154	0	0.487047	0	G|0.982;A|0.018	0.018	strong	.	FLT4	356	.	NM_182925	exon23	c.C3147T	p.D1049D	CACCACGTCGCTT	.	PASS	Atlas-SNP
GOLGA7	51125	hgsc.bcm.edu	37	8	41355096	41355096	+	Silent	SNP	C	C	T	rs17656952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	22	53	0	0.34375	0	C|0.876;T|0.124	0.124	strong	.	GOLGA7	10	.	NM_001002296	exon2	c.C180T	p.L60L	GAAGCTCGGCGGC	.	PASS	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95537572	95537572	+	Missense_Mutation	SNP	C	C	T	rs4854235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	39	12	0	1	0	C|0.646;T|0.354	0.354	strong	.	TEKT4	72	.	NM_144705	exon1	c.C248T	p.T83M	AGCGCACGCAGCA	.	PASS	Atlas-SNP
ADAM12	8038	hgsc.bcm.edu	37	10	127824167	127824167	+	Silent	SNP	C	C	T	rs12098586	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	61	143	0	0.488	0	C|0.960;T|0.040	0.040	strong	.	ADAM12	388	.	NM_021641	exon5	c.G411A	p.T137T	AGAACACGTGCTG	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	35	96	0	0.364583	0	G|0.916;C|0.084	0.084	strong	.	ZNF366	108	.	NM_152625	exon5	c.C2216G	p.A739G	AGCACTGCTTGTT	.	PASS	Atlas-SNP
SIK2	23235	hgsc.bcm.edu	37	11	111594520	111594520	+	Silent	SNP	G	G	A	rs75997369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	36	82	0	0.631579	0	G|0.997;A|0.003	0.003	strong	.	SIK2	89	.	NM_015191	exon15	c.G2448A	p.T816T	GCCCACGCAGCTA	.	PASS	Atlas-SNP
PPM1H	57460	hgsc.bcm.edu	37	12	63083521	63083521	+	Silent	SNP	G	G	A	rs11174604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	84	168	0	0.587413	0	G|0.858;A|0.141	0.141	strong	PPM1H,NS,carcinoma,-2,1	PPM1H	42	1	NM_020700	exon8	c.C1203T	p.D401D	GTTGGAGTCATGC	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71838661	71838661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	31	79	0	0.469697	0	.	.	none	DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	2	NM_001130982	exon39	c.G4168A	p.V1390M	AGCCTCGTGGTAG	.	PASS	Atlas-SNP
KSR1	8844	hgsc.bcm.edu	37	17	25932816	25932816	+	Silent	SNP	G	G	A	rs55938675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	81	109	0	0.547297	0	G|0.964;A|0.036	0.036	strong	.	KSR1	151	.	NM_014238	exon15	c.G1626A	p.P542P	GAACCCGCCCCAC	.	PASS	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	37	9	119739015	119739015	+	Silent	SNP	G	G	A	rs10983437	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	102	96	0	0.723404	0	G|0.856;A|0.144	0.144	strong	.	ASTN2	307	.	NM_014010	exon7	c.C1488T	p.H496H	ACACAGGTGTCTG	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24802204	24802204	+	Silent	SNP	C	C	T	rs113288384	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	26	49	0	0.5	0	C|0.999;T|0.001	0.001	strong	.	TNRC6A	171	.	NM_014494	exon6	c.C2241T	p.D747D	GACTGACAATGGG	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5210762	5210762	+	Silent	SNP	G	G	A	rs1143699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	63	124	0	0.504	0	G|0.874;A|0.126	0.126	strong	.	PTPRS	169	.	NM_002850	exon34	c.C5289T	p.D1763D	CCAGAAGTCTTCC	.	PASS	Atlas-SNP
ZNF474	133923	hgsc.bcm.edu	37	5	121487954	121487954	+	Missense_Mutation	SNP	G	G	A	rs116158782	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	56	131	0	0.4375	0	G|0.988;A|0.012	0.012	strong	.	ZNF474	43	.	NM_207317	exon2	c.G269A	p.R90H	CGGCCCGCAGGCC	.	PASS	Atlas-SNP
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	40	75	0	0.39604	0	C|0.721;T|0.279	0.279	strong	.	MTOR	327	.	NM_004958	exon49	c.G6909A	p.L2303L	CAGCCACAGCAGC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721272	54721272	+	Missense_Mutation	SNP	C	C	T	rs114189491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	418	208	602	0	0.497608	0	C|0.961;T|0.039	0.039	strong	.	LILRB3	67	.	NM_001081450	exon12	c.G1668A	p.M556I	AGAGGCCATTTCT	.	PASS	Atlas-SNP
ASPSCR1	79058	hgsc.bcm.edu	37	17	79943475	79943475	+	Silent	SNP	A	A	G	rs4796860	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	82	177	0	0.460674	0	A|0.983;G|0.017	0.017	strong	.	ASPSCR1	27	.	NM_001251888	exon4	c.A366G	p.P122P	TTTTCCACAGATC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46760037	46760037	+	Missense_Mutation	SNP	G	G	A	rs6008777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	85	122	0	0.534591	0	G|0.971;A|0.029	0.029	strong	CELSR1,colon,carcinoma,+1,1	CELSR1	242	1	NM_014246	exon34	c.C8891T	p.S2964L	GTGCGCGAGGATG	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112309123	112309123	+	Missense_Mutation	SNP	C	C	A	rs197414	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	102	0	1	0	C|0.846;A|0.154	0.154	strong	.	DDX20	50	.	NM_007204	exon11	c.C2077A	p.R693S	GATGATCGTATTT	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	72	156	0	0.48	0	C|0.823;T|0.177	0.177	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon13	c.G1608A	p.K536K	TTGACTCTTGGTG	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285404	16285404	+	Silent	SNP	C	C	T	rs9908960	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	82	147	0	0.458101	0	C|0.947;T|0.053	0.053	strong	.	UBB	30	.	NM_018955	exon2	c.C183T	p.I61I	CAACATCCAGAAG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22952111	22952111	+	Missense_Mutation	SNP	A	A	G	rs34726149	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	157	0	1	0	A|0.809;G|0.191	0.191	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon2	c.T19C	p.W7R	CATCCCAAAATGT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	18	37	0	0.4	0	T|0.406;C|0.594	0.594	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon32	c.T5078C	p.V1693A	CAGGCGTTGAGCC	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154504741	154504741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	481	5	457	1	0.010395	0.00218818	.	.	none	KIAA0922,colon,carcinoma,+1,1	KIAA0922	214	1	NM_001131007	exon11	c.A977G	p.D326G	AGAGAGATGCTCT	.	scavenged	Atlas-SNP
VAV3	10451	hgsc.bcm.edu	37	1	108138961	108138961	+	Silent	SNP	T	T	C	rs17229705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	63	136	0	0.440559	0	T|0.950;C|0.050	0.050	strong	.	VAV3	176	.	NM_006113	exon25	c.A2223G	p.E741E	CACAAGTTCCTTT	.	PASS	Atlas-SNP
PLEKHG4	25894	hgsc.bcm.edu	37	16	67316234	67316234	+	Missense_Mutation	SNP	C	C	T	rs11860295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	35	44	0	0.686275	0	C|0.752;T|0.248	0.248	strong	.	PLEKHG4	94	.	NM_001129728	exon9	c.C1235T	p.T412I	AGGTGACCCTGAG	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42631928	42631928	+	Silent	SNP	T	T	C	rs36023127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	95	73	1	0.989583	0.0136986	T|0.910;C|0.090	0.090	strong	GANC,brain,glioma,0,1	GANC	57	1	NM_198141	exon17	c.T1905C	p.A635A	CCAGGCTGGAGCC	.	scavenged	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30704725	30704725	+	Silent	SNP	C	C	T	rs62000451	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	91	0	1	0	C|0.886;T|0.114	0.114	strong	.	TEX15	350	.	NM_031271	exon1	c.G1809A	p.Q603Q	AGCTATCTGTATT	.	PASS	Atlas-SNP
DYRK4	8798	hgsc.bcm.edu	37	12	4702173	4702173	+	Silent	SNP	C	C	T	rs2240763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	49	72	0	0.453704	0	C|0.897;T|0.103	0.103	strong	DYRK4,NS,carcinoma,-2,1	DYRK4	75	1	NM_003845	exon4	c.C124T	p.L42L	GAGGCCCTAAAGC	.	PASS	Atlas-SNP
BBS12	166379	hgsc.bcm.edu	37	4	123663098	123663098	+	Silent	SNP	A	A	G	rs17006077	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	162	273	0	0.496933	0	A|0.927;G|0.073	0.073	strong	.	BBS12	63	.	NM_001178007	exon3	c.A51G	p.Q17Q	ACTTCAACAACTT	.	PASS	Atlas-SNP
CIB4	130106	hgsc.bcm.edu	37	2	26805761	26805761	+	Silent	SNP	C	C	T	rs7595964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	39	107	0	0.4875	0	C|0.951;T|0.049	0.049	strong	.	CIB4	15	.	NM_001029881	exon6	c.G459A	p.L153L	ATTGTCCAGATCC	.	PASS	Atlas-SNP
PRKCH	5583	hgsc.bcm.edu	37	14	61857969	61857969	+	Silent	SNP	A	A	G	rs2230499	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	25	53	0	0.409836	0	A|0.743;G|0.257	0.257	strong	.	PRKCH	89	.	NM_006255	exon2	c.A390G	p.V130V	GAAAGTATTTGTG	.	PASS	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	37	1	87012929	87012929	+	Missense_Mutation	SNP	C	C	T	rs2231580	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	50	95	0	0.531915	0	C|0.971;T|0.029	0.029	strong	.	CLCA4	131	.	NM_012128	exon1	c.C127T	p.P43S	AGTGTGCCAGAAG	.	PASS	Atlas-SNP
CDH26	60437	hgsc.bcm.edu	37	20	58571064	58571064	+	Missense_Mutation	SNP	G	G	T	rs194998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	57	0	0.467742	0	A|0.001;C|0.008	.	strong	.	CDH26	229	.	NM_177980	exon12	c.G1843T	p.V615L	CTTCATGTGGGGG	.	PASS	Atlas-SNP
SLC14A1	6563	hgsc.bcm.edu	37	18	43307338	43307338	+	Silent	SNP	C	C	A	rs11877086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	67	85	0	1	0	C|0.566;A|0.434	0.434	strong	.	SLC14A1	84	.	NM_001146037	exon1	c.C102A	p.G34G	CAGAGGCATCGCC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124409630	124409630	+	Missense_Mutation	SNP	G	G	T	rs74845458	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	136	258	0	0.482269	0	G|0.958;T|0.042	0.042	strong	DNAH10_same_name,NS,carcinoma,0,2	DNAH10	888	2	NM_207437	exon67	c.G11446T	p.V3816F	TTTCCCGTCCCCT	.	PASS	Atlas-SNP
PRKAG3	53632	hgsc.bcm.edu	37	2	219691801	219691801	+	Missense_Mutation	SNP	G	G	A	rs33985460	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	82	146	0	0.465909	0	G|0.961;A|0.039	0.039	strong	.	PRKAG3	47	.	NM_017431	exon10	c.C1018T	p.R340W	AGGGCCGGGGCAG	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135440203	135440203	+	Missense_Mutation	SNP	A	A	T	rs200661929	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1297	230	1248	0	0.177332	0	A|0.986;T|0.014	0.014	strong	FRG2B,NS,haematopoietic_neoplasm,0,1	FRG2B	47	1	NM_001080998	exon1	c.T44A	p.I15N	CACTGGATGGAGG	.	scavenged	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23929189	23929189	+	Missense_Mutation	SNP	C	C	G	rs190617851	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	44	86	0	0.473118	0	C|1.000;G|0.000	0.000	strong	.	SACS	871	.	NM_014363	exon8	c.G1562C	p.S521T	TCAGAGCTCTTTT	.	PASS	Atlas-SNP
MPG	4350	hgsc.bcm.edu	37	16	129654	129654	+	Silent	SNP	C	C	T	rs710081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	54	90	0	0.519231	0	C|0.762;T|0.238	0.238	strong	MPG,NS,carcinoma,0,1	MPG	26	1	NM_002434	exon3	c.C270T	p.F90F	GGAGTTCTTCGAC	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518297	161518297	+	Missense_Mutation	SNP	G	G	T	rs52820103	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	770	215	638	0	0.279221	0	G|0.994;T|0.006	0.006	strong	FCGR3A,NS,carcinoma,-1,1	FCGR3A	38	1	NM_000569	exon3	c.C341A	p.A114D	GTGGCAGCGTCAA	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91744348	91744348	+	Missense_Mutation	SNP	C	C	T	rs114849211	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	57	77	0	0.553398	0	C|0.994;T|0.006	0.006	strong	KIAA1509,caecum,carcinoma,-1,6	CCDC88C	192	6	NM_001080414	exon29	c.G4976A	p.R1659Q	CAGGGCCGCACTC	.	PASS	Atlas-SNP
WNT4	54361	hgsc.bcm.edu	37	1	22446768	22446768	+	Silent	SNP	G	G	A	rs34228276	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	103	179	0	0.504902	0	G|0.968;A|0.032	0.032	strong	.	WNT4	33	.	NM_030761	exon5	c.C831T	p.P277P	GAAGTCGGGGCTA	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88504483	88504483	+	Silent	SNP	C	C	G	rs375672779		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	50	77	0	0.617284	0	.	.	weak	.	ZNF469	121	.	NM_001127464	exon2	c.C10521G	p.T3507T	CGTGACCCACCCG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464465	10464465	+	Silent	SNP	G	G	A	rs112520779	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	43	52	0	0.661538	0	A|0.002;G|0.998;T|0.000	0.002	strong	RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	NM_178857	exon4	c.C7143T	p.L2381L	GGGGGCGAGACTT	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180335743	180335743	+	Silent	SNP	C	C	T	rs112784813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	163	123	0	1	0	C|0.866;T|0.134	0.134	strong	.	BTNL8	114	.	NM_001159708	exon2	c.C207T	p.D69D	CAGGGACGGGAAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11959	11959	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	8	8	0	0.888889	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.A1200G	p.M400M	CAACATACTAGTC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179434516	179434516	+	Missense_Mutation	SNP	C	C	T	rs3813243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	40	62	0	0.588235	0	C|0.918;T|0.082	0.082	strong	.	TTN	18412	.	NM_001267550	exon326	c.G76343A	p.S25448N	CCAACACTCACAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678481	100678481	+	Missense_Mutation	SNP	A	A	T	rs73168389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	22	123	0	0.165414	0	A|0.973;T|0.027	0.027	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3784T	p.T1262S	CCTACAACCGCTG	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143823112	143823112	+	Missense_Mutation	SNP	G	G	A	rs3762001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	26	59	0	0.361111	0	G|0.804;A|0.196	0.196	strong	FUCA2,NS,carcinoma,0,1	FUCA2	28	1	NM_032020	exon5	c.C1111T	p.H371Y	AGGTATGGGTTTC	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87696470	87696470	+	Silent	SNP	A	A	G	rs12507034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	74	142	0	0.451219	0	A|0.906;G|0.094	0.094	strong	.	PTPN13	203	.	NM_080685	exon34	c.A5670G	p.T1890T	CATAACACTAACG	.	PASS	Atlas-SNP
GOLT1A	127845	hgsc.bcm.edu	37	1	204172096	204172096	+	Silent	SNP	G	G	A	rs6689607	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	99	177	0	0.510309	0	G|0.898;A|0.102	0.102	strong	GOLT1A,caecum,carcinoma,0,1	GOLT1A	15	1	NM_198447	exon2	c.C45T	p.T15T	GAAACCGGTGATC	.	PASS	Atlas-SNP
ROBO1	6091	hgsc.bcm.edu	37	3	79174619	79174619	+	Silent	SNP	C	C	T	rs139237706	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	94	192	0	0.482051	0	C|0.998;T|0.002	0.002	strong	.	ROBO1	833	.	NM_002941	exon3	c.G159A	p.S53S	GCCCAGCGAATTG	.	PASS	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	46	104	0	0.464646	0	G|0.859;A|0.141	0.141	strong	.	KANK3	35	.	NM_198471	exon4	c.C1359T	p.D453D	TGTGCCGTCTCTC	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102466430	102466430	+	Silent	SNP	G	G	A	rs34690489	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	87	0	0.463636	0	G|0.984;A|0.016	0.016	strong	DYNC1H1,colon,carcinoma,+1,1	DYNC1H1	395	1	NM_001376	exon17	c.G3909A	p.A1303A	GGAGGCGCTGGAA	.	PASS	Atlas-SNP
ALDH1L2	160428	hgsc.bcm.edu	37	12	105434467	105434467	+	Silent	SNP	C	C	T	rs11112330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	52	94	0	0.547368	0	C|0.698;T|0.302	0.302	strong	ALDH1L2,NS,carcinoma,0,1	ALDH1L2	71	1	NM_001034173	exon16	c.G1869A	p.T623T	CAAGGGCGTGACC	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16260916	16260916	+	Silent	SNP	C	C	T	rs848211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	25	65	0	0.362319	0	C|0.897;T|0.103	0.103	strong	SPEN,NS,carcinoma,+1,1	SPEN	374	1	NM_015001	exon11	c.C8181T	p.A2727A	CAATGCCGCTGCG	.	PASS	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2411118	2411118	+	Missense_Mutation	SNP	T	T	A	rs142406714	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	41	57	0	0.585714	0	T|1.000;A|0.000	0.000	weak	.	TGM6	126	.	NM_198994	exon11	c.T1705A	p.Y569N	ATATCTTACTCTA	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55524314	55524314	+	Silent	SNP	T	T	C	rs7137261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	87	124	0	0.557692	0	T|0.674;C|0.326	0.326	strong	.	OR9K2	63	.	NM_001005243	exon1	c.T762C	p.H254H	GATACATTCTACT	.	PASS	Atlas-SNP
RFC5	5985	hgsc.bcm.edu	37	12	118465820	118465820	+	Silent	SNP	T	T	C	rs5745873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	23	64	0	0.45098	0	T|0.884;C|0.116	0.116	strong	.	RFC5	35	.	NM_007370	exon9	c.T856C	p.L286L	ATACACTTGTTTG	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19500830	19500830	+	Missense_Mutation	SNP	T	T	G	rs143098074	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	49	0	0.5	0	T|0.999;G|0.001	0.001	strong	.	UBR4	415	.	NM_020765	exon22	c.A2965C	p.K989Q	CATTCTTGTTTTC	.	PASS	Atlas-SNP
DEFA3	1668	hgsc.bcm.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	T	G	rs2230231	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	696	29	689	28	0.0416667	0.0406386	T|0.167;G|0.833	0.833	strong	DEFA3,NS,carcinoma,0,1	DEFA3	7	1	NM_005217	exon3	c.A194C	p.D65A	TAGCAGTCCATGT	.	scavenged	Atlas-SNP
SHROOM4	57477	hgsc.bcm.edu	37	X	50350674	50350674	+	Silent	SNP	T	T	C	rs3747282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	45	67	0	0.5	0	T|0.703;C|0.297	0.297	strong	.	SHROOM4	171	.	NM_020717	exon6	c.A3468G	p.E1156E	CTCCTCTTCCTCC	.	PASS	Atlas-SNP
MINOS1	440574	hgsc.bcm.edu	37	1	19950062	19950062	+	Silent	SNP	T	T	C	rs1737428	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	37	75	0	0.536232	0	T|0.661;C|0.339	0.339	strong	.	.	.	.	NM_001032363	exon3	c.T207C	p.H69H	TCTACATGGAAAA	.	PASS	Atlas-SNP
ZNF841	284371	hgsc.bcm.edu	37	19	52568422	52568422	+	Missense_Mutation	SNP	T	T	G	rs61743893	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	135	220	0	0.548781	0	T|0.938;G|0.062	0.062	strong	.	ZNF841	183	.	NM_001136499	exon7	c.A2713C	p.T905P	TAGTTGTAAGGTT	.	PASS	Atlas-SNP
ALDH1B1	219	hgsc.bcm.edu	37	9	38396002	38396002	+	Missense_Mutation	SNP	C	C	T	rs2228093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	27	58	0	0.5	0	C|0.831;A|0.001	.	strong	ALDH1B1,NS,carcinoma,+1,1	ALDH1B1	50	1	NM_000692	exon2	c.C257T	p.A86V	GGGAAGCCTTCCG	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549420	158549420	+	Silent	SNP	C	C	T	rs863361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	157	142	0	1	0	C|0.471;T|0.529	0.529	strong	OR10X1,face,carcinoma,-2,1	OR10X1	96	1	NM_001004477	exon1	c.G270A	p.T90T	GGTCAGCGTATAG	.	PASS	Atlas-SNP
EIF2AK2	5610	hgsc.bcm.edu	37	2	37353464	37353464	+	Silent	SNP	A	A	G	rs2307478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	79	196	0	0.519737	0	A|0.985;G|0.015	0.015	strong	.	EIF2AK2	54	.	NM_001135651	exon11	c.T876C	p.T292T	AACGTAAGTCTTT	.	PASS	Atlas-SNP
FTSJD2	23070	hgsc.bcm.edu	37	6	37426429	37426429	+	Silent	SNP	T	T	C	rs35608753	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	67	99	0	0.429487	0	T|0.986;C|0.014	0.014	strong	.	FTSJD2	64	.	NM_015050	exon9	c.T819C	p.F273F	GTACTTTGCTGAT	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219508988	219508988	+	Missense_Mutation	SNP	T	T	C	rs3770214	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	313	309	0	0.996815	0	C|0.742;N|0.000	0.742	strong	.	ZNF142	190	.	NM_001105537	exon8	c.A2251G	p.S751G	CAGCACTCAAGTC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82834299	82834299	+	Missense_Mutation	SNP	G	G	A	rs188703	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	49	91	1	0.5	0.010989	G|0.623;A|0.377	0.377	strong	VCAN,NS,carcinoma,-1,1	VCAN	498	1	NM_004385	exon8	c.G5477A	p.R1826H	TCCCACGTAGTCC	.	scavenged	Atlas-SNP
ANKRD40	91369	hgsc.bcm.edu	37	17	48774319	48774319	+	Silent	SNP	G	G	A	rs3815378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	44	123	0	0.382609	0	G|0.963;A|0.037	0.037	strong	.	ANKRD40	35	.	NM_052855	exon4	c.C942T	p.P314P	AGTATTGGGTAAC	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32000302	32000302	+	Silent	SNP	C	C	T	rs372606333		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	5	256	0	0.017301	0	.	.	weak	PDZD2,NS,carcinoma,+2,1	PDZD2	306	1	NM_178140	exon4	c.C1179T	p.V393V	ACTGGTCGGGCTC	.	scavenged	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	16	154	0	0.142857	0	.	.	weak	.	HOMEZ	80	.	NM_020834	exon2	c.G1608A	p.E536E	ATCTTCCTCCTCC	.	PASS	Atlas-SNP
FUCA1	2517	hgsc.bcm.edu	37	1	24189740	24189740	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	63	0	0.486486	0	.	.	none	.	FUCA1	24	.	NM_000147	exon3	c.C546T	p.Y182Y	TGAGTGGTATAGT	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580958	140580958	+	Silent	SNP	C	C	A	rs74949746	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	433	213	284	0	0.491917	0	C|0.991;A|0.009	0.009	strong	PCDHB11,right_upper_lobe,carcinoma,+2,2	PCDHB11	162	2	NM_018931	exon1	c.C1611A	p.G537G	CCGCGGCTCCCCG	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7231280	7231280	+	Missense_Mutation	SNP	T	T	C	rs115093903	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	85	0	0.486486	0	T|0.989;C|0.011	0.011	strong	.	RREB1	242	.	NM_001003700	exon10	c.T2948C	p.L983S	TAACTTTGGGGCC	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123886681	123886681	+	Missense_Mutation	SNP	A	A	G	rs1893766	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	902	204	1152	2	0.226164	0.00173611	A|0.567;G|0.433	0.433	strong	OR10G4,NS,malignant_melanoma,-2,2	OR10G4	77	2	NM_001004462	exon1	c.A400G	p.M134V	ACCAGCATGATGA	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108754260	108754260	+	Silent	SNP	A	A	G	rs3762696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	86	0	1	0	G|0.422;A|0.578	0.422	strong	.	MORC1	211	.	NM_014429	exon15	c.T1386C	p.D462D	CTCCACATCGATG	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158612236	158612236	+	Missense_Mutation	SNP	A	A	G	rs863931	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	407	186	387	1	0.457002	0.00258398	A|0.379;G|0.621	0.621	strong	.	SPTA1	720	.	NM_003126	exon33	c.T4702C	p.C1568R	CGCTACACTCAAT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382368	43382368	+	Missense_Mutation	SNP	T	T	G	rs707745	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	344	316	334	0	0.918605	0	T|0.708;G|0.292	0.292	strong	.	PSG1	196	.	NM_001184826	exon2	c.A127C	p.T43P	CTTTGGTTGGCTC	.	PASS	Atlas-SNP
EMR2	30817	hgsc.bcm.edu	37	19	14877820	14877820	+	Missense_Mutation	SNP	G	G	A	rs74182239		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	15	63	2	1	0.031746	A|1.000;|0.000	1.000	weak	EMR2,larynx,carcinoma,+2,1	EMR2	99	1	NM_001271052	exon5	c.C457T	p.L153F	GTTTGAGCTTGAA	.	scavenged	Atlas-SNP
ARMC12	221481	hgsc.bcm.edu	37	6	35705059	35705059	+	Silent	SNP	G	G	A	rs56183341	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	56	116	0	0.482759	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_145028	exon1	c.G174A	p.P58P	GTGTCCGGGCCCT	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1008704	1008704	+	Missense_Mutation	SNP	G	G	A	rs61744375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	26	21	0	0.684211	0	G|0.965;A|0.035	0.035	strong	.	GRIN3B	46	.	NM_138690	exon7	c.G2554A	p.E852K	CTGGGCGAGCACG	.	PASS	Atlas-SNP
C2CD4D	100191040	hgsc.bcm.edu	37	1	151810486	151810486	+	Missense_Mutation	SNP	G	G	A	rs188475396	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	53	97	0	0.464912	0	G|0.994;A|0.006	0.006	strong	.	C2CD4D	3	.	NM_001136003	exon2	c.C980T	p.T327M	AGGGGCGTCTCGC	.	PASS	Atlas-SNP
RBM15	64783	hgsc.bcm.edu	37	1	110884493	110884493	+	Silent	SNP	T	T	C	rs61745292	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	60	120	0	0.428571	0	T|0.974;C|0.026	0.026	strong	.	RBM15	93	.	NM_022768	exon1	c.T2466C	p.T822T	TTCAACTGGAGGC	.	PASS	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	37	20	20340872	20340872	+	Missense_Mutation	SNP	A	A	G	rs75487354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	63	0	0.467742	0	A|0.984;G|0.016	0.016	strong	.	C20orf26	188	.	NM_015585	exon27	c.A3532G	p.I1178V	CCTTCCATAGAGC	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183696387	183696387	+	Silent	SNP	G	G	A	rs1053386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	49	46	0	1	0	G|0.913;A|0.087	0.087	strong	.	ABCC5	142	.	NM_005688	exon9	c.C1200T	p.S400S	AGTGATGCTCTGG	.	PASS	Atlas-SNP
UNC5D	137970	hgsc.bcm.edu	37	8	35583692	35583692	+	Silent	SNP	T	T	C	rs6983275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	36	94	0	0.444444	0	T|0.826;C|0.174	0.174	strong	.	UNC5D	393	.	NM_080872	exon10	c.T1326C	p.S442S	GAATTCTGCCATG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T	rs6508919	bycluster;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	28	141	0	0.202899	0	.	.	weak	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon13	c.G6187A	p.G2063S	GGCAGCCGTGCTG	.	scavenged	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123419573	123419573	+	Missense_Mutation	SNP	G	G	T	rs3732487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	86	135	0	0.534162	0	G|0.879;T|0.121	0.121	strong	.	MYLK	224	.	NM_053025	exon18	c.C2742A	p.D914E	CTTCAGGTCGTCT	.	PASS	Atlas-SNP
PTGFRN	5738	hgsc.bcm.edu	37	1	117484581	117484581	+	Silent	SNP	C	C	T	rs77895792	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	100	205	0	0.502513	0	C|0.995;T|0.005	0.005	strong	.	PTGFRN	91	.	NM_020440	exon2	c.C294T	p.A98A	GACTGCCAACGAC	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883680	152883680	+	Silent	SNP	A	A	G	rs7535306	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	211	161	1	0.99061	0.00621118	A|0.667;G|0.333	0.333	strong	IVL,NS,lymphoid_neoplasm,+1,1	IVL	100	1	NM_005547	exon2	c.A1407G	p.Q469Q	GAAGCAACTGGAG	.	PASS	Atlas-SNP
WBP1	23559	hgsc.bcm.edu	37	2	74687550	74687550	+	Silent	SNP	T	T	C	rs8469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	302	262	0	1	0	T|0.633;C|0.367	0.367	strong	.	WBP1	35	.	NM_012477	exon4	c.T552C	p.P184P	CCCCCCTCATCAG	.	PASS	Atlas-SNP
SLC12A9	56996	hgsc.bcm.edu	37	7	100456506	100456506	+	Silent	SNP	C	C	T	rs78261122	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	90	148	0	0.459184	0	C|0.994;T|0.006	0.006	strong	.	SLC12A9	81	.	NM_001267812	exon6	c.C807T	p.S269S	TGCCAGCGTCTTT	.	PASS	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	184005719	184005719	+	Missense_Mutation	SNP	G	G	A	rs35875049	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	30	65	1	0.46875	0.0153846	G|0.967;A|0.033	0.033	strong	ECE2_ENST00000402825,colon,carcinoma,0,3	ECE2	303	3	NM_014693	exon11	c.G1712A	p.R571Q	TTGACCGGCAAAG	.	scavenged	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139911983	139911983	+	Silent	SNP	T	T	G	rs12348881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	39	56	0	0.65	0	T|0.905;G|0.095	0.095	strong	.	ABCA2	113	.	NM_212533	exon17	c.A2463C	p.A821A	GTAGACTGCCAGG	.	PASS	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206892933	206892933	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	3	142	0	0.024	0	.	.	none	INO80D,colon,carcinoma,-2,1	INO80D	134	1	NM_017759	exon6	c.T1200C	p.H400H	AAACGTATGCCGG	.	scavenged	Atlas-SNP
ANKRD13B	124930	hgsc.bcm.edu	37	17	27939427	27939427	+	Silent	SNP	G	G	C	rs147156385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	104	249	1	0.488263	0.00401606	G|0.998;C|0.002	0.002	strong	ANKRD13B,NS,carcinoma,0,1	ANKRD13B	39	1	NM_152345	exon12	c.G1266C	p.P422P	AATCCCGATCTTC	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	201	19	0	0.913636	0	C|0.597;G|0.403	0.403	strong	TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	NM_176884	exon1	c.G104C	p.W35S	TTGAACCACTCAA	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11887	11887	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	6	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.G1128A	p.L376L	CCTACTGGGAGAA	.	PASS	Atlas-SNP
PHKB	5257	hgsc.bcm.edu	37	16	47697618	47697618	+	Missense_Mutation	SNP	A	A	G	rs16945474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	108	231	0	0.461538	0	A|0.929;G|0.071	0.071	strong	PHKB_ENST00000323584,NS,carcinoma,0,3	PHKB	298	3	NM_000293	exon24	c.A2309G	p.Y770C	GAGTCTATAGAAG	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	37	14	101010204	101010204	+	Silent	SNP	T	T	C	rs4073549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	42	89	0	0.488372	0	T|0.915;C|0.085	0.085	strong	.	BEGAIN	32	.	NM_020836	exon5	c.A342G	p.S114S	GTCCTCTGACAGC	.	PASS	Atlas-SNP
PCDHA7	56141	hgsc.bcm.edu	37	5	140216125	140216125	+	Silent	SNP	G	G	A	rs61730621	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	183	302	1	0.54142	0.00331126	G|0.982;A|0.018	0.018	strong	.	PCDHA7	367	.	NM_031852	exon1	c.G2157A	p.T719T	GTACACGGCGTTG	.	PASS	Atlas-SNP
NOD2	64127	hgsc.bcm.edu	37	16	50746191	50746191	+	Missense_Mutation	SNP	G	G	A	rs5743279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	67	102	0	0.536	0	G|0.989;A|0.011	0.011	strong	NOD2,colon,carcinoma,+1,2	NOD2	118	2	NM_022162	exon4	c.G2369A	p.R790Q	ACCTCCGGCGGCC	.	PASS	Atlas-SNP
SLC37A3	84255	hgsc.bcm.edu	37	7	140048445	140048445	+	Silent	SNP	G	G	A	rs73472776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	57	0	0.517857	0	G|0.961;A|0.039	0.039	strong	.	SLC37A3	80	.	NM_207113	exon10	c.C1005T	p.Y335Y	AACGTCGTACCAA	.	PASS	Atlas-SNP
TBC1D24	57465	hgsc.bcm.edu	37	16	2546356	2546356	+	Silent	SNP	T	T	C	rs13339237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	116	1	1	0.00862069	T|0.941;C|0.059	0.059	strong	.	TBC1D24	35	.	NM_001199107	exon2	c.T207C	p.P69P	CACGCCTGACGCC	.	PASS	Atlas-SNP
ABL1	25	hgsc.bcm.edu	37	9	133759546	133759546	+	Silent	SNP	G	G	A	rs34717358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	63	52	0	0.7875	0	G|0.971;A|0.029	0.029	strong	.	ABL1	1632	.	NM_007313	exon11	c.G1926A	p.E642E	CCGGGAGATGGAC	.	PASS	Atlas-SNP
CCDC107	203260	hgsc.bcm.edu	37	9	35661088	35661088	+	Silent	SNP	G	G	A	rs10441686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	64	133	0	0.477612	0	G|0.925;A|0.075	0.075	strong	.	CCDC107	12	.	NM_174923	exon5	c.G756A	p.R252R	GAGAAGGTGCAGC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1148	138	983	92	0.120209	0.093591	C|0.500;T|0.500	0.500	strong	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5226A	p.T1742T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
VAT1L	57687	hgsc.bcm.edu	37	16	78011559	78011559	+	Silent	SNP	C	C	T	rs3751769	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	81	177	0	0.519231	0	C|0.873;T|0.127	0.127	strong	.	VAT1L	68	.	NM_020927	exon9	c.C1227T	p.S409S	AGACAGCGAGAAC	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36487060	36487060	+	Missense_Mutation	SNP	C	C	T	rs78470373	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	26	47	0	0.565217	0	C|0.995;T|0.005	0.005	strong	.	GPR179	170	.	NM_001004334	exon11	c.G2392A	p.A798T	GAGAGGCCTTCTT	.	PASS	Atlas-SNP
CLDND2	125875	hgsc.bcm.edu	37	19	51871157	51871157	+	Missense_Mutation	SNP	G	G	A	rs74538792	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	41	61	0	0.5125	0	G|0.968;A|0.032	0.032	strong	.	CLDND2	11	.	NM_152353	exon2	c.C293T	p.A98V	AGGAAGGCGCTCG	.	PASS	Atlas-SNP
SPRTN	83932	hgsc.bcm.edu	37	1	231487133	231487133	+	Silent	SNP	G	G	A	rs73116379	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	48	95	0	0.461538	0	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_032018	exon4	c.G534A	p.P178P	GCCACCGTATTAC	.	PASS	Atlas-SNP
PASD1	139135	hgsc.bcm.edu	37	X	150840185	150840185	+	Silent	SNP	T	T	C	rs6627174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	115	162	1	0.625	0.00617284	0|0.003;C|0.271	0.271	strong	.	PASD1	286	.	NM_173493	exon13	c.T1371C	p.G457G	CTGTGGTTTATCT	.	PASS	Atlas-SNP
TFAP2A	7020	hgsc.bcm.edu	37	6	10398707	10398707	+	Silent	SNP	G	G	A	rs3734391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	442	196	354	1	0.443439	0.00282486	G|0.883;A|0.117	0.117	strong	.	TFAP2A	129	.	NM_003220	exon7	c.C1257T	p.N419N	GTGGCTGTTGGGG	.	PASS	Atlas-SNP
FAM210B	116151	hgsc.bcm.edu	37	20	54941268	54941268	+	Silent	SNP	G	G	A	rs6099116	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	127	240	0	0.481061	0	G|0.885;A|0.115	0.115	strong	.	.	.	.	NM_080821	exon3	c.G504A	p.T168T	CATTACGCTAGTC	.	PASS	Atlas-SNP
DICER1	23405	hgsc.bcm.edu	37	14	95572111	95572111	+	Silent	SNP	A	A	C	rs12018992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	47	127	0	0.408696	0	A|0.977;C|0.023	0.023	strong	.	DICER1	181	.	NM_030621	exon20	c.T2997G	p.L999L	TGTCAAAAGATTA	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120594802	120594802	+	Silent	SNP	A	A	G	rs4871364	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	174	189	0	1	0	A|0.735;G|0.265	0.265	strong	.	ENPP2	254	.	NM_006209	exon19	c.T1740C	p.H580H	ACTTCCATGGGTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677586	100677586	+	Silent	SNP	A	A	G	rs189731103	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	46	144	0	0.202643	0	A|0.999;G|0.001	0.001	weak	.	MUC17	804	.	NM_001040105	exon3	c.A2889G	p.S963S	CACTTCATCTCCT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1028	143	930	100	0.139105	0.107527	C|0.500;T|0.500	0.500	weak	MUC6,NS,carcinoma,-1,1	MUC6	408	1	NM_005961	exon31	c.G5733A	p.T1911T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
ZNF233	353355	hgsc.bcm.edu	37	19	44778799	44778799	+	Silent	SNP	G	G	A	rs2884016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	52	51	0	0.981132	0	G|0.901;A|0.099	0.099	strong	.	ZNF233	73	.	NM_001207005	exon5	c.G1986A	p.L662L	TTCGTTGTCTTCA	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156878737	156878737	+	Silent	SNP	T	T	C	rs6671392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	34	90	0	0.441558	0	T|0.809;C|0.191	0.191	strong	.	PEAR1	118	.	NM_001080471	exon11	c.T1320C	p.P440P	TCCTCCTGACACC	.	PASS	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168098235	168098235	+	Silent	SNP	A	A	G	rs2277933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	26	119	0	0.305882	0	A|0.689;G|0.311	0.311	strong	.	SLIT3	224	.	NM_001271946	exon34	c.T4116C	p.D1372D	CTCCTGATCGCAG	.	PASS	Atlas-SNP
C1orf106	55765	hgsc.bcm.edu	37	1	200860731	200860731	+	Silent	SNP	G	G	A	rs141245080	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	106	182	0	0.56383	0	A|0.008;C|0.001;G|0.991	0.008	strong	.	C1orf106	59	.	NM_018265	exon1	c.G105A	p.R35R	GGCTCGGGGGGAG	.	PASS	Atlas-SNP
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719294	140719294	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	26	64	0	0.541667	0	.	.	none	.	PCDHGA2	205	.	NM_018915	exon1	c.G756A	p.P252P	CATTCCGGAGAAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411700	105411700	+	Missense_Mutation	SNP	A	A	G	rs4264326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	247	245	1	0.995968	0.00408163	A|0.454;G|0.546	0.546	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	NM_138420	exon7	c.T10088C	p.V3363A	AGGTCCACAGAAG	.	PASS	Atlas-SNP
PREPL	9581	hgsc.bcm.edu	37	2	44550528	44550528	+	Missense_Mutation	SNP	T	T	C	rs75128515	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	68	89	0	0.5	0	T|0.987;C|0.013	0.013	strong	.	PREPL	69	.	NM_001171603	exon12	c.A1769G	p.N590S	ATGGTGTTGAGAA	.	PASS	Atlas-SNP
TBX4	9496	hgsc.bcm.edu	37	17	59557600	59557600	+	Missense_Mutation	SNP	C	C	T	rs3744438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	95	111	1	0.959596	0.00900901	C|0.789;T|0.211	0.211	strong	TBX4,mouth,carcinoma,-1,1	TBX4	69	1	NM_018488	exon7	c.C941T	p.A314V	AGCTCGCGGAGCC	.	PASS	Atlas-SNP
CYP4B1	1580	hgsc.bcm.edu	37	1	47283814	47283814	+	Silent	SNP	T	T	C	rs74072926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	95	202	0	0.508021	0	T|0.995;C|0.005	0.005	strong	CYP4B1,bladder,carcinoma,+1,2	CYP4B1	81	2	NM_001099772	exon11	c.T1284C	p.S428S	TGACTCTCTGCGC	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109656946	109656946	+	Silent	SNP	T	T	C	rs667524	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	224	236	0	0.995556	0	T|0.512;C|0.488	0.488	strong	.	KIAA1324	77	.	NM_020775	exon1	c.T141C	p.H47H	GCTTCATGCCTGC	.	PASS	Atlas-SNP
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	34	59	0	0.507463	0	A|0.800;G|0.200	0.200	strong	.	CCT2	49	.	NM_006431	exon9	c.A783G	p.T261T	CTCTACAGCAAAG	.	PASS	Atlas-SNP
OPRK1	4986	hgsc.bcm.edu	37	8	54142157	54142157	+	Silent	SNP	T	T	C	rs702764	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	177	160	0	0.994382	0	T|0.752;C|0.248	0.248	strong	.	OPRK1	90	.	NM_000912	exon4	c.A843G	p.A281A	GAAGACTGCCACC	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053577	33053577	+	Missense_Mutation	SNP	G	G	A	rs9276	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	92	97	0	0.989247	0	A|0.132;C|0.000;G|0.868;T|0.000	0.132	strong	.	HLA-DPB1	28	.	NM_002121	exon4	c.G668A	p.R223Q	CTGCCCGGAGTAA	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52478206	52478206	+	Silent	SNP	C	C	T	rs3743796	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	55	77	1	0.617977	0.012987	C|0.891;T|0.109	0.109	strong	TOX3_ENST00000407228,caecum,carcinoma,-1,3	TOX3	121	3	NM_001080430	exon6	c.G969A	p.R323R	GCTGGCCCTGTAT	.	scavenged	Atlas-SNP
LAMC3	10319	hgsc.bcm.edu	37	9	133951230	133951230	+	Silent	SNP	C	C	T	rs3818800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	49	0	0.431373	0	C|0.830;T|0.170	0.170	strong	.	LAMC3	167	.	NM_006059	exon21	c.C3507T	p.T1169T	AGACACCGCCACC	.	PASS	Atlas-SNP
RTL1	388015	hgsc.bcm.edu	37	14	101347090	101347090	+	Missense_Mutation	SNP	C	C	T	rs73349352	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	86	153	0	0.49711	0	C|0.966;T|0.034	0.034	strong	.	RTL1	120	.	NM_001134888	exon1	c.G4036A	p.E1346K	GCTCTTCTAGCCT	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3475490	3475490	+	Silent	SNP	C	C	T	rs877610	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	55	123	0	0.436508	0	C|0.927;T|0.073	0.073	strong	.	TRPV1	99	.	NM_018727	exon14	c.G2157A	p.K719K	GAAGGCCTTCCTC	.	PASS	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	140952690	140952690	+	Silent	SNP	G	G	A	rs2229950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	149	1	1	0.00671141	G|0.843;A|0.157	0.157	strong	.	CACNA1B	266	.	NM_001243812	exon28	c.G4296A	p.L1432L	CAGCCTGGAGAAG	.	PASS	Atlas-SNP
PCDH11X	27328	hgsc.bcm.edu	37	X	91090533	91090533	+	Silent	SNP	C	C	T	rs56704613	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	479	477	517	0	0.995825	0	C|0.922;T|0.078	0.078	strong	.	PCDH11X	714	.	NM_001168363	exon1	c.C30T	p.F10F	CATTTTCGCGGTC	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31250875	31250875	+	Missense_Mutation	SNP	G	G	C	rs74912343		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	385	48	250	0	0.124675	0	.	.	weak	DDX11_ENST00000407793,NS,haematopoietic_neoplasm,0,6	DDX11	188	6	NM_030653	exon18	c.G1819C	p.A607P	CACTTTGCCCAAG	.	scavenged	Atlas-SNP
CD1E	913	hgsc.bcm.edu	37	1	158326645	158326645	+	Missense_Mutation	SNP	G	G	A	rs61734680	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	48	97	0	0.484848	0	G|0.978;A|0.022	0.022	strong	.	CD1E	129	.	NM_030893	exon6	c.G1126A	p.V376I	AACAGAGTATTGA	.	PASS	Atlas-SNP
NPY2R	4887	hgsc.bcm.edu	37	4	156135250	156135250	+	Silent	SNP	C	C	T	rs2342674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	133	262	0	0.488971	0	C|0.967;T|0.033	0.033	strong	.	NPY2R	87	.	NM_000910	exon2	c.C159T	p.L53L	TGTTCTCATATTG	.	PASS	Atlas-SNP
ADAMTS9	56999	hgsc.bcm.edu	37	3	64672474	64672474	+	Missense_Mutation	SNP	A	A	T	rs36115950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	79	160	0	0.429348	0	A|0.886;T|0.114	0.114	strong	.	ADAMTS9	206	.	NM_182920	exon2	c.T286A	p.S96T	CCTGGGAGGAGGT	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207827220	207827220	+	Missense_Mutation	SNP	G	G	A	rs62617140	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	68	158	0	0.459459	0	G|0.965;A|0.035	0.035	strong	.	CPO	42	.	NM_173077	exon7	c.G659A	p.S220N	TTGCCAGCTTCAT	.	PASS	Atlas-SNP
REV1	51455	hgsc.bcm.edu	37	2	100055158	100055158	+	Missense_Mutation	SNP	T	T	C	rs3087399	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	57	100	0	0.471074	0	T|0.866;C|0.134	0.134	strong	.	REV1	100	.	NM_001037872	exon6	c.A1118G	p.N373S	AGGGTATTGACAA	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060021	16060021	+	Silent	SNP	C	C	T	rs16980821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	372	372	370	0	1	0	C|0.723;T|0.277	0.277	strong	.	OR10H4	48	.	NM_001004465	exon1	c.C204T	p.S68S	CCTCTCCGTCTCT	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15853150	15853150	+	Silent	SNP	C	C	T	rs16980824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	32	68	0	0.484848	0	C|0.720;T|0.280	0.280	strong	.	OR10H3	53	.	NM_013938	exon1	c.C948T	p.S316S	AAGCTCCTAATGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548534	32548534	+	Missense_Mutation	SNP	C	C	T	rs71547382	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	439	28	191	0	0.0637813	0	C|1.000;|0.000	.	weak	.	HLA-DRB1	41	.	NM_002124	exon4	c.G752A	p.R251K	TGATTCCTGAAGT	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	107	141	0	1	0	G|0.750;A|0.250	0.250	strong	.	VIPR2	53	.	NM_003382	exon4	c.C288T	p.D96D	CCATCCGTCACTC	.	PASS	Atlas-SNP
SLC35G3	146861	hgsc.bcm.edu	37	17	33520904	33520904	+	Silent	SNP	G	G	A	rs61753879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	104	195	0	0.492891	0	G|0.977;A|0.023	0.023	strong	.	.	.	.	NM_152462	exon1	c.C423T	p.C141C	GGCGGAGCAGACG	.	PASS	Atlas-SNP
OR4F6	390648	hgsc.bcm.edu	37	15	102346030	102346030	+	Silent	SNP	G	G	A	rs401632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	135	267	1	0.483871	0.00374532	G|0.944;A|0.056	0.056	strong	.	OR4F6	45	.	NM_001005326	exon1	c.G108A	p.V36V	CTATGTGTCAAGC	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145296510	145296510	+	Silent	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	391	18	323	3	0.0460358	0.00928793	.	.	none	NBPF10,right_lower_lobe,carcinoma,0,1	NBPF10	221	1	NM_001039703	exon3	c.C432G	p.L144L	GGACCTCCAAGAA	.	scavenged	Atlas-SNP
TNFSF10	8743	hgsc.bcm.edu	37	3	172224303	172224303	+	Silent	SNP	A	A	G	rs1131532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	269	254	1	1	0.00393701	G|0.691;C|0.000;A|0.309	0.691	strong	.	TNFSF10	30	.	NM_003810	exon5	c.T825C	p.F275F	GGCCCCAAAAAAA	.	PASS	Atlas-SNP
SPDYA	245711	hgsc.bcm.edu	37	2	29063342	29063342	+	Missense_Mutation	SNP	T	T	C	rs6747208	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	56	110	0	0.513761	0	T|0.993;C|0.007	0.007	strong	.	SPDYA	41	.	NM_001008779	exon5	c.T857C	p.I286T	GTATGATTTAGTA	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117130561	117130561	+	Silent	SNP	T	T	G	rs76688215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	63	113	0	0.466667	0	T|0.984;G|0.016	0.016	strong	.	GPRC6A	152	.	NM_148963	exon2	c.A414C	p.P138P	AACTCTTGGCATG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16673800	16673800	+	Silent	SNP	G	G	A	rs3188408	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	65	125	0	0.481481	0	G|0.980;A|0.020	0.020	strong	.	MYO10	198	.	NM_012334	exon36	c.C5163T	p.T1721T	CCCAGCGGTGGTG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76528591	76528591	+	Silent	SNP	C	C	T	rs11868065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	111	111	0	0.973684	0	C|0.509;T|0.491	0.491	strong	.	DNAH17	347	.	NM_173628	exon20	c.G3087A	p.P1029P	GGTGGGCGGTGTC	.	PASS	Atlas-SNP
FAM9A	171482	hgsc.bcm.edu	37	X	8764370	8764370	+	Missense_Mutation	SNP	C	C	T	rs148031370	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	65	148	0	0.464286	0	C|0.996;T|0.004	0.004	strong	.	FAM9A	57	.	NM_174951	exon6	c.G427A	p.A143T	AAGCTGCTTTATC	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	6	267	2	0.0213523	0.00749064	G|0.540;A|0.460	0.460	strong	UBB,NS,carcinoma,0,1	UBB	30	1	NM_018955	exon2	c.G321A	p.Q107Q	GATCCAGGATAAA	.	scavenged	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61830256	61830256	+	Silent	SNP	T	T	C	rs61732400	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	62	114	0	0.516667	0	T|0.970;C|0.030	0.030	strong	.	ANK3	703	.	NM_020987	exon37	c.A10383G	p.Q3461Q	TTTACTTTGGCTA	.	PASS	Atlas-SNP
TSHR	7253	hgsc.bcm.edu	37	14	81562998	81562998	+	Silent	SNP	T	T	C	rs2075179	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	73	143	0	0.528986	0	T|0.711;C|0.289	0.289	strong	TSHR_ENST00000554435,NS,carcinoma,+2,3	TSHR	462	3	NM_000369	exon7	c.T561C	p.N187N	CAACAATGGCTTT	.	PASS	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205884274	205884274	+	Missense_Mutation	SNP	T	T	C	rs6669481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	81	116	0	0.554795	0	T|0.807;C|0.193	0.193	strong	.	SLC26A9	176	.	NM_134325	exon22	c.A2410G	p.R804G	CACTCCTGTAAGG	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85780536	85780536	+	Missense_Mutation	SNP	C	C	T	rs699664	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	66	115	0	0.428571	0	C|0.580;T|0.420	0.420	strong	.	GGCX	44	.	NM_000821	exon8	c.G974A	p.R325Q	AACCTTCGGGGGC	.	PASS	Atlas-SNP
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	32	71	0	0.426667	0	A|0.712;C|0.002	.	strong	.	LSS	50	.	NM_001001438	exon20	c.T1950C	p.H650H	TGTGTTATGGATC	.	PASS	Atlas-SNP
AP2A2	161	hgsc.bcm.edu	37	11	993907	993907	+	Silent	SNP	C	C	G	rs11538725	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	25	57	0	0.438596	0	C|0.832;G|0.168	0.168	strong	.	AP2A2	50	.	NM_001242837	exon13	c.C1707G	p.L569L	CCAGCTCAGGAAC	.	PASS	Atlas-SNP
GHRHR	2692	hgsc.bcm.edu	37	7	31011677	31011677	+	Silent	SNP	C	C	T	rs740336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	55	115	0	0.458333	0	C|0.943;T|0.057	0.057	strong	.	GHRHR	55	.	NM_000823	exon6	c.C564T	p.H188H	TTTCCACAGCGAC	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18768850	18768850	+	Silent	SNP	A	A	G	rs16985306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	35	103	0	0.486111	0	A|0.677;G|0.323	0.323	strong	.	NT5C1B	72	.	NM_001199088	exon2	c.T39C	p.P13P	CATTCCAGGCTCA	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3594296	3594296	+	Silent	SNP	C	C	T	rs35402060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	88	0	0.460674	0	C|0.947;T|0.053	0.053	strong	.	NLRC3	103	.	NM_178844	exon17	c.G2805A	p.A935A	CGCACACGCTCCG	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94772429	94772429	+	Silent	SNP	G	G	A	rs2228543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	40	135	0	0.421053	0	G|0.677;T|0.043	.	strong	SERPINA6_ENST00000341584,NS,carcinoma,-2,2	SERPINA6	102	2	NM_001756	exon4	c.C1011T	p.D337D	CTGGGCGTCCTGG	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52484317	52484317	+	Missense_Mutation	SNP	C	C	T	rs114182621	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	70	118	0	0.5	0	C|0.992;T|0.008	0.008	strong	.	TOX3	121	.	NM_001080430	exon4	c.G550A	p.A184T	ACTGGGCGCTGAG	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17152994	17152994	+	Silent	SNP	G	G	A	rs1801223	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	98	0	1	0	G|0.680;T|0.036	.	strong	.	CUBN	515	.	NM_001081	exon9	c.C939T	p.N313N	GCCGCCGTTATTT	.	PASS	Atlas-SNP
ZNF800	168850	hgsc.bcm.edu	37	7	127026184	127026184	+	Silent	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	72	0	0.506024	0	.	.	none	.	ZNF800	78	.	NM_176814	exon3	c.T87G	p.P29P	CAAAGGAGGATCT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512534	4512534	+	Missense_Mutation	SNP	C	C	T	rs61730732	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	100	182	0	0.440529	0	C|0.991;T|0.009	0.009	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G1396A	p.A466T	CTTTGGCCACATT	.	PASS	Atlas-SNP
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259818	71259818	+	Missense_Mutation	SNP	G	G	A	rs146869772	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	145	293	0	0.447531	0	G|0.999;A|0.001	0.001	strong	KRTAP5-9,caecum,carcinoma,0,1	KRTAP5-9	19	1	NM_005553	exon1	c.G115A	p.V39I	GCACCCGTCTACT	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187088170	187088170	+	Missense_Mutation	SNP	G	G	A	rs141044925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	51	119	0	0.395349	0	G|0.995;A|0.005	0.005	strong	.	FAM149A	52	.	NM_001006655	exon11	c.G1213A	p.G405S	CCTGACGGTACAG	.	PASS	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37480797	37480797	+	Silent	SNP	C	C	T	rs2111833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	50	134	0	0.42735	0	C|0.669;T|0.331	0.331	strong	TMPRSS6_ENST00000442782,NS,carcinoma,-1,2	TMPRSS6	99	2	NM_153609	exon9	c.G1083A	p.S361S	TTGGGGCGAGTAG	.	PASS	Atlas-SNP
TEKT2	27285	hgsc.bcm.edu	37	1	36551495	36551495	+	Missense_Mutation	SNP	T	T	C	rs419653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	65	143	0	0.40625	0	T|0.990;C|0.010	0.010	strong	.	TEKT2	32	.	NM_014466	exon4	c.T341C	p.I114T	TGGCCATTGAGTG	.	PASS	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	37	8	121259862	121259862	+	Silent	SNP	G	G	A	rs2305605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	38	33	0	0.59375	0	G|0.897;A|0.103	0.103	strong	.	COL14A1	292	.	NM_021110	exon21	c.G2490A	p.S830S	ATCCTCGGGGCCC	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	28	49	0	0.491228	0	C|0.717;T|0.283	0.283	strong	.	STAB2	370	.	NM_017564	exon49	c.C5100T	p.N1700N	TATAAACAATAAG	.	PASS	Atlas-SNP
NEU2	4759	hgsc.bcm.edu	37	2	233899377	233899377	+	Silent	SNP	C	C	T	rs2233394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	119	237	0	0.526549	0	C|0.833;T|0.167	0.167	strong	.	NEU2	42	.	NM_005383	exon2	c.C753T	p.D251D	CAATGACGGGCTT	.	PASS	Atlas-SNP
GATA4	2626	hgsc.bcm.edu	37	8	11614559	11614559	+	Silent	SNP	A	A	G	rs112435835	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	132	301	0	0.509652	0	A|0.993;G|0.007	0.007	strong	.	GATA4	29	.	NM_002052	exon6	c.A1113G	p.S371S	CCTGTCATCTCAC	.	PASS	Atlas-SNP
C6orf57	135154	hgsc.bcm.edu	37	6	71289189	71289189	+	Missense_Mutation	SNP	A	A	G	rs1048886	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	75	85	0	1	0	A|0.787;G|0.213	0.213	strong	.	C6orf57	13	.	NM_145267	exon2	c.A137G	p.Q46R	TCAAACAGTCCCT	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	13357331	13357331	+	Missense_Mutation	SNP	C	C	T	rs35173269	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	34	63	0	0.523077	0	C|0.981;T|0.019	0.019	strong	.	DLC1	411	.	NM_182643	exon2	c.G250A	p.D84N	CCACATCCTTTGA	.	PASS	Atlas-SNP
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	103	116	0	0.990385	0	C|0.701;N|0.001	0.701	strong	.	SLC2A4	44	.	NM_001042	exon4	c.T390C	p.N130N	GGCCAATGCTGCT	.	PASS	Atlas-SNP
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458893	39458893	+	Missense_Mutation	SNP	G	G	A	rs758741	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	47	88	0	0.412281	0	G|0.768;A|0.232	0.232	strong	.	KRTAP29-1	2	.	NM_001257309	exon1	c.C211T	p.R71C	GAAGGCGGGTAGG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	129	338	0	0.383929	0	C|0.695;G|0.305	0.305	strong	.	PSG1	196	.	NM_001184826	exon2	c.G121C	p.E41Q	TTGGCTCGGCTTC	.	PASS	Atlas-SNP
TMEM150A	129303	hgsc.bcm.edu	37	2	85826721	85826721	+	Silent	SNP	G	G	A	rs11891495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	115	201	0	0.477178	0	G|0.810;A|0.190	0.190	strong	.	TMEM150A	15	.	NM_001031738	exon7	c.C501T	p.T167T	CGGGGCGGTGGCC	.	PASS	Atlas-SNP
IFNA6	3443	hgsc.bcm.edu	37	9	21350487	21350487	+	Silent	SNP	G	G	A	rs61736258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	179	371	0	0.495845	0	G|0.971;A|0.029	0.029	strong	.	IFNA6	27	.	NM_021002	exon1	c.C400T	p.L134L	TCATCAGGGGAGT	.	PASS	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	37	15	95019926	95019926	+	Silent	SNP	C	C	T	rs79112132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	25	39	0	0.581395	0	C|0.953;T|0.047	0.047	strong	.	MCTP2	122	.	NM_018349	exon21	c.C2472T	p.G824G	TTCAGGCATAAAT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133981760	133981760	+	Missense_Mutation	SNP	T	T	C	rs56230101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	58	115	0	0.504348	0	T|0.869;C|0.131	0.131	strong	.	TG	416	.	NM_003235	exon32	c.T5921C	p.M1974T	AACTGATGGGGAT	.	PASS	Atlas-SNP
MIA2	117153	hgsc.bcm.edu	37	14	39717002	39717002	+	Silent	SNP	A	A	G	rs17109049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	41	0	1	0	A|0.921;G|0.079	0.079	strong	.	MIA2	82	.	NM_054024	exon4	c.A1224G	p.A408A	TGGGGCAGATGAA	.	PASS	Atlas-SNP
EHHADH	1962	hgsc.bcm.edu	37	3	184922267	184922267	+	Missense_Mutation	SNP	T	T	C	rs115754857	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	21	61	0	0.375	0	T|0.986;C|0.014	0.014	strong	.	EHHADH	73	.	NM_001966	exon6	c.A847G	p.T283A	AGGGAGTTGACCA	.	PASS	Atlas-SNP
AADACL3	126767	hgsc.bcm.edu	37	1	12785494	12785494	+	Missense_Mutation	SNP	G	G	T	rs7513079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	48	57	0	1	0	G|0.302;N|0.001	.	strong	.	AADACL3	84	.	NM_001103170	exon4	c.G584T	p.C195F	GCTACTGTTTTTT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15498181	15498181	+	Silent	SNP	A	A	G	rs12601532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	195	226	0	0.984848	0	A|0.715;G|0.285	0.285	strong	.	CDRT1	83	.	NM_006382	exon10	c.T1728C	p.A576A	TTTCACAGCTCCC	.	PASS	Atlas-SNP
FAM111A	63901	hgsc.bcm.edu	37	11	58919813	58919813	+	Silent	SNP	A	A	G	rs10896928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	30	56	0	0.5	0	A|0.739;G|0.261	0.261	strong	.	FAM111A	57	.	NM_001142520	exon5	c.A672G	p.A224A	GGATGCACTGTGC	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239010719	239010719	+	Silent	SNP	T	T	C	rs36066915	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	78	0	1	0	T|0.377;C|0.623	0.623	strong	.	ESPNL	63	.	NM_194312	exon2	c.T432C	p.A144A	CCACGCTGCCGTC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410411	105410411	+	Missense_Mutation	SNP	C	C	T	rs11160825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	250	267	0	0.992063	0	C|0.480;T|0.520	0.520	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G11377A	p.D3793N	CCTTGTCGGCCAG	.	PASS	Atlas-SNP
URGCP-MRPS24	0	hgsc.bcm.edu	37	7	43908661	43908661	+	Missense_Mutation	SNP	G	G	T	rs17854882	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	73	83	0	0.483444	0	G|0.971;T|0.029	0.029	strong	.	.	.	.	NM_001204871	exon6	c.C257A	p.P86Q	GTACTCGGGCCGC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891554	44891554	+	Missense_Mutation	SNP	T	T	C	rs61358479	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	40	135	0	0.38835	0	T|0.952;C|0.048	0.048	strong	.	ZNF285	86	.	NM_152354	exon4	c.A853G	p.K285E	GAGTCTTGCCAGA	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66678182	66678182	+	Missense_Mutation	SNP	C	C	A	rs17080065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	50	97	0	0.568182	0	C|0.972;A|0.028	0.028	strong	.	CCDC102B	92	.	NM_001093729	exon9	c.C1275A	p.N425K	ACTGAACCTTCAA	.	PASS	Atlas-SNP
CXCR7	57007	hgsc.bcm.edu	37	2	237489796	237489796	+	Missense_Mutation	SNP	G	G	A	rs35095494	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	90	136	0	0.523256	0	G|0.984;A|0.016	0.016	strong	.	CXCR7	72	.	NM_020311	exon2	c.G688A	p.V230I	ATCGCTGTCTTCT	.	PASS	Atlas-SNP
GSTA2	2939	hgsc.bcm.edu	37	6	52615415	52615415	+	Missense_Mutation	SNP	T	T	G	rs6577	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	154	153	0	1	0	T|0.753;G|0.247	0.247	strong	GSTA2,NS,carcinoma,0,1	GSTA2	33	1	NM_000846	exon7	c.A629C	p.E210A	GATTTCTCATCCA	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931737	116931737	+	Silent	SNP	C	C	T	rs2808771	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	10	22	0	0.5	0	C|0.745;T|0.255	0.255	strong	.	COL27A1	200	.	NM_032888	exon3	c.C1902T	p.G634G	CTGTGGCTTGCCG	.	PASS	Atlas-SNP
GPR148	344561	hgsc.bcm.edu	37	2	131487691	131487691	+	Missense_Mutation	SNP	C	C	T	rs143265147	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	58	78	0	0.508772	0	C|0.996;T|0.004	0.004	strong	GPR148,NS,carcinoma,0,1	GPR148	54	1	NM_207364	exon1	c.C967T	p.R323C	CTGCTCCGCTACC	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24251659	24251659	+	Missense_Mutation	SNP	T	T	C	rs7007084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	32	76	0	0.492308	0	T|0.967;C|0.033	0.033	strong	.	ADAMDEC1	69	.	NM_014479	exon4	c.T362C	p.M121T	AGAACATGGTAGG	.	PASS	Atlas-SNP
TEX11	56159	hgsc.bcm.edu	37	X	70073159	70073159	+	Missense_Mutation	SNP	T	T	C	rs6525433	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	84	146	0	0.545455	0	0|0.003;C|0.200	0.200	strong	.	TEX11	132	.	NM_001003811	exon7	c.A389G	p.K130R	CATTCTTTTCCTA	.	PASS	Atlas-SNP
CCT8L2	150160	hgsc.bcm.edu	37	22	17072347	17072347	+	Nonsense_Mutation	SNP	C	C	T	rs139948519	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	29	69	0	0.54717	0	C|0.982;T|0.018	0.018	strong	.	CCT8L2	150	.	NM_014406	exon1	c.G1094A	p.W365X	CATTCCCATTCAA	.	PASS	Atlas-SNP
TTC24	164118	hgsc.bcm.edu	37	1	156555577	156555577	+	Missense_Mutation	SNP	C	C	T	rs147693801	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	65	123	0	0.419355	0	C|0.994;T|0.006	0.006	strong	TTC24,right_upper_lobe,carcinoma,-1,1	TTC24	46	1	NM_001105669	exon9	c.C1529T	p.T510M	AGCACACGCCCTG	.	PASS	Atlas-SNP
U2SURP	23350	hgsc.bcm.edu	37	3	142747230	142747230	+	Silent	SNP	G	G	A	rs80238215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	85	232	0	0.461957	0	G|0.991;A|0.009	0.009	strong	.	U2SURP	66	.	NM_001080415	exon15	c.G1428A	p.K476K	GTGGAAGCTTTAT	.	PASS	Atlas-SNP
HTR3E	285242	hgsc.bcm.edu	37	3	183824398	183824398	+	Missense_Mutation	SNP	G	G	A	rs13324468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	146	328	0	0.515901	0	G|0.941;A|0.059	0.059	strong	.	HTR3E	65	.	NM_001256614	exon7	c.G1366A	p.A456T	AGCCACGCGATGG	.	PASS	Atlas-SNP
LARGE	9215	hgsc.bcm.edu	37	22	33679238	33679238	+	Silent	SNP	T	T	C	rs11913417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	88	139	0	0.578947	0	T|0.970;C|0.030	0.030	strong	.	LARGE	98	.	NM_004737	exon14	c.A1827G	p.S609S	CGCTTTTGACTTG	.	PASS	Atlas-SNP
ZFP69B	65243	hgsc.bcm.edu	37	1	40928145	40928145	+	Silent	SNP	G	G	A	rs61740805	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	57	125	0	0.487179	0	G|0.950;A|0.050	0.050	strong	ZNF643_ENST00000411995,NS,carcinoma,+1,4	.	.	4	NM_023070	exon5	c.G489A	p.S163S	TATTTCGTGGGAA	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65241228	65241228	+	Silent	SNP	A	A	G	rs229592	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	64	132	0	0.503937	0	A|0.516;G|0.484	0.484	strong	.	SPTB	378	.	NM_001024858	exon23	c.T4860C	p.I1620I	CATCACAATGGCG	.	PASS	Atlas-SNP
CBL	867	hgsc.bcm.edu	37	11	119170480	119170480	+	Missense_Mutation	SNP	G	G	A	rs17122769	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	30	72	0	0.434783	0	G|0.993;A|0.007	0.007	strong	.	CBL	408	.	NM_005188	exon16	c.G2710A	p.V904I	GCCCATGTAGCTA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679254	100679254	+	Missense_Mutation	SNP	A	A	G	rs199808245	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	26	142	0	0.167742	0	A|0.955;G|0.045	0.045	strong	.	MUC17	804	.	NM_001040105	exon3	c.A4557G	p.I1519M	AAGTATACCTGTC	.	PASS	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	37	17	21203907	21203907	+	Silent	SNP	T	T	C	rs73311539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	63	155	0	0.366279	0	T|0.741;C|0.259	0.259	strong	MAP2K3_ENST00000316920,NS,carcinoma,0,4	MAP2K3	135	4	NM_145109	exon4	c.T216C	p.R72R	GGGCCGTGGAGCC	.	PASS	Atlas-SNP
ZYG11A	440590	hgsc.bcm.edu	37	1	53326421	53326421	+	Missense_Mutation	SNP	A	A	G	rs61744306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	103	255	0	0.418699	0	A|0.983;G|0.017	0.017	strong	.	ZYG11A	46	.	NM_001004339	exon4	c.A1027G	p.M343V	GCCAGTATGAGTC	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30762140	30762140	+	Missense_Mutation	SNP	G	G	A	rs740223	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	66	0	0.473684	0	G|0.814;A|0.186	0.186	strong	.	CCDC157	86	.	NM_001017437	exon3	c.G151A	p.D51N	GACCTCGACATGG	.	PASS	Atlas-SNP
MRPL23	6150	hgsc.bcm.edu	37	11	1977552	1977552	+	Missense_Mutation	SNP	G	G	A	rs12812	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	24	35	0	0.615385	0	G|0.874;A|0.126	0.126	strong	MRPL23,NS,carcinoma,0,1	MRPL23	14	1	NM_021134	exon5	c.G364A	p.A122T	GGCAGCGCTGCCG	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641328	55641328	+	Missense_Mutation	SNP	G	G	A	rs6581025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	71	210	0	0.375661	0	G|0.760;A|0.240	0.240	strong	.	OR6C74	52	.	NM_001005490	exon1	c.G257A	p.G86D	CAACAGGTGATAA	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12858028	12858028	+	Missense_Mutation	SNP	T	T	C	rs3732675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	120	1	1	0.00833333	C|0.609;G|0.000;T|0.391	0.609	strong	CAND2_ENST00000456430,NS,carcinoma,0,2	CAND2	138	2	NM_001162499	exon10	c.T1597C	p.S533P	GCTGACTCTTTCT	.	PASS	Atlas-SNP
OR7E24	26648	hgsc.bcm.edu	37	19	9362343	9362343	+	Silent	SNP	C	C	T	rs2240927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	112	0	1	0	C|0.488;T|0.512	0.512	strong	.	OR7E24	48	.	NM_001079935	exon1	c.C624T	p.S208S	GTGTTCCGACACC	.	PASS	Atlas-SNP
DKC1	1736	hgsc.bcm.edu	37	X	154004584	154004584	+	Silent	SNP	C	C	T	rs1127051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	96	143	0	0.666667	0	C|0.921;T|0.079	0.079	strong	.	DKC1	41	.	NM_001363	exon14	c.C1461T	p.A487A	CGGGGCCGAGCCT	.	PASS	Atlas-SNP
EIF3K	27335	hgsc.bcm.edu	37	19	39125677	39125677	+	Missense_Mutation	SNP	G	G	A	rs138580388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	46	70	0	0.433962	0	G|0.998;A|0.002	0.002	strong	.	EIF3K	22	.	NM_013234	exon7	c.G544A	p.D182N	AGTGCCGACGAGT	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	37	7	102106459	102106459	+	Silent	SNP	G	G	A	rs146433593	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	96	0	0.518519	0	G|0.995;A|0.005	0.005	strong	.	LRWD1	41	.	NM_152892	exon2	c.G276A	p.K92K	CCCCAAGCTCGAG	.	PASS	Atlas-SNP
ZNF611	81856	hgsc.bcm.edu	37	19	53219140	53219140	+	Missense_Mutation	SNP	C	C	T	rs146379839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	13	54	0	0.351351	0	C|0.999;T|0.001	0.001	strong	.	ZNF611	72	.	NM_030972	exon5	c.G8A	p.R3H	TCCTCACGTAACA	.	PASS	Atlas-SNP
MND1	84057	hgsc.bcm.edu	37	4	154276856	154276856	+	Silent	SNP	A	A	G	rs10471075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	73	154	0	0.489933	0	A|0.926;G|0.074	0.074	strong	.	MND1	18	.	NM_001253861	exon3	c.A120G	p.K40K	AGAGAAAGGCATT	.	PASS	Atlas-SNP
ZSWIM1	90204	hgsc.bcm.edu	37	20	44511627	44511627	+	Silent	SNP	C	C	T	rs11086984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	109	219	1	0.550505	0.00456621	C|0.930;T|0.070	0.070	strong	.	ZSWIM1	35	.	NM_080603	exon2	c.C396T	p.F132F	AGTATTCAAGAAG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	38	65	0	0.527778	0	T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong	.	MYOM1	192	.	NM_003803	exon8	c.C1146T	p.H382H	CCCAGCGTGGAAG	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	842972	842972	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	63	0	0.490196	0	.	.	none	.	CHTF18	52	.	NM_022092	exon13	c.C1579G	p.L527V	GTCTCCCTGCGGC	.	PASS	Atlas-SNP
CPM	1368	hgsc.bcm.edu	37	12	69252715	69252715	+	Silent	SNP	A	A	G	rs1143653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	48	64	0	1	0	T|0.153;G|0.175;C|0.041;A|0.631	0.175	strong	.	CPM	30	.	NM_001005502	exon8	c.T1077C	p.S359S	TATATAAGACCCA	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117114025	117114025	+	Silent	SNP	G	G	A	rs6901250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	53	123	1	0.441667	0.00813008	G|0.686;A|0.314	0.314	strong	GPRC6A,NS,carcinoma,0,2	GPRC6A	152	2	NM_148963	exon6	c.C2061T	p.A687A	GCTGAAGGCTAGC	.	scavenged	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17927327	17927327	+	Missense_Mutation	SNP	T	T	C	rs1049874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	24	66	0	0.436364	0	T|0.579;C|0.421	0.421	strong	.	ASAH1	71	.	NM_004315	exon4	c.A325G	p.I109V	GCATAATTTTTCC	.	PASS	Atlas-SNP
ZC3H18	124245	hgsc.bcm.edu	37	16	88643806	88643806	+	Missense_Mutation	SNP	C	C	G	rs114866066	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	18	43	0	0.580645	0	C|0.999;G|0.001	0.001	strong	.	ZC3H18	90	.	NM_144604	exon2	c.C275G	p.P92R	GGGGCCCGACCAG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129904474	129904474	+	Missense_Mutation	SNP	G	G	A	rs61738284	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	448	226	432	1	0.504464	0.00231481	G|0.915;A|0.085	0.085	strong	.	MKI67	363	.	NM_002417	exon13	c.C5630T	p.P1877L	CTCTTGGGCCGTT	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447640	10447640	+	Missense_Mutation	SNP	A	A	G	rs10016702	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	97	0	0.419753	0	A|0.793;G|0.207	0.207	strong	ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	NM_053042	exon3	c.T313C	p.S105P	CACTGGAATTATT	.	PASS	Atlas-SNP
KLHL24	54800	hgsc.bcm.edu	37	3	183368216	183368216	+	Silent	SNP	A	A	T	rs3755648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	62	204	0	0.413333	0	A|0.647;T|0.353	0.353	strong	KLHL24,caecum,carcinoma,+1,2	KLHL24	56	2	NM_017644	exon3	c.A72T	p.R24R	TAAGCGAAAAGTT	.	PASS	Atlas-SNP
ETV7	51513	hgsc.bcm.edu	37	6	36339176	36339176	+	Missense_Mutation	SNP	C	C	T	rs34306145	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	20	58	0	0.408163	0	C|0.987;T|0.013	0.013	strong	.	ETV7	31	.	NM_001207035	exon5	c.G595A	p.G199S	TGCAGCCGAGCTC	.	PASS	Atlas-SNP
GJD2	57369	hgsc.bcm.edu	37	15	35044940	35044940	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	3	142	0	0.0154639	0	.	.	none	GJD2,NS,carcinoma,0,1	GJD2	49	1	NM_020660	exon2	c.C705T	p.P235P	GATGCAGGGGTAG	.	scavenged	Atlas-SNP
ZNF658	26149	hgsc.bcm.edu	37	9	40774091	40774091	+	Missense_Mutation	SNP	C	C	T	rs79262629	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	543	183	532	2	0.337017	0.0037594	C|0.990;T|0.010	0.010	strong	ZNF658,lower_third,carcinoma,-1,1	ZNF658	100	1	NM_033160	exon5	c.G1184A	p.R395Q	GCTTTCCGGTAAA	.	scavenged	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7605067	7605067	+	Missense_Mutation	SNP	C	C	T	rs3824658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	98	175	0	0.510417	0	C|0.373;T|0.627	0.627	strong	.	ITIH5	343	.	NM_030569	exon15	c.G2807A	p.R936Q	ATTCCCCGGCCAA	.	PASS	Atlas-SNP
MTA1	9112	hgsc.bcm.edu	37	14	105931109	105931109	+	Silent	SNP	C	C	T	rs36015555	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	39	42	0	0.65	0	C|0.947;T|0.053	0.053	strong	.	MTA1	61	.	NM_004689	exon15	c.C1443T	p.I481I	GCGGATCGCCCGG	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62172281	62172281	+	Missense_Mutation	SNP	C	C	T	rs310655	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	86	55	0	0.966292	0	C|0.826;T|0.174	0.174	strong	.	SRMS	48	.	NM_080823	exon8	c.G1357A	p.A453T	CCTCCGCCGGGCA	.	PASS	Atlas-SNP
POLH	5429	hgsc.bcm.edu	37	6	43582091	43582091	+	Missense_Mutation	SNP	A	A	T	rs6941583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	77	158	0	0.411765	0	A|0.875;T|0.125	0.125	strong	.	POLH	54	.	NM_006502	exon11	c.A1939T	p.M647L	TGGGATATGCCAG	.	PASS	Atlas-SNP
TRIP11	9321	hgsc.bcm.edu	37	14	92474136	92474136	+	Missense_Mutation	SNP	C	C	T	rs372171033		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	127	0	0.421687	0	.	.	weak	.	TRIP11	184	.	NM_004239	exon10	c.G1375A	p.A459T	TTGTAGCTGTACT	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120591143	120591143	+	Silent	SNP	A	A	G	rs12312562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	61	116	0	0.508333	0	A|0.657;G|0.343	0.343	strong	GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	NM_006836	exon33	c.T3936C	p.Y1312Y	AGCATCATAGCTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284457	152284457	+	Missense_Mutation	SNP	T	T	A	rs3120652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	538	214	446	0	0.39777	0	T|0.942;A|0.058	0.058	strong	.	FLG	900	.	NM_002016	exon3	c.A2905T	p.N969Y	GATGGTTTCTGGA	.	PASS	Atlas-SNP
SPG7	6687	hgsc.bcm.edu	37	16	89623301	89623301	+	Missense_Mutation	SNP	A	A	G	rs35749032	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	45	91	0	0.483871	0	A|0.982;G|0.018	0.018	strong	.	SPG7	75	.	NM_003119	exon17	c.A2188G	p.N730D	CTGGCAAACGCCC	.	PASS	Atlas-SNP
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	20	41	0	0.512821	0	A|0.835;G|0.165	0.165	strong	.	KLHL23	52	.	NM_144711	exon2	c.A1185G	p.K395K	AGAGAAATGGATT	.	PASS	Atlas-SNP
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190830	39190830	+	Missense_Mutation	SNP	C	C	T	rs62622849	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	70	136	0	0.496454	0	C|0.888;T|0.112	0.112	strong	.	KRTAP1-3	18	.	NM_030966	exon1	c.G244A	p.G82R	CAGTTCCGCAGGA	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41815063	41815063	+	Missense_Mutation	SNP	C	C	T	rs61748721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	29	44	0	0.568627	0	C|0.958;T|0.042	0.042	strong	.	RPAP1	111	.	NM_015540	exon19	c.G2642A	p.R881H	CTGAGACGGGGGC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81208473	81208473	+	Missense_Mutation	SNP	G	G	T	rs115666278	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	43	84	0	0.477778	0	G|0.963;T|0.037	0.037	strong	.	PKD1L2	361	.	NM_001076780	exon16	c.C2630A	p.A877D	GACACGGCAGCCT	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	284299	284299	+	Silent	SNP	A	A	G	rs7108261	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	42	67	1	0.446809	0.0149254	A|0.837;G|0.163	0.163	strong	NALP6,NS,carcinoma,+1,1	NLRP6	4	1	NM_138329	exon6	c.A2271G	p.A757A	CCCCGCACTGACG	.	scavenged	Atlas-SNP
COPG1	22820	hgsc.bcm.edu	37	3	128984409	128984409	+	Silent	SNP	G	G	A	rs78889622	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	63	126	0	0.45	0	G|0.973;A|0.027	0.027	strong	.	.	.	.	NM_016128	exon14	c.G1242A	p.K414K	GTATAAGCGCGCT	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	37	14	45693648	45693648	+	Silent	SNP	G	G	A	rs35223850	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	115	0	0.494118	0	G|0.954;A|0.046	0.046	strong	.	MIS18BP1	92	.	NM_018353	exon11	c.C2142T	p.C714C	TTCATCGCAATCT	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93460264	93460264	+	Missense_Mutation	SNP	C	C	G	rs61740994	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	83	185	0	0.51875	0	C|0.989;G|0.011	0.011	strong	.	KIAA1731	173	.	NM_033395	exon24	c.C6622G	p.Q2208E	AAAAATCAGAACT	.	PASS	Atlas-SNP
TP53BP2	7159	hgsc.bcm.edu	37	1	223984072	223984072	+	Silent	SNP	G	G	A	rs141654811	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	112	283	0	0.453441	0	G|1.000;A|0.000	0.000	strong	.	TP53BP2	144	.	NM_001031685	exon13	c.C2169T	p.D723D	TTCTAGGTCAGCA	.	PASS	Atlas-SNP
TSPO	706	hgsc.bcm.edu	37	22	43558972	43558972	+	Missense_Mutation	SNP	G	G	A	rs6972	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	80	0	0.431193	0	G|0.812;A|0.188	0.188	strong	.	TSPO	6	.	NM_001256531	exon4	c.G485A	p.R162H	GCTGGCGTGGGGG	.	PASS	Atlas-SNP
RNF152	220441	hgsc.bcm.edu	37	18	59483514	59483514	+	Silent	SNP	A	A	G	rs9319985	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	85	1	1	0.0117647	A|0.767;G|0.233	0.233	strong	RNF152,caecum,carcinoma,0,1	RNF152	37	1	NM_173557	exon2	c.T183C	p.P61P	GCCGGGAGGCAGC	.	scavenged	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44175293	44175293	+	Silent	SNP	G	G	A	rs35881858	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	19	32	0	0.358491	0	G|0.983;A|0.017	0.017	strong	.	LRPPRC	105	.	NM_133259	exon18	c.C1888T	p.L630L	TTTCCAGGAGATT	.	PASS	Atlas-SNP
TJP1	7082	hgsc.bcm.edu	37	15	30012209	30012209	+	Silent	SNP	A	A	C	rs376115263	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	80	0	0.476744	0	.	.	weak	.	TJP1	140	.	NM_003257	exon20	c.T2775G	p.A925A	AGATGAAGCTTCT	.	PASS	Atlas-SNP
FUT7	2529	hgsc.bcm.edu	37	9	139925459	139925459	+	Silent	SNP	G	G	A	rs11145973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	71	76	0	0.72449	0	G|0.993;A|0.007	0.007	strong	.	FUT7	24	.	NM_004479	exon2	c.C732T	p.N244N	CAGTGCGTTGCGC	.	PASS	Atlas-SNP
ANO2	57101	hgsc.bcm.edu	37	12	5841733	5841733	+	Missense_Mutation	SNP	A	A	C	rs1860961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	90	164	0	0.529412	0	A|0.870;C|0.130	0.130	strong	ANO2,NS,carcinoma,0,1	ANO2	309	1	NM_020373	exon15	c.T1498G	p.S500A	CAGCAGACTGGTT	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541141	12541141	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	4	244	3	0.015873	0.0122951	.	.	none	ZNF443,lower_third,carcinoma,-1,1	ZNF443	63	1	NM_005815	exon4	c.G1845A	p.P615P	TTCATACGGGTTC	.	scavenged	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249458	71249458	+	Silent	SNP	T	T	C	rs372455775		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	9	181	6	0.0382979	0.0331492	.	.	weak	KRTAP5-8,NS,carcinoma,0,1	KRTAP5-8	28	1	NM_021046	exon1	c.T357C	p.C119C	CAGCTGTTGTAAG	.	scavenged	Atlas-SNP
CLEC2L	154790	hgsc.bcm.edu	37	7	139225215	139225215	+	Silent	SNP	T	T	C	rs112553913	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	67	139	0	0.531746	0	T|0.972;C|0.028	0.028	strong	.	CLEC2L	14	.	NM_001080511	exon3	c.T414C	p.I138I	TGTGATTCAGAGC	.	PASS	Atlas-SNP
CYTH2	9266	hgsc.bcm.edu	37	19	48977189	48977189	+	Silent	SNP	C	C	T	rs28582663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	89	0	1	0	C|0.982;T|0.018	0.018	strong	.	CYTH2	33	.	NM_017457	exon6	c.C462T	p.P154P	CCTACCCGGAGAG	.	PASS	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108072298	108072298	+	Missense_Mutation	SNP	T	T	C	rs6779254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	27	34	0	0.509434	0	T|0.430;C|0.570	0.570	strong	.	HHLA2	95	.	NM_007072	exon4	c.T89C	p.I30T	TCTTCATTTATGT	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112045709	112045709	+	Missense_Mutation	SNP	G	G	C	rs77883500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	135	262	0	0.463918	0	G|0.985;C|0.015	0.015	strong	.	ADORA3	104	.	NM_020683	exon1	c.C268G	p.L90V	TAAGCAGTAGGCA	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72008421	72008421	+	Missense_Mutation	SNP	T	T	C	rs11541286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	21	47	0	0.381818	0	T|0.956;C|0.044	0.044	strong	.	ZFC3H1	172	.	NM_144982	exon30	c.A5420G	p.K1807R	AAAAATTTGAATT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17264920	17264920	+	Missense_Mutation	SNP	C	C	T	rs4463721	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	464	145	293	1	0.3125	0.00341297	C|0.713;T|0.287	0.287	strong	CROCC,NS,carcinoma,0,3	CROCC	185	3	NM_014675	exon11	c.C1316T	p.A439V	AGCAGGCGGCCCT	.	scavenged	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	15139	15139	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	17	15	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.T393C	p.Y131Y	AGGCTATGTCCTC	.	PASS	Atlas-SNP
CBLC	23624	hgsc.bcm.edu	37	19	45281375	45281375	+	Missense_Mutation	SNP	C	C	T	rs115775900	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	8	6	0	0.8	0	C|0.983;T|0.017	0.017	strong	.	CBLC	41	.	NM_001130852	exon1	c.C187T	p.R63W	TCTCGGCGGGCGG	.	PASS	Atlas-SNP
ETNK2	55224	hgsc.bcm.edu	37	1	204109238	204109238	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	53	100	0	0.477477	0	.	.	none	ETNK2_ENST00000367202,NS,carcinoma,0,2	ETNK2	48	2	NM_018208	exon5	c.C793T	p.R265W	TGAACCGCACGTG	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26688662	26688662	+	Silent	SNP	C	C	T	rs2272071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	104	161	0	0.536082	0	C|0.951;T|0.049	0.049	strong	OTOF_ENST00000361394,NS,carcinoma,0,2	OTOF	524	2	NM_194248	exon38	c.G4677A	p.V1559V	CACAGCCACCGTC	.	PASS	Atlas-SNP
COL1A2	1278	hgsc.bcm.edu	37	7	94028386	94028386	+	Missense_Mutation	SNP	G	G	A	rs139528613	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	44	81	0	0.578947	0	G|0.996;A|0.004	0.004	strong	.	COL1A2	240	.	NM_000089	exon4	c.G122A	p.R41H	GACCACGTGGAGA	.	PASS	Atlas-SNP
RETSAT	54884	hgsc.bcm.edu	37	2	85570440	85570440	+	Silent	SNP	G	G	A	rs150706527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	73	299	0	0.222561	0	G|0.996;A|0.004	0.004	strong	RETSAT,NS,carcinoma,-2,1	RETSAT	56	1	NM_017750	exon11	c.C1758T	p.A586A	CAGGATGGCGCTG	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182827297	182827297	+	Silent	SNP	G	G	A	rs73063095	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	76	178	0	0.439306	0	G|0.986;A|0.014	0.014	strong	.	DHX9	114	.	NM_001357	exon8	c.G732A	p.L244L	TGCCCTGTCACTT	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	159992751	159992751	+	Silent	SNP	A	A	G	rs4921150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	73	142	7	0.453416	0.0492958	A|0.867;G|0.133	0.133	strong	ATP10B,colon,carcinoma,0,1	ATP10B	201	1	NM_025153	exon26	c.T4095C	p.T1365T	GTGGTGAGTTGGT	.	scavenged	Atlas-SNP
GALNT9	50614	hgsc.bcm.edu	37	12	132681664	132681664	+	Silent	SNP	G	G	A	rs111344752	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	64	134	0	0.496124	0	G|0.990;A|0.010	0.010	strong	.	GALNT9	74	.	NM_001122636	exon11	c.C1800T	p.H600H	CCGTGCGTGTTTG	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924696	70924696	+	Silent	SNP	G	G	A	rs77892318	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	21	97	0	0.253012	0	G|0.946;A|0.054	0.054	strong	ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.G480A	p.K160K	TTATAAGATAAAC	.	PASS	Atlas-SNP
EPB41	2035	hgsc.bcm.edu	37	1	29391505	29391505	+	Silent	SNP	G	G	A	rs79677225	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	25	79	0	0.403226	0	G|0.991;A|0.009	0.009	strong	.	EPB41	118	.	NM_001166005	exon16	c.G2019A	p.K673K	AGACAAGAGTCAA	.	PASS	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	37	13	52520435	52520435	+	Silent	SNP	C	C	T	rs1801248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	37	83	0	0.440476	0	C|0.984;T|0.016	0.016	strong	.	ATP7B	123	.	NM_000053	exon13	c.G3045A	p.L1015L	CATCTCCAGGGGC	.	PASS	Atlas-SNP
OR52K2	119774	hgsc.bcm.edu	37	11	4471276	4471276	+	Missense_Mutation	SNP	G	G	A	rs331537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	128	248	0	0.505929	0	G|0.792;A|0.208	0.208	strong	.	OR52K2	61	.	NM_001005172	exon1	c.G707A	p.R236H	AGGCCCGCTACAA	.	PASS	Atlas-SNP
RAB17	64284	hgsc.bcm.edu	37	2	238483751	238483751	+	Missense_Mutation	SNP	T	T	C	rs34311889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	75	132	0	0.510204	0	T|0.884;C|0.116	0.116	strong	.	RAB17	17	.	NM_022449	exon6	c.A550G	p.S184G	CGTCGCTTCTCTG	.	PASS	Atlas-SNP
PPP6R3	55291	hgsc.bcm.edu	37	11	68341661	68341661	+	Silent	SNP	C	C	A	rs114505709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	23	54	0	0.338235	0	C|0.991;A|0.009	0.009	strong	.	PPP6R3	159	.	NM_001164162	exon13	c.C1428A	p.P476P	GGGCCCCAACAGT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1269835	1269835	+	Missense_Mutation	SNP	G	G	A	rs2943521	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	474	234	476	1	0.493671	0.00210084	G|0.614;A|0.386	0.386	strong	.	MUC5B	473	.	NM_002458	exon31	c.G11725A	p.V3909I	TCCTCCGTCCCGG	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	119	0	1	0	C|0.834;G|0.166	0.166	strong	.	ADAMTS5	184	.	NM_007038	exon1	c.G413C	p.G138A	GGACTACCGTCCA	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113376388	113376388	+	Missense_Mutation	SNP	G	G	A	rs1859330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	35	38	0	1	0	G|0.326;A|0.674	0.674	strong	.	OAS3	63	.	NM_006187	exon1	c.G53A	p.R18K	CCAGAAGGCTGCA	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70505162	70505162	+	Missense_Mutation	SNP	G	G	A	rs28404221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	52	100	0	0.40625	0	G|0.956;A|0.044	0.044	strong	.	UGT2A1	131	.	NM_001252274	exon3	c.C800T	p.A267V	AGAGTTGCTGATG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284382	152284382	+	Missense_Mutation	SNP	C	C	T	rs149595328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	674	50	581	0	0.074184	0	C|0.995;T|0.005	0.005	strong	FLG,NS,carcinoma,+1,2	FLG	900	2	NM_002016	exon3	c.G2980A	p.G994S	CGTGACCGGCTCT	.	PASS	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49701523	49701523	+	Missense_Mutation	SNP	A	A	G	rs495335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	66	139	0	0.554622	0	A|0.322;G|0.678	0.678	strong	.	CRISP3	67	.	NM_001190986	exon5	c.T385C	p.S129P	AGCTGGAGGCACT	.	PASS	Atlas-SNP
UBC	7316	hgsc.bcm.edu	37	12	125396377	125396377	+	Silent	SNP	A	A	G	rs16918544	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	172	323	0	0.504399	0	A|0.976;G|0.024	0.024	strong	UBC,NS,carcinoma,0,1	UBC	79	1	NM_021009	exon2	c.T1941C	p.D647D	CTGCTGATCAGGA	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64604634	64604634	+	Silent	SNP	T	T	C	rs8007874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	51	107	0	0.536842	0	T|0.941;C|0.059	0.059	strong	.	SYNE2	577	.	NM_182914	exon79	c.T14776C	p.L4926L	CAGTGGTTGTCCC	.	PASS	Atlas-SNP
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389813	2389813	+	Silent	SNP	C	C	T	rs8100380	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	45	81	0	0.523256	0	C|0.948;T|0.052	0.052	strong	.	TMPRSS9	79	.	NM_182973	exon1	c.C30T	p.L10L	ACACCTCGTGCCC	.	PASS	Atlas-SNP
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	54	95	0	0.490909	0	G|0.766;A|0.234	0.234	strong	.	MEF2D	43	.	NM_005920	exon4	c.C303T	p.P101P	CCCGTCGGGCTCG	.	PASS	Atlas-SNP
APOL5	80831	hgsc.bcm.edu	37	22	36124860	36124860	+	Missense_Mutation	SNP	C	C	G	rs2076673	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	56	105	0	0.533333	0	C|0.692;G|0.308	0.308	strong	.	APOL5	45	.	NM_030642	exon4	c.C1217G	p.S406C	CAGTCTCTGCCCC	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6269021	6269021	+	Silent	SNP	C	C	T	rs114798118	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	7	3	0	1	0	C|0.894;T|0.106	0.106	strong	.	RNF207	45	.	NM_207396	exon4	c.C405T	p.R135R	AGCACGCATGTTC	.	PASS	Atlas-SNP
METTL5	29081	hgsc.bcm.edu	37	2	170681093	170681093	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	3	271	0	0.0114943	0	.	.	none	METTL5,NS,carcinoma,0,1	METTL5	24	1	NM_014168	exon1	c.G15A	p.R5R	CTTAAGCCTTACT	.	scavenged	Atlas-SNP
PTGES	9536	hgsc.bcm.edu	37	9	132515247	132515247	+	Silent	SNP	G	G	A	rs11792431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	11	28	0	0.37931	0	G|0.905;A|0.095	0.095	strong	.	PTGES	7	.	NM_004878	exon1	c.C45T	p.A15A	CAGGAAGGCCGGG	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117552560	117552560	+	Silent	SNP	T	T	C	rs7554376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	91	0	0.991304	0	T|0.915;C|0.085	0.085	strong	.	CD101	95	.	NM_001256109	exon2	c.T132C	p.N44N	CTGCAATGTAACT	.	PASS	Atlas-SNP
P2RY4	5030	hgsc.bcm.edu	37	X	69478749	69478749	+	Silent	SNP	G	G	T	rs3829708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	122	0	0.401869	0	G|0.866;0|0.003	.	strong	.	P2RY4	39	.	NM_002565	exon1	c.C726A	p.R242R	GAGAGAGCGGAGG	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53989945	53989945	+	Silent	SNP	G	G	A	rs74708552	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	18	64	0	0.209302	0	G|0.500;A|0.500	0.500	strong	.	ZNF813	81	.	NM_001004301	exon3	c.G75A	p.L25L	ATGCCTGGACCCT	.	PASS	Atlas-SNP
PRTG	283659	hgsc.bcm.edu	37	15	55970041	55970041	+	Silent	SNP	A	A	G	rs11854213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	104	0	1	0	A|0.787;G|0.213	0.213	strong	.	PRTG	110	.	NM_173814	exon8	c.T1335C	p.N445N	GTCTGAATTATAA	.	PASS	Atlas-SNP
KIAA0825	285600	hgsc.bcm.edu	37	5	93859799	93859799	+	Missense_Mutation	SNP	T	T	C	rs2044909	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	72	124	0	0.549618	0	T|0.874;C|0.126	0.126	strong	.	KIAA0825	172	.	NM_173665	exon4	c.A136G	p.K46E	AATGTTTTATGCT	.	PASS	Atlas-SNP
CEP104	9731	hgsc.bcm.edu	37	1	3745924	3745924	+	Missense_Mutation	SNP	G	G	A	rs2275831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	14	33	0	0.388889	0	G|0.873;A|0.127	0.127	strong	.	CEP104	79	.	NM_014704	exon15	c.C2057T	p.A686V	GTAGCCGCTTTTC	.	PASS	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121701681	121701681	+	Silent	SNP	G	G	A	rs2230776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	53	112	0	0.509615	0	G|0.911;A|0.089	0.089	strong	.	CAMKK2	87	.	NM_153500	exon6	c.C687T	p.P229P	CTCAATGGGGCCC	.	PASS	Atlas-SNP
CENPQ	55166	hgsc.bcm.edu	37	6	49459978	49459978	+	Missense_Mutation	SNP	A	A	G	rs2501968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	11	57	0	0.244444	0	A|0.545;C|0.003	.	strong	CENPQ,colon,carcinoma,0,2	CENPQ	23	2	NM_018132	exon9	c.A797G	p.D266G	AACTGGATGCATC	.	PASS	Atlas-SNP
PCDH12	51294	hgsc.bcm.edu	37	5	141329059	141329059	+	Missense_Mutation	SNP	T	T	G	rs61737141	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	52	93	0	0.553191	0	T|0.989;G|0.011	0.011	strong	.	PCDH12	133	.	NM_016580	exon3	c.A3068C	p.E1023A	AGGTCCTCTTCAG	.	PASS	Atlas-SNP
LRCH3	84859	hgsc.bcm.edu	37	3	197579466	197579466	+	Missense_Mutation	SNP	C	C	T	rs36078463	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	67	127	0	0.503759	0	C|0.913;T|0.087	0.087	strong	.	LRCH3	96	.	NM_032773	exon13	c.C1565T	p.P522L	AGCACCCGCTCCT	.	PASS	Atlas-SNP
AKAP4	8852	hgsc.bcm.edu	37	X	49957346	49957346	+	Missense_Mutation	SNP	G	G	C	rs12012704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	98	169	0	0.52973	0	A|0.000;C|0.063;G|0.936	0.063	strong	.	AKAP4	131	.	NM_003886	exon5	c.C2018G	p.A673G	TCTTCCGCTTTGT	.	PASS	Atlas-SNP
ZNF257	113835	hgsc.bcm.edu	37	19	22256358	22256358	+	Missense_Mutation	SNP	A	A	G	rs73930397	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	27	57	0	0.473684	0	A|0.967;G|0.033	0.033	strong	.	ZNF257	156	.	NM_033468	exon3	c.A218G	p.K73R	TAGCCAAACCCCC	.	PASS	Atlas-SNP
DHX58	79132	hgsc.bcm.edu	37	17	40255812	40255812	+	Missense_Mutation	SNP	C	C	T	rs2074160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	26	28	0	0.577778	0	C|0.886;T|0.114	0.114	strong	.	DHX58	39	.	NM_024119	exon12	c.G1568A	p.R523Q	AGATCCCGGATCT	.	PASS	Atlas-SNP
IMPA2	3613	hgsc.bcm.edu	37	18	12009913	12009913	+	Missense_Mutation	SNP	G	G	A	rs16976948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	55	98	0	0.495495	0	G|0.979;A|0.021	0.021	strong	.	IMPA2	27	.	NM_014214	exon3	c.G262A	p.A88T	TCTGGGGCCAAGT	.	PASS	Atlas-SNP
CACNG1	786	hgsc.bcm.edu	37	17	65052343	65052343	+	Missense_Mutation	SNP	C	C	T	rs371885900		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	73	177	0	0.521429	0	.	.	weak	CACNG1,colon,carcinoma,0,1	CACNG1	24	1	NM_000727	exon4	c.C625T	p.R209W	ATGCCCCGGAACC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139149406	139149406	+	Silent	SNP	G	G	A	rs6577876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	55	102	0	0.419847	0	G|0.777;A|0.223	0.223	strong	.	FAM135B	423	.	NM_015912	exon19	c.C3999T	p.L1333L	GTCTTTGAGGGCA	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109394564	109394564	+	Silent	SNP	T	T	C	rs17030016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	59	119	0	0.531532	0	T|0.935;C|0.065	0.065	strong	.	AKNAD1	83	.	NM_152763	exon2	c.A723G	p.A241A	TGAATTTGCTTTT	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324410	39324410	+	Silent	SNP	G	G	A	rs73985507	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	211	148	0	1	0	G|0.944;A|0.056	0.056	strong	.	KRTAP4-3	40	.	NM_033187	exon1	c.C15T	p.C5C	GCCACAGCAGGAG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82835724	82835724	+	Missense_Mutation	SNP	T	T	A	rs160278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	37	89	0	0.377551	0	T|0.507;G|0.000;N|0.000;A|0.493	0.493	strong	.	VCAN	498	.	NM_004385	exon8	c.T6902A	p.F2301Y	AAGACTTTAACAG	.	PASS	Atlas-SNP
CCL4L1	9560	hgsc.bcm.edu	37	17	34641448	34641448	+	Splice_Site	SNP	A	A	G	rs4796195	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	28	871	0	0.0838323	0	G|1.000;|0.000	1.000	weak	CCL4L2,NS,carcinoma,0,1	.	.	1	NM_001001435	exon3	c.192-2A>G	.	TTCTACAGATTCC	.	scavenged	Atlas-SNP
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219661	28219661	+	Missense_Mutation	SNP	G	G	A	rs9986596	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	54	0	1	0	G|0.842;A|0.158	0.158	strong	.	ZKSCAN4	42	.	NM_019110	exon1	c.C98T	p.S33F	AAGGCGGAGGCTT	.	PASS	Atlas-SNP
ALOX5AP	241	hgsc.bcm.edu	37	13	31309719	31309719	+	Missense_Mutation	SNP	C	C	T	rs17245407	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	75	77	0	0.590551	0	C|0.968;T|0.032	0.032	strong	.	ALOX5AP	12	.	NM_001204406	exon2	c.C148T	p.L50F	GCAGTCCTCTCTG	.	PASS	Atlas-SNP
ACAD8	27034	hgsc.bcm.edu	37	11	134131033	134131033	+	Silent	SNP	C	C	T	rs36115758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	132	0	0.483051	0	C|0.993;T|0.007	0.007	strong	.	ACAD8	33	.	NM_014384	exon7	c.C801T	p.L267L	CTTCCTCATTGCC	.	PASS	Atlas-SNP
OR2AE1	81392	hgsc.bcm.edu	37	7	99474427	99474427	+	Missense_Mutation	SNP	A	A	G	rs2572023	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	127	109	0	0.984496	0	G|0.588;N|0.000	0.588	strong	.	OR2AE1	32	.	NM_001005276	exon1	c.T230C	p.I77T	AGGATGATTGTGG	.	PASS	Atlas-SNP
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840079	1840079	+	Missense_Mutation	SNP	C	C	T	rs143202933	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	71	129	0	0.449367	0	C|0.997;T|0.003	0.003	strong	.	RTN4RL1	21	.	NM_178568	exon2	c.G1037A	p.R346Q	CCGGGCCGGGGGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	29	48	0	0.42029	0	C|0.879;T|0.121	0.121	strong	.	OBSCN	2142	.	NM_001271223	exon79	c.C19893T	p.A6631A	GGGGGCCGCTGAG	.	PASS	Atlas-SNP
OR2H2	7932	hgsc.bcm.edu	37	6	29555778	29555778	+	Silent	SNP	A	A	G	rs2235698	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	128	252	1	0.483019	0.00396825	A|0.764;G|0.236	0.236	strong	OR2H2,NS,carcinoma,+1,1	OR2H2	29	1	NM_007160	exon1	c.A57G	p.P19P	ACACCCAGGGCTG	.	PASS	Atlas-SNP
OR5B2	390190	hgsc.bcm.edu	37	11	58190112	58190112	+	Missense_Mutation	SNP	A	A	G	rs10466659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	41	103	0	0.445652	0	A|0.781;G|0.219	0.219	strong	OR5B2,NS,carcinoma,0,1	OR5B2	75	1	NM_001005566	exon1	c.T623C	p.V208A	AGAAGAACAAAAA	.	PASS	Atlas-SNP
SLC4A4	8671	hgsc.bcm.edu	37	4	72338467	72338467	+	Silent	SNP	C	C	T	rs35169468	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	52	117	0	0.419355	0	C|0.988;T|0.012	0.012	strong	.	SLC4A4	269	.	NM_001098484	exon14	c.C1683T	p.S561S	GTGGTCCGCCTTC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73466709	73466709	+	Silent	SNP	T	T	C	rs10823829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	142	132	0	0.986111	0	T|0.793;C|0.207	0.207	strong	.	CDH23	365	.	NM_022124	exon25	c.T3009C	p.S1003S	TGTGTCTGTGTCC	.	PASS	Atlas-SNP
SEMA4A	64218	hgsc.bcm.edu	37	1	156146218	156146218	+	Silent	SNP	C	C	T	rs12401573	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	58	96	0	0.508772	0	C|0.508;T|0.492	0.492	strong	.	SEMA4A	75	.	NM_001193300	exon15	c.C1716T	p.P572P	TGTCCCCAACTCC	.	PASS	Atlas-SNP
OR10G8	219869	hgsc.bcm.edu	37	11	123900916	123900916	+	Missense_Mutation	SNP	C	C	T	rs75240316	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	410	211	416	0	0.514634	0	C|0.966;T|0.034	0.034	strong	OR10G8,NS,carcinoma,-1,2	OR10G8	132	2	NM_001004464	exon1	c.C587T	p.T196I	TAGAGACTGTCAT	.	PASS	Atlas-SNP
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	103	0	1	0	T|0.531;G|0.469	0.469	strong	NRF1,NS,adenoma,0,1	NRF1	40	1	NM_005011	exon2	c.T141G	p.S47S	TTCTTCTCCCGAG	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	33	66	0	0.559322	0	T|0.694;C|0.306	0.306	strong	.	AKNAD1	83	.	NM_152763	exon14	c.A2184G	p.K728K	GATCCGTTTGGGT	.	PASS	Atlas-SNP
ADAM33	80332	hgsc.bcm.edu	37	20	3650234	3650234	+	Missense_Mutation	SNP	A	A	G	rs2280091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	71	149	0	0.503546	0	A|0.871;G|0.129	0.129	strong	.	ADAM33	76	.	NM_025220	exon20	c.T2291C	p.M764T	AACTCCATGGGGT	.	PASS	Atlas-SNP
LUZP1	7798	hgsc.bcm.edu	37	1	23419806	23419806	+	Missense_Mutation	SNP	A	A	C	rs12091554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	79	216	0	0.467456	0	A|0.952;C|0.048	0.048	strong	.	LUZP1	83	.	NM_033631	exon4	c.T949G	p.S317A	TTTTGGACTTCAT	.	PASS	Atlas-SNP
MNT	4335	hgsc.bcm.edu	37	17	2290222	2290222	+	Silent	SNP	G	G	A	rs61733100	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	95	160	0	0.582822	0	G|0.953;A|0.047	0.047	strong	.	MNT	35	.	NM_020310	exon6	c.C1722T	p.F574F	GACTGGGAAGGAG	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	40	65	0	0.526316	0	C|0.436;T|0.564	0.564	strong	MYO9B_ENST00000319396,NS,carcinoma,+2,2	MYO9B	264	2	NM_001130065	exon28	c.C4716T	p.V1572V	GATCGTCGTCAGC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78942956	78942956	+	Silent	SNP	A	A	G	rs2259969	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	118	152	0	0.702381	0	A|0.492;G|0.508	0.508	strong	.	PCSK5	329	.	NM_001190482	exon32	c.A4290G	p.S1430S	CTCATCATCTGGG	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235949877	235949877	+	Missense_Mutation	SNP	T	T	C	rs3731644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	40	67	0	0.56338	0	T|0.747;C|0.253	0.253	strong	SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	NM_014521	exon4	c.T464C	p.M155T	GCAGAATGTACAG	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55790414	55790414	+	Missense_Mutation	SNP	G	G	T	rs16976354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	53	110	0	0.401515	0	G|0.928;T|0.072	0.072	strong	.	DYX1C1	54	.	NM_001033560	exon2	c.C114A	p.N38K	CAGATAGTTTTCC	.	PASS	Atlas-SNP
NPR3	4883	hgsc.bcm.edu	37	5	32712119	32712119	+	Silent	SNP	T	T	C	rs6859964	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	61	99	0	0.491935	0	T|0.956;C|0.044	0.044	strong	.	NPR3	65	.	NM_000908	exon1	c.T237C	p.A79A	GTATGCTCTGCGC	.	PASS	Atlas-SNP
WDR96	80217	hgsc.bcm.edu	37	10	105906077	105906077	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	85	127	0	0.508982	0	.	.	none	WDR96,NS,carcinoma,+1,1	WDR96	183	1	NM_025145	exon30	c.A3799G	p.R1267G	CTTCTCTAGATTT	.	PASS	Atlas-SNP
CCNI	10983	hgsc.bcm.edu	37	4	77976374	77976374	+	Missense_Mutation	SNP	C	C	T	rs4252903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	102	171	0	0.463636	0	C|0.992;T|0.008	0.008	strong	.	CCNI	22	.	NM_006835	exon6	c.G619A	p.V207I	GACTAACCATGGC	.	PASS	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16459745	16459745	+	Silent	SNP	G	G	A	rs10907223	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	73	132	0	0.506944	0	G|0.827;A|0.173	0.173	strong	.	EPHA2	102	.	NM_004431	exon11	c.C1983T	p.L661L	CTCGCCGAGGAAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179416659	179416659	+	Missense_Mutation	SNP	C	C	T	rs11887722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	56	84	0	0.513761	0	C|0.949;T|0.051	0.051	strong	.	TTN	18412	.	NM_001267550	exon335	c.G90968A	p.R30323K	GGAATCCTGAACT	.	PASS	Atlas-SNP
ENAM	10117	hgsc.bcm.edu	37	4	71509431	71509431	+	Missense_Mutation	SNP	G	G	A	rs3796704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	67	134	0	0.503759	0	G|0.873;A|0.127	0.127	strong	ENAM_ENST00000396073,colon,carcinoma,0,2	ENAM	140	2	NM_031889	exon9	c.G2288A	p.R763Q	CTTCACGGAATTC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17083797	17083797	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	339	162	221	0	0.477876	0	.	.	none	.	.	.	.	NM_001271733	exon15	c.G2000A	p.R667H	GGCCAGCGCGACC	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924693	70924693	+	Silent	SNP	T	T	C	rs45480894	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	19	94	0	0.234568	0	T|0.945;C|0.055	0.055	strong	ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.T477C	p.Y159Y	GGTTTATAAGATA	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3480910	3480910	+	Silent	SNP	A	A	G	rs34378673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	31	86	0	0.449275	0	A|0.934;G|0.066	0.066	strong	.	TRPV1	99	.	NM_018727	exon11	c.T1695C	p.Y565Y	GACGGCATAGATG	.	PASS	Atlas-SNP
EBI3	10148	hgsc.bcm.edu	37	19	4237067	4237067	+	Silent	SNP	A	A	G	rs4905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	40	0	1	0	A|0.585;G|0.415	0.415	strong	.	EBI3	15	.	NM_005755	exon5	c.A672G	p.T224T	TGCCACAATGAGC	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123838882	123838882	+	Silent	SNP	C	C	T	rs138596900	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	40	131	0	0.3125	0	C|0.979;T|0.021	0.021	strong	.	.	.	.	NM_001163278	exon5	c.G996A	p.L332L	TAGTAACAAGGCC	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939664	12939664	+	Missense_Mutation	SNP	A	A	T	rs78455617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	50	156	0	0.352113	0	A|0.881;T|0.119	0.119	strong	PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	NM_001009611	exon4	c.T1138A	p.F380I	GCTCAAAGCAGCG	.	scavenged	Atlas-SNP
AVPR2	554	hgsc.bcm.edu	37	X	153171993	153171993	+	Silent	SNP	A	A	G	rs5201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	199	224	1	1	0.00446429	A|0.412;0|0.001	.	strong	.	AVPR2	43	.	NM_000054	exon3	c.A927G	p.L309L	TGTGCTACTCATG	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912406	45912406	+	Missense_Mutation	SNP	G	G	A	rs2336219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	31	72	0	0.508197	0	G|0.767;A|0.233	0.233	strong	.	CD3EAP	27	.	NM_012099	exon3	c.G1180A	p.D394N	CAGCAAGATGCCA	.	PASS	Atlas-SNP
PGAM2	5224	hgsc.bcm.edu	37	7	44104913	44104913	+	Silent	SNP	G	G	A	rs111656877	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	57	109	0	0.471074	0	G|0.984;A|0.016	0.016	strong	.	PGAM2	20	.	NM_000290	exon1	c.C216T	p.D72D	CGTGCCGTCCAGG	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2911352	2911352	+	Silent	SNP	C	C	T	rs36016465	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	72	74	0	0.5625	0	C|0.988;T|0.012	0.012	strong	.	RAP1GAP2	90	.	NM_015085	exon17	c.C1407T	p.H469H	GCTCCACGCCCAC	.	PASS	Atlas-SNP
DNAJA3	9093	hgsc.bcm.edu	37	16	4492415	4492415	+	Silent	SNP	C	C	T	rs141270066		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	66	144	0	0.519685	0	C|1.000;T|0.000	0.000	weak	.	DNAJA3	52	.	NM_001135110	exon5	c.C777T	p.S259S	CGGCTCCGGCATG	.	PASS	Atlas-SNP
PCDHGA5	56110	hgsc.bcm.edu	37	5	140745333	140745333	+	Missense_Mutation	SNP	C	C	T	rs6882138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	31	78	0	0.397436	0	C|0.944;T|0.056	0.056	strong	.	PCDHGA5	215	.	NM_032054	exon1	c.C1436T	p.P479L	ATGACCCCGACAG	.	PASS	Atlas-SNP
ARHGEF15	22899	hgsc.bcm.edu	37	17	8216468	8216468	+	Missense_Mutation	SNP	T	T	C	rs871841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	43	72	0	0.573333	0	T|0.398;G|0.003	.	strong	.	ARHGEF15	97	.	NM_025014	exon3	c.T830C	p.L277P	TGCCACTCCTCAA	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43152366	43152366	+	Silent	SNP	C	C	A	rs41274928	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	95	156	0	0.516304	0	C|0.948;A|0.052	0.052	strong	.	CUL9	248	.	NM_015089	exon2	c.C318A	p.G106G	AGGAGGCCTGGAT	.	PASS	Atlas-SNP
HMGXB3	22993	hgsc.bcm.edu	37	5	149404213	149404213	+	Missense_Mutation	SNP	G	G	T	rs115942845	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	34	57	0	0.566667	0	G|0.995;T|0.005	0.005	strong	.	HMGXB3	31	.	NM_014983	exon7	c.G1430T	p.S477I	CCTCCAGTCCACT	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55451083	55451083	+	Silent	SNP	A	A	G	rs1654636	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	18	199	0	0.191489	0	A|0.949;G|0.051	0.051	strong	NLRP7_ENST00000328092,NS,carcinoma,-2,2	NLRP7	411	2	NM_001127255	exon4	c.T1104C	p.I368I	GCACACAATCCAG	.	scavenged	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22137603	22137603	+	Missense_Mutation	SNP	G	G	A	rs55732851	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	67	142	0	0.465278	0	G|0.908;A|0.092	0.092	strong	.	VWA3A	115	.	NM_173615	exon17	c.G1637A	p.C546Y	AGGACTGTTTCAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910581	29910581	+	Missense_Mutation	SNP	C	C	A	rs1059423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	20	82	0	0.215054	0	A|0.089;C|0.911	0.089	strong	.	HLA-A	89	.	NM_001242758	exon2	c.C121A	p.R41S	CCCGGCCGCGGGG	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744456	31744456	+	Missense_Mutation	SNP	G	G	A	rs16986753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	116	273	0	0.469636	0	G|0.989;A|0.011	0.011	strong	.	KRTAP13-2	29	.	NM_181621	exon1	c.C76T	p.R26C	AGCCACGTGAGGA	.	PASS	Atlas-SNP
THSD4	79875	hgsc.bcm.edu	37	15	72040774	72040774	+	Silent	SNP	C	C	T	rs1872056	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	230	210	0	1	0	C|0.782;T|0.218	0.218	strong	.	THSD4	75	.	NM_024817	exon13	c.C2256T	p.C752C	GCCCTGCGGCGTG	.	PASS	Atlas-SNP
OC90	729330	hgsc.bcm.edu	37	8	133053909	133053909	+	Silent	SNP	G	G	C	rs115883855	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	70	121	0	0.503597	0	G|0.989;C|0.011	0.011	strong	OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	2	NM_001080399	exon5	c.C207G	p.V69V	GGTGAAGACAGCC	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506749	11506749	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	489	150	104	2	0.306748	0.0192308	.	.	none	PRB1,NS,carcinoma,0,1	PRB1	33	1	NM_199353	exon3	c.A288G	p.K96K	TTGTGGTTTTCCT	.	scavenged	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45817713	45817713	+	Silent	SNP	G	G	A	rs45622331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	81	138	0	0.519231	0	G|0.947;A|0.053	0.053	strong	.	TRPM2	196	.	NM_003307	exon13	c.G2016A	p.S672S	CAGCTCGGAGGAG	.	PASS	Atlas-SNP
MLANA	2315	hgsc.bcm.edu	37	9	5892525	5892525	+	Silent	SNP	C	C	T	rs2233178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	57	105	0	0.463415	0	C|0.863;T|0.137	0.137	strong	.	MLANA	16	.	NM_005511	exon2	c.C51T	p.H17H	GGGGCACGGCCAC	.	PASS	Atlas-SNP
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	18	28	0	0.5625	0	A|0.766;G|0.234	0.234	strong	FAM83F,NS,carcinoma,0,1	FAM83F	29	1	NM_138435	exon4	c.A1306G	p.R436G	CCCGCCAGGCGCT	.	PASS	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120793332	120793332	+	Silent	SNP	T	T	C	rs28619538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	36	75	0	0.580645	0	T|0.977;C|0.023	0.023	strong	.	TAF2	204	.	NM_003184	exon17	c.A2214G	p.T738T	GTTGTTTGTTTTC	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38777173	38777173	+	Silent	SNP	A	A	T	rs10856838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	137	0	1	0	A|0.721;T|0.279	0.279	strong	.	TLR10	87	.	NM_001017388	exon2	c.T39A	p.I13I	CATAACAATACTA	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32093079	32093079	+	Silent	SNP	A	A	G	rs16889443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	100	144	0	0.515464	0	A|0.932;G|0.068	0.068	strong	.	PDZD2	306	.	NM_178140	exon20	c.A7794G	p.G2598G	AGTGGGATCGAAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417774	105417774	+	Silent	SNP	G	G	A	rs2013228	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	263	378	0	1	0	G|0.700;A|0.300	0.300	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4014T	p.F1338F	CACCCCGAACGAC	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746722	143746722	+	Silent	SNP	G	G	A	rs60195180	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	99	0	0.401869	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_003724	exon2	c.C756T	p.V252V	ATAGGCGACGGGC	.	PASS	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140201604	140201604	+	Missense_Mutation	SNP	C	C	T	rs28685844	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	87	74	1	0.783784	0.0135135	C|0.957;T|0.043	0.043	strong	EXD3_ENST00000340951,NS,carcinoma,0,1	EXD3	86	1	NM_017820	exon22	c.G2429A	p.R810Q	TGCAGCCGGGTGC	.	scavenged	Atlas-SNP
ADRBK1	156	hgsc.bcm.edu	37	11	67052322	67052322	+	Silent	SNP	C	C	T	rs115867067	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	25	52	0	0.328947	0	C|0.987;T|0.013	0.013	strong	.	ADRBK1	51	.	NM_001619	exon19	c.C1659T	p.Y553Y	AGACTACGCCCTG	.	PASS	Atlas-SNP
CNGB3	54714	hgsc.bcm.edu	37	8	87588248	87588248	+	Silent	SNP	T	T	C	rs3735970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	304	165	289	0	0.542763	0	T|0.918;C|0.082	0.082	strong	.	CNGB3	176	.	NM_019098	exon18	c.A2214G	p.E738E	TTTATCTTCATTT	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17700792	17700792	+	Silent	SNP	C	C	T	rs35686634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	49	139	0	0.398374	0	C|0.916;T|0.084	0.084	strong	.	RAI1	121	.	NM_030665	exon3	c.C4530T	p.P1510P	CCAGCCCCCGGAG	.	PASS	Atlas-SNP
C17orf82	388407	hgsc.bcm.edu	37	17	59489787	59489787	+	Missense_Mutation	SNP	G	G	C	rs58036240	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	31	45	0	0.469697	0	G|0.930;C|0.070	0.070	strong	.	C17orf82	16	.	NM_203425	exon1	c.G451C	p.A151P	GGCCGCGCCTGGT	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15517415	15517415	+	Silent	SNP	C	C	T	rs11970076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	74	78	0	0.544118	0	C|0.983;T|0.017	0.017	strong	.	JARID2	135	.	NM_004973	exon17	c.C3474T	p.V1158V	AAACGTCGTGTTC	.	PASS	Atlas-SNP
HSD11B2	3291	hgsc.bcm.edu	37	16	67469733	67469733	+	Silent	SNP	C	C	A	rs5479	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	39	72	0	0.609375	0	C|0.902;A|0.098	0.098	strong	.	HSD11B2	13	.	NM_000196	exon2	c.C468A	p.T156T	CCACACCACCAGC	.	PASS	Atlas-SNP
ZNF582	147948	hgsc.bcm.edu	37	19	56901457	56901457	+	Missense_Mutation	SNP	C	C	T	rs61743722	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	44	83	0	0.473118	0	C|0.972;T|0.028	0.028	strong	.	ZNF582	56	.	NM_144690	exon4	c.G145A	p.V49I	TGGAAACGGCAAG	.	PASS	Atlas-SNP
LMLN	89782	hgsc.bcm.edu	37	3	197712759	197712759	+	Silent	SNP	T	T	C	rs7373242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	58	120	0	0.563107	0	T|0.785;C|0.215	0.215	strong	.	LMLN	53	.	NM_001136049	exon8	c.T927C	p.Y309Y	TAATTATAGGTAT	.	PASS	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	37	5	57753116	57753116	+	Silent	SNP	C	C	T	rs17710502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	47	0	0.545455	0	C|0.868;T|0.132	0.132	strong	.	PLK2	71	.	NM_006622	exon7	c.G900A	p.P300P	TGAGGACGGCATT	.	PASS	Atlas-SNP
TTC8	123016	hgsc.bcm.edu	37	14	89343670	89343670	+	Silent	SNP	G	G	C	rs142073418	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	54	119	0	0.45	0	G|0.997;C|0.003	0.003	strong	TTC8,NS,carcinoma,+2,1	TTC8	42	1	NM_144596	exon15	c.G1464C	p.A488A	TGCTGCGCAGAAG	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327912	16327912	+	Missense_Mutation	SNP	C	C	A	rs368218879		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	8	72	1	0.119403	0.0138889	.	.	weak	ATXN1,colon,carcinoma,0,2	ATXN1	117	2	NM_001128164	exon7	c.G630T	p.Q210H	CTGATGCTGATGC	.	scavenged	Atlas-SNP
POLM	27434	hgsc.bcm.edu	37	7	44116207	44116207	+	Missense_Mutation	SNP	C	C	A	rs28382653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	69	0	0.451613	0	C|0.983;A|0.017	0.017	strong	.	POLM	50	.	NM_013284	exon6	c.G736T	p.V246F	CACCGACCCCGAA	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009620	46009620	+	Silent	SNP	C	C	T	rs34147726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	59	149	0	0.42446	0	C|0.907;T|0.093	0.093	strong	.	FYCO1	115	.	NM_024513	exon8	c.G1206A	p.E402E	CCCTAGCTCCTGC	.	PASS	Atlas-SNP
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507003	24507003	+	Silent	SNP	A	A	C	rs28599797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	317	169	283	1	0.533123	0.00353357	A|0.751;C|0.249	0.249	strong	.	.	.	.	NM_001082488	exon2	c.A180C	p.V60V	CGTGGTAGTCAGC	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156354367	156354367	+	Missense_Mutation	SNP	A	A	G	rs6668857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	138	142	0	0.985714	0	A|0.291;G|0.709	0.709	strong	.	RHBG	133	.	NM_020407	exon10	c.A1283G	p.H428R	CCCAGCACTACGA	.	PASS	Atlas-SNP
CTBS	1486	hgsc.bcm.edu	37	1	85040069	85040069	+	Silent	SNP	G	G	A	rs2911592	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	12	21	0	0.6	0	G|0.761;A|0.239	0.239	strong	.	CTBS	24	.	NM_004388	exon1	c.C30T	p.R10R	GACGAGGCGCCAG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379109	31379109	+	Missense_Mutation	SNP	G	G	A	rs1051794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	99	0	1	0	G|0.642;A|0.358	0.358	strong	.	MICA	21	.	NM_001177519	exon3	c.G586A	p.E196K	TATCTAGAATCCG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684550	100684550	+	Missense_Mutation	SNP	A	A	G	rs35090328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	73	149	0	0.459119	0	A|0.904;G|0.096	0.096	strong	.	MUC17	804	.	NM_001040105	exon3	c.A9853G	p.S3285G	TTAACAAGTATGC	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233489682	233489682	+	Silent	SNP	G	G	A	rs56268427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	107	200	0	0.504717	0	G|0.951;A|0.049	0.049	strong	.	KIAA1804	129	.	NM_032435	exon3	c.G1116A	p.P372P	TGAGCCGTTTGCC	.	PASS	Atlas-SNP
CDK11A	728642	hgsc.bcm.edu	37	1	1638925	1638925	+	Missense_Mutation	SNP	C	C	T	rs200982240	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	114	226	0	0.425373	0	C|0.960;T|0.040	0.040	strong	CDK11B,caecum,carcinoma,0,2	CDK11A	38	2	NM_024011	exon11	c.G1168A	p.D390N	CATAGTCGCCCTC	.	PASS	Atlas-SNP
ZSWIM1	90204	hgsc.bcm.edu	37	20	44512013	44512013	+	Missense_Mutation	SNP	C	C	G	rs115926000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	106	172	0	0.522168	0	C|0.998;G|0.002	0.002	strong	.	ZSWIM1	35	.	NM_080603	exon2	c.C782G	p.T261S	AGGTCACCACCCA	.	PASS	Atlas-SNP
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507010	24507010	+	Missense_Mutation	SNP	C	C	A	rs12587718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	179	289	0	0.550769	0	C|0.731;A|0.269	0.269	strong	.	.	.	.	NM_001082488	exon2	c.C187A	p.R63S	GTCAGCCGCCGGA	.	PASS	Atlas-SNP
RBM46	166863	hgsc.bcm.edu	37	4	155720349	155720349	+	Silent	SNP	C	C	A	rs12651031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	143	268	0	0.537594	0	C|0.880;A|0.120	0.120	strong	.	RBM46	76	.	NM_144979	exon4	c.C1035A	p.G345G	TCTAGGCAAGCTG	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3631241	3631241	+	Missense_Mutation	SNP	A	A	G	rs2976230	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	125	220	0	0.570776	0	A|0.678;G|0.322	0.322	strong	.	ITGAE	96	.	NM_002208	exon26	c.T3056C	p.V1019A	ACTGCTACAACCT	.	PASS	Atlas-SNP
NEIL2	252969	hgsc.bcm.edu	37	8	11643731	11643731	+	Silent	SNP	G	G	A	rs113110839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	126	199	0	0.53617	0	G|0.996;A|0.004	0.004	strong	.	NEIL2	14	.	NM_001135746	exon5	c.G948A	p.P316P	GTGCCCGCAGTGC	.	PASS	Atlas-SNP
OR10Z1	128368	hgsc.bcm.edu	37	1	158576394	158576394	+	Missense_Mutation	SNP	C	C	A	rs116792162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	182	316	0	0.494565	0	C|0.992;A|0.008	0.008	strong	OR10Z1,right_upper_lobe,carcinoma,-1,1	OR10Z1	99	1	NM_001004478	exon1	c.C166A	p.H56N	CATCTGCACACCC	.	PASS	Atlas-SNP
STAMBP	10617	hgsc.bcm.edu	37	2	74057995	74057995	+	Silent	SNP	T	T	C	rs919629	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	30	66	0	0.517241	0	T|0.896;C|0.104	0.104	strong	.	STAMBP	37	.	NM_006463	exon3	c.T12C	p.H4H	TGACCATGGAGAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678622	100678622	+	Missense_Mutation	SNP	G	G	A	rs77299546	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	22	111	0	0.15942	0	G|0.936;A|0.064	0.064	strong	.	MUC17	804	.	NM_001040105	exon3	c.G3925A	p.V1309M	GGTCCTGTGGTCA	.	PASS	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31411184	31411184	+	Missense_Mutation	SNP	C	C	A	rs1465972	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	62	0	1	0	C|0.704;A|0.296	0.296	strong	CAPN14,NS,carcinoma,0,1	CAPN14	36	1	NM_001145122	exon14	c.G1530T	p.K510N	ACTCACCTTTGAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1271429	1271429	+	Missense_Mutation	SNP	C	C	T	rs2943516	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	470	208	443	1	0.442553	0.00225734	C|0.521;T|0.479	0.479	strong	.	MUC5B	473	.	NM_002458	exon31	c.C13319T	p.P4440L	CCACCCCGTCCTC	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133887676	133887676	+	Missense_Mutation	SNP	T	T	C	rs35356262	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	37	99	0	0.45679	0	T|0.999;C|0.001	0.001	strong	.	NCKAP5	322	.	NM_207481	exon6	c.A215G	p.K72R	ATCAGCTTCTCAT	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154523373	154523373	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	2	132	0	0.0148148	0	.	.	none	KIAA0922_ENST00000409959,NS,malignant_melanoma,0,2	KIAA0922	214	2	NM_001131007	exon22	c.C2336T	p.P779L	CTCTTCCTATAAC	.	scavenged	Atlas-SNP
MAGEA8	4107	hgsc.bcm.edu	37	X	149013963	149013963	+	Missense_Mutation	SNP	C	C	T	rs12010332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	293	284	0	1	0	C|0.947;T|0.053	0.053	strong	.	MAGEA8	40	.	NM_005364	exon3	c.C917T	p.S306F	ACCCATCCCTGCA	.	PASS	Atlas-SNP
ZNF500	26048	hgsc.bcm.edu	37	16	4810583	4810583	+	Missense_Mutation	SNP	C	C	T	rs151148153	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	45	103	0	0.416667	0	C|0.995;T|0.005	0.005	strong	.	ZNF500	45	.	NM_021646	exon5	c.G670A	p.V224M	AGTTCACGGGCAC	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5085758	5085758	+	Silent	SNP	G	G	A	rs144567321	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	16	138	0	0.173913	0	G|0.994;A|0.006	0.006	strong	ZNF594,colon,carcinoma,-2,3	ZNF594	89	3	NM_032530	exon2	c.C1794T	p.C598C	TTCTTTGCATTCA	.	PASS	Atlas-SNP
AADACL3	126767	hgsc.bcm.edu	37	1	12779618	12779618	+	Missense_Mutation	SNP	T	T	C	rs3010877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	142	173	0	0.97931	0	T|0.150;C|0.850	0.850	strong	.	AADACL3	84	.	NM_001103170	exon2	c.T139C	p.S47P	TACCAATCCAAGG	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6901891	6901891	+	Missense_Mutation	SNP	G	G	A	rs897738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	72	128	0	0.517986	0	G|0.597;T|0.003	.	strong	.	EMR1	153	.	NM_001256253	exon6	c.G520A	p.D174N	GACGTGGATGAAT	.	PASS	Atlas-SNP
COMMD8	54951	hgsc.bcm.edu	37	4	47462210	47462210	+	Missense_Mutation	SNP	A	A	C	rs114141818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	119	0	1	0	A|0.985;C|0.015	0.015	strong	.	COMMD8	15	.	NM_017845	exon2	c.T173G	p.I58S	TTGGCAATATCTT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114152755	114152755	+	Silent	SNP	C	C	T	rs2260218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	14	50	0	0.466667	0	C|0.795;T|0.205	0.205	strong	.	TMCO3	77	.	NM_017905	exon3	c.C543T	p.D181D	GCTTGACGAGATT	.	PASS	Atlas-SNP
FJX1	24147	hgsc.bcm.edu	37	11	35641428	35641428	+	Missense_Mutation	SNP	G	G	A	rs12286850	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	27	57	0	0.574468	0	G|0.908;A|0.092	0.092	strong	.	FJX1	32	.	NM_014344	exon1	c.G1244A	p.R415H	TACAGCGCCGCCT	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	10	21	0	0.625	0	G|0.607;A|0.393	0.393	strong	.	SLC6A5	151	.	NM_004211	exon2	c.G304A	p.G102S	GCGCAAGGCGCGC	.	PASS	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231065630	231065630	+	Missense_Mutation	SNP	G	G	A	rs59573011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	86	167	0	0.438776	0	G|0.980;A|0.020	0.020	strong	.	SP110	105	.	NM_001185015	exon11	c.C1118T	p.T373M	CTAGGCGTCTTCT	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42740369	42740369	+	Silent	SNP	C	C	T	rs3742996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	110	187	0	0.516432	0	C|0.911;T|0.089	0.089	strong	.	ZFP106	117	.	NM_022473	exon3	c.G2967A	p.A989A	GGAGATCGCAAGG	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43762196	43762196	+	Missense_Mutation	SNP	C	C	T	rs689647	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	85	0	0.490196	0	C|0.671;N|0.000	.	strong	.	TP53BP1	157	.	NM_001141980	exon11	c.G1249A	p.G417S	GTTCACCACTTTG	.	PASS	Atlas-SNP
LHFP	10186	hgsc.bcm.edu	37	13	40175311	40175311	+	Silent	SNP	G	G	A	rs34616166	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	70	89	0	0.569106	0	G|0.941;A|0.059	0.059	strong	.	LHFP	31	.	NM_005780	exon2	c.C43T	p.L15L	AAGACAGCAAAGC	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444607	20444607	+	Missense_Mutation	SNP	C	C	G	rs10135467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	207	169	0	0.990431	0	C|0.770;G|0.230	0.230	strong	.	OR4K15	82	.	NM_001005486	exon1	c.C930G	p.I310M	TGTAATCTACACG	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	rs41310553	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	63	121	0	0.547826	0	G|0.986;A|0.014	0.014	strong	.	URB2	152	.	NM_014777	exon8	c.G4223A	p.R1408Q	AAGGGCGGCAGAA	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140264091	140264091	+	Silent	SNP	G	G	C	rs10076265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	83	153	0	0.522013	0	G|0.982;C|0.018	0.018	strong	PCDHA13,colon,carcinoma,+2,1	PCDHA13	213	1	NM_031865	exon1	c.G2238C	p.G746G	GGCAGGGAGTTGG	.	PASS	Atlas-SNP
VCPIP1	80124	hgsc.bcm.edu	37	8	67577670	67577670	+	Silent	SNP	G	G	A	rs3808602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	117	260	1	0.446565	0.00384615	G|0.858;A|0.142	0.142	strong	.	VCPIP1	110	.	NM_025054	exon1	c.C1524T	p.Y508Y	AAAGCTGTAATTT	.	PASS	Atlas-SNP
AMBN	258	hgsc.bcm.edu	37	4	71472426	71472426	+	Silent	SNP	A	A	G	rs7680880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	161	270	0	0.570922	0	A|0.762;G|0.238	0.238	strong	.	AMBN	73	.	NM_016519	exon13	c.A1323G	p.A441A	TGACGCATGGCAT	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7783172	7783172	+	Silent	SNP	G	G	A	rs77207711	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	96	210	0	0.442396	0	G|0.870;A|0.130	0.130	strong	.	AFAP1	93	.	NM_001134647	exon13	c.C1713T	p.Y571Y	GGCAGGGTATTTG	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A	rs75200561	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	35	254	0	0.123239	0	.	.	weak	TDG,pharynx,carcinoma,0,1	TDG	43	1	NM_003211	exon3	c.C387A	p.T129T	TTTGACCTTCAAT	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30680562	30680562	+	Missense_Mutation	SNP	G	G	A	rs28986465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	73	133	0	0.521429	0	G|0.939;A|0.061	0.061	strong	.	MDC1	218	.	NM_014641	exon5	c.C1157T	p.P386L	GCCTGTGGGGCCT	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014492	53014492	+	Silent	SNP	T	T	A	rs145508251	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	68	106	0	0.444444	0	T|0.993;A|0.007	0.007	strong	.	.	.	.	NM_001099694	exon6	c.T858A	p.P286P	GAAACCTTACAAG	.	PASS	Atlas-SNP
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736328	140736328	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	73	129	0	0.514085	0	.	.	none	.	PCDHGA4	150	.	NM_018917	exon1	c.G1561A	p.D521N	TCCTTCGACTATG	.	PASS	Atlas-SNP
C17orf77	146723	hgsc.bcm.edu	37	17	72588806	72588806	+	Nonsense_Mutation	SNP	C	C	A	rs545652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	72	118	0	0.507042	0	C|0.751;A|0.249	0.249	strong	C17orf77,colon,carcinoma,0,1	C17orf77	31	1	NM_152460	exon3	c.C621A	p.C207X	CCCATGCCCCAGG	.	PASS	Atlas-SNP
KRT37	8688	hgsc.bcm.edu	37	17	39577215	39577215	+	Missense_Mutation	SNP	G	G	A	rs8071814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	31	58	0	0.442857	0	G|0.935;A|0.065	0.065	strong	.	KRT37	61	.	NM_003770	exon7	c.C1265T	p.T422M	GCAGGCGTGGAAC	.	PASS	Atlas-SNP
SAMD4B	55095	hgsc.bcm.edu	37	19	39873877	39873877	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	76	169	0	0.475	0	.	.	none	SAMD4B,NS,carcinoma,0,2	SAMD4B	48	2	NM_018028	exon15	c.A2002G	p.I668V	CTGGAGATCAATC	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33738752	33738752	+	Missense_Mutation	SNP	A	A	G	rs12946189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	123	251	0	0.448905	0	A|0.962;G|0.038	0.038	strong	SLFN12,NS,malignant_melanoma,+1,3	SLFN12	56	3	NM_018042	exon4	c.T1342C	p.S448P	CCTGGGAAATCAG	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153418514	153418514	+	Missense_Mutation	SNP	G	G	A	rs79866052	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1100	325	468	0	0.295455	0	G|0.870;A|0.130	0.130	strong	.	OPN1LW	87	.	NM_020061	exon3	c.G511A	p.V171M	GCCATCGTGGGCA	.	PASS	Atlas-SNP
FRMD7	90167	hgsc.bcm.edu	37	X	131212512	131212512	+	Silent	SNP	A	A	G	rs5977623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	88	208	0	0.425121	0	A|0.670;0|0.003	.	strong	.	FRMD7	69	.	NM_194277	exon12	c.T1533C	p.I511I	TGCTCTAATTGGG	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13650	13650	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	8	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.C1314T	p.P438P	CTTCCCCACCCTT	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30071357	30071357	+	Silent	SNP	G	G	A	rs17194258	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	33	55	0	0.464789	0	G|0.980;A|0.020	0.020	strong	TRIM31,right_upper_lobe,carcinoma,+2,1	TRIM31	40	1	NM_007028	exon9	c.C1234T	p.L412L	CTGTCAGCCACTC	.	PASS	Atlas-SNP
IL4I1	259307	hgsc.bcm.edu	37	19	50393269	50393269	+	Silent	SNP	A	A	G	rs56359967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	16	37	0	0.340426	0	A|0.881;G|0.119	0.119	strong	.	IL4I1	50	.	NM_172374	exon10	c.T1428C	p.F476F	TACCACAAAGCCA	.	PASS	Atlas-SNP
ACOX1	51	hgsc.bcm.edu	37	17	73949540	73949540	+	Missense_Mutation	SNP	G	G	C	rs1135640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	101	196	0	0.467593	0	G|0.477;C|0.523	0.523	strong	.	ACOX1	85	.	NM_007292	exon7	c.C936G	p.I312M	TGGCTTGATTTCA	.	PASS	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	37	2	171713564	171713564	+	Silent	SNP	C	C	T	rs769392	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	27	65	0	0.369863	0	C|0.959;T|0.041	0.041	strong	.	GAD1	79	.	NM_000817	exon15	c.C1450T	p.L484L	AAATGCCTGGAAC	.	PASS	Atlas-SNP
NEUROG3	50674	hgsc.bcm.edu	37	10	71332480	71332480	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	3	258	0	0.0109091	0	.	.	none	NEUROG3,NS,carcinoma,+1,1	NEUROG3	33	1	NM_020999	exon2	c.G320A	p.R107H	ACACCGCGCAGGG	.	scavenged	Atlas-SNP
ERO1LB	56605	hgsc.bcm.edu	37	1	236381833	236381833	+	Silent	SNP	A	A	G	rs11811758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	121	244	0	0.560185	0	A|0.961;G|0.039	0.039	strong	.	ERO1LB	48	.	NM_019891	exon16	c.T1387C	p.L463L	GTTGTAATAAGAC	.	PASS	Atlas-SNP
PPP1R3F	89801	hgsc.bcm.edu	37	X	49126714	49126714	+	Silent	SNP	C	C	T	rs111938103	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	14	16	0	0.875	0	C|0.941;T|0.059	0.059	strong	.	PPP1R3F	56	.	NM_033215	exon1	c.C382T	p.L128L	GGCCGTCTGGAGC	.	PASS	Atlas-SNP
GXYLT2	727936	hgsc.bcm.edu	37	3	72971414	72971414	+	Silent	SNP	A	A	G	rs61741329	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	60	148	0	0.458015	0	A|0.976;G|0.024	0.024	strong	.	GXYLT2	43	.	NM_001080393	exon3	c.A528G	p.T176T	CATCACATTTTCT	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145004185	145004185	+	Silent	SNP	C	C	T	rs78012434	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	37	51	0	0.425287	0	C|0.963;T|0.037	0.037	strong	.	PLEC	1144	.	NM_201380	exon22	c.G3069A	p.L1023L	CACGTGCAACTGG	.	PASS	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23873463	23873463	+	Silent	SNP	T	T	C	rs1677016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	126	281	0	0.533898	0	T|0.474;C|0.526	0.526	strong	TAF4B,NS,carcinoma,+1,1	TAF4B	71	1	NM_005640	exon9	c.T1800C	p.N600N	GAAAAATAGAATA	.	PASS	Atlas-SNP
TTC39B	158219	hgsc.bcm.edu	37	9	15191209	15191209	+	Silent	SNP	A	A	G	rs74818741	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	49	110	0	0.5	0	A|0.969;G|0.031	0.031	strong	.	TTC39B	83	.	NM_001168340	exon10	c.T975C	p.F325F	TCCAATAAATTCT	.	PASS	Atlas-SNP
ADRB2	154	hgsc.bcm.edu	37	5	148206440	148206440	+	Missense_Mutation	SNP	G	G	A	rs1042713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	57	101	0	0.522936	0	G|0.576;A|0.424	0.424	strong	.	ADRB2	42	.	NM_000024	exon1	c.G46A	p.G16R	CCCAATGGAAGCC	.	PASS	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238461	71238461	+	Missense_Mutation	SNP	G	G	A	rs200128074	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	365	19	338	0	0.0520548	0	G|0.999;A|0.001	0.001	weak	.	KRTAP5-7	23	.	NM_001012503	exon1	c.G115A	p.V39I	GTGCCCGTCTGCT	.	PASS	Atlas-SNP
CHSY1	22856	hgsc.bcm.edu	37	15	101718097	101718097	+	Silent	SNP	C	C	G	rs28364839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	50	89	0	0.561798	0	C|0.724;G|0.276	0.276	strong	.	CHSY1	60	.	NM_014918	exon3	c.G1905C	p.V635V	AGTAAACACGAGG	.	PASS	Atlas-SNP
FAM208A	23272	hgsc.bcm.edu	37	3	56667213	56667213	+	Silent	SNP	T	T	C	rs34828128	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	68	179	0	0.435897	0	T|0.987;C|0.013	0.013	strong	.	FAM208A	113	.	NM_001112736	exon18	c.A3606G	p.Q1202Q	AGCTGGTTGAGCA	.	PASS	Atlas-SNP
TADA2A	6871	hgsc.bcm.edu	37	17	35771468	35771468	+	Missense_Mutation	SNP	C	C	T	rs7211875	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	63	0	1	0	C|0.135;N|0.000	.	strong	.	TADA2A	91	.	NM_001488	exon2	c.C16T	p.P6S	TTGGGTCCCTTTA	.	PASS	Atlas-SNP
ENTPD2	954	hgsc.bcm.edu	37	9	139943112	139943112	+	Silent	SNP	A	A	G	rs17853460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	58	86	0	0.651685	0	A|0.802;G|0.198	0.198	strong	.	ENTPD2	30	.	NM_203468	exon9	c.T1485C	p.I495I	CCCCTAAATGGTG	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201058428	201058428	+	Silent	SNP	G	G	A	rs61734621	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	125	220	1	0.478927	0.00454545	G|0.984;A|0.016	0.016	strong	.	CACNA1S	249	.	NM_000069	exon6	c.C858T	p.Y286Y	GCACTGGTACACG	.	PASS	Atlas-SNP
SNAPC2	6618	hgsc.bcm.edu	37	19	7987428	7987428	+	Missense_Mutation	SNP	C	C	T	rs116635738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	55	0	0.5	0	C|0.991;T|0.009	0.009	strong	SNAPC2,colon,carcinoma,0,1	SNAPC2	20	1	NM_003083	exon5	c.C784T	p.R262C	TACCTACGCCTGA	.	PASS	Atlas-SNP
CFI	3426	hgsc.bcm.edu	37	4	110681527	110681527	+	Missense_Mutation	SNP	C	C	T	rs112534524	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	49	157	0	0.365672	0	C|0.998;G|0.000;T|0.002	0.002	strong	.	CFI	59	.	NM_000204	exon6	c.G782A	p.G261D	CCTTTGCCTTGGC	.	PASS	Atlas-SNP
CPN1	1369	hgsc.bcm.edu	37	10	101824954	101824954	+	Silent	SNP	G	G	A	rs3750717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	26	52	0	0.481481	0	G|0.957;A|0.043	0.043	strong	.	CPN1	62	.	NM_001308	exon4	c.C750T	p.L250L	CTGGAAGAGCTTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414238	105414238	+	Missense_Mutation	SNP	C	C	A	rs60754080	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	282	279	1	0.996466	0.00358423	C|0.609;A|0.391	0.391	strong	AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.G7550T	p.G2517V	AGGCTCCCGTCGG	.	PASS	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68938185	68938185	+	Missense_Mutation	SNP	C	C	T	rs1438391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	28	54	0	0.482759	0	C|0.960;T|0.040	0.040	strong	.	TMPRSS11F	79	.	NM_207407	exon5	c.G370A	p.D124N	GAATATCCACACC	.	PASS	Atlas-SNP
ZNF600	162966	hgsc.bcm.edu	37	19	53270623	53270623	+	Missense_Mutation	SNP	G	G	C	rs79890896	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	80	182	0	0.479042	0	G|0.938;C|0.062	0.062	strong	ZNF600,colon,carcinoma,0,1	ZNF600	75	1	NM_198457	exon3	c.C386G	p.P129R	GGCCTAGGAGAAA	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43097765	43097765	+	Missense_Mutation	SNP	G	G	A	rs3732858	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	73	122	0	0.45625	0	G|0.865;A|0.135	0.135	strong	.	FAM198A	23	.	NM_001129908	exon5	c.G1615A	p.G539S	AGCCAAGGCGGAG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79229302	79229302	+	Silent	SNP	A	A	G	rs345528	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	244	236	0	0.987854	0	A|0.864;G|0.136	0.136	strong	.	FRAS1	779	.	NM_001166133	exon15	c.A1617G	p.R539R	GCTGAGAGATGGC	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80750659	80750659	+	Missense_Mutation	SNP	G	G	A	rs11836060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	104	181	0	0.568306	0	G|0.823;A|0.177	0.177	strong	.	OTOGL	235	.	NM_173591	exon48	c.G5957A	p.R1986Q	AAGTTCGACAGGA	.	PASS	Atlas-SNP
ZNF609	23060	hgsc.bcm.edu	37	15	64967654	64967654	+	Silent	SNP	C	C	T	rs16948170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	36	39	0	0.507042	0	C|0.871;T|0.129	0.129	strong	.	ZNF609	106	.	NM_015042	exon4	c.C2601T	p.A867A	GGACGCCGAACAG	.	PASS	Atlas-SNP
RASA3	22821	hgsc.bcm.edu	37	13	114773022	114773022	+	Missense_Mutation	SNP	C	C	T	rs74116414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	20	47	0	0.416667	0	C|0.976;T|0.024	0.024	strong	.	RASA3	83	.	NM_007368	exon18	c.G1729A	p.V577M	TAAGCACGATGGG	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7585795	7585795	+	Missense_Mutation	SNP	C	C	A	rs34884895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	49	90	0	0.544444	0	C|0.991;A|0.009	0.009	strong	.	DSP	306	.	NM_004415	exon24	c.C8300A	p.T2767N	AAGACACCAGCAG	.	PASS	Atlas-SNP
IFT74	80173	hgsc.bcm.edu	37	9	27062721	27062721	+	Missense_Mutation	SNP	C	C	T	rs3429	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	54	157	0	0.457627	0	C|0.900;T|0.100	0.100	strong	.	IFT74	46	.	NM_001099222	exon20	c.C1790T	p.T597I	ATAGCACCAGCGG	.	PASS	Atlas-SNP
CD3G	917	hgsc.bcm.edu	37	11	118221349	118221349	+	Silent	SNP	T	T	C	rs71469175	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	104	236	0	0.527919	0	CT|0.500;TG|0.500	.	alt	.	CD3G	31	.	NM_000073	exon4	c.T390C	p.A130A	CCTTGCTGTTGGG	.	PASS	Atlas-SNP
AKT1	207	hgsc.bcm.edu	37	14	105238783	105238783	+	Silent	SNP	G	G	A	rs11555434	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	60	103	0	0.461538	0	G|0.992;A|0.008	0.008	strong	.	AKT1	379	.	NM_005163	exon12	c.C1179T	p.G393G	GCCCCCGCCAAGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	75	88	0	0.572519	0	G|0.776;A|0.224	0.224	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon58	c.G15540A	p.T5180T	CGTGACGCCCGAG	.	PASS	Atlas-SNP
SIAE	54414	hgsc.bcm.edu	37	11	124539273	124539273	+	Missense_Mutation	SNP	T	T	C	rs12282107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	97	172	0	0.638158	0	T|0.906;C|0.094	0.094	strong	.	SIAE	37	.	NM_170601	exon2	c.A212G	p.K71R	GTCACTTTCTTCA	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	67	140	0	0.515385	0	G|0.907;A|0.093	0.093	strong	.	ZNF407	231	.	NM_001146190	exon1	c.G1578A	p.T526T	TCAGACGTTGTGT	.	PASS	Atlas-SNP
PDCD2	5134	hgsc.bcm.edu	37	6	170892759	170892759	+	Silent	SNP	T	T	A	rs73258640	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	43	90	0	0.452632	0	T|0.985;A|0.015	0.015	strong	.	PDCD2	13	.	NM_002598	exon2	c.A360T	p.T120T	TTCTCCTGTTTCT	.	PASS	Atlas-SNP
CAMSAP3	57662	hgsc.bcm.edu	37	19	7682862	7682862	+	Silent	SNP	C	C	G	rs4134883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	42	126	0	0.4375	0	C|0.969;G|0.031	0.031	strong	.	CAMSAP3	131	.	NM_001080429	exon19	c.C3750G	p.V1250V	GAGCGTCGATGCC	.	PASS	Atlas-SNP
FOXO3	2309	hgsc.bcm.edu	37	6	108882570	108882570	+	Silent	SNP	C	C	T	rs11757217	bycluster;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	10	52	0	0.263158	0	.	.	weak	FOXO3,brain,glioma,0,4	FOXO3	67	4	NM_001455	exon1	c.C159T	p.A53A	GGCCGCCGACTCC	.	scavenged	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26868289	26868289	+	Silent	SNP	C	C	T	rs2230383	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	65	56	0	0.984848	0	C|0.931;T|0.069	0.069	strong	.	ITPR2	270	.	NM_002223	exon8	c.G798A	p.T266T	CAAGGTCGTACGA	.	PASS	Atlas-SNP
IFNA10	3446	hgsc.bcm.edu	37	9	21206916	21206916	+	Missense_Mutation	SNP	T	T	A	rs28368145	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	329	342	1	0.99697	0.00292398	T|0.962;A|0.038	0.038	strong	.	IFNA10	29	.	NM_002171	exon1	c.A181T	p.I61F	GGGGGATTCGGAA	.	PASS	Atlas-SNP
MMP11	4320	hgsc.bcm.edu	37	22	24124471	24124471	+	Silent	SNP	C	C	A	rs28382569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	46	87	0	0.547619	0	A|0.014;C|0.986	0.014	strong	.	MMP11	53	.	NM_005940	exon7	c.C1134A	p.T378T	CCTCACCGAGCTG	.	PASS	Atlas-SNP
PRTG	283659	hgsc.bcm.edu	37	15	55972797	55972797	+	Missense_Mutation	SNP	T	T	C	rs16976466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	173	175	0	0.994253	0	C|0.201;N|0.000	0.201	strong	.	PRTG	110	.	NM_173814	exon5	c.A706G	p.T236A	TAATTGTTGGTGT	.	PASS	Atlas-SNP
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104280	26104280	+	Silent	SNP	T	T	C	rs2229768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	97	0	0.508065	0	T|0.790;C|0.210	0.210	strong	.	HIST1H4C	14	.	NM_003542	exon1	c.T105C	p.I35I	GGCTATTCGCCGT	.	PASS	Atlas-SNP
SRP68	6730	hgsc.bcm.edu	37	17	74036544	74036544	+	Missense_Mutation	SNP	C	C	T	rs75353721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	127	225	2	0.51626	0.00888889	C|0.993;T|0.007	0.007	strong	SRP68,colon,carcinoma,+2,1	SRP68	61	1	NM_014230	exon15	c.G1612A	p.A538T	GATGAGCGTCGTT	.	scavenged	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186148	12186148	+	Silent	SNP	T	T	C	rs10424893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	15	31	0	0.517241	0	T|0.725;C|0.275	0.275	strong	ZNF844,NS,NS,+2,1	ZNF844	69	1	NM_001136501	exon4	c.T213C	p.V71V	GAGAGTTGATGAA	.	scavenged	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6138575	6138575	+	Missense_Mutation	SNP	C	C	T	rs141087261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	74	90	0	0.564885	0	C|0.992;T|0.008	0.008	strong	.	VWF	338	.	NM_000552	exon22	c.G2900A	p.G967D	GCTTTGCCCAGCA	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218683139	218683139	+	Missense_Mutation	SNP	G	G	A	rs34291329	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	30	63	0	0.38961	0	G|0.932;A|0.068	0.068	strong	.	TNS1	251	.	NM_022648	exon24	c.C3604T	p.P1202S	TGCTGGGATTGAT	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782395	54782395	+	Missense_Mutation	SNP	A	A	G	rs7246737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	76	205	0	0.397906	0	A|0.971;G|0.029	0.029	strong	.	LILRB2	94	.	NM_005874	exon7	c.T977C	p.F326S	GAGATGAAGGGTG	.	PASS	Atlas-SNP
HSD17B4	3295	hgsc.bcm.edu	37	5	118877660	118877660	+	Missense_Mutation	SNP	A	A	G	rs28943594	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	87	222	0	0.505814	0	A|0.967;G|0.033	0.033	strong	.	HSD17B4	63	.	NM_001199291	exon25	c.A2257G	p.M753V	CTTCAGATGATTC	.	PASS	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24797913	24797913	+	Silent	SNP	C	C	T	rs1220546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	36	79	0	0.439024	0	C|0.720;T|0.280	0.280	strong	.	SPATA13	92	.	NM_001166271	exon2	c.C846T	p.D282D	CCATGACGCACGG	.	PASS	Atlas-SNP
NUGGC	389643	hgsc.bcm.edu	37	8	27925220	27925220	+	Silent	SNP	A	A	G	rs114951850	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	130	212	0	0.526316	0	A|0.985;G|0.015	0.015	strong	.	.	.	.	NM_001010906	exon6	c.T522C	p.H174H	CGTCCTATGCAGG	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	37	12	1955786	1955786	+	Silent	SNP	G	G	A	rs11836202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	35	33	0	0.636364	0	G|0.860;A|0.140	0.140	strong	.	CACNA2D4	220	.	NM_172364	exon24	c.C2316T	p.F772F	GCCCACGAACAAG	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95923644	95923644	+	Missense_Mutation	SNP	C	C	T	rs74082143	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	38	77	0	0.44186	0	C|0.989;T|0.011	0.011	strong	.	SYNE3	130	.	NM_152592	exon4	c.G659A	p.R220Q	TGCTCCCGGGCCA	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167095881	167095881	+	Missense_Mutation	SNP	G	G	A	rs3795605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	99	186	0	0.469194	0	G|0.731;A|0.269	0.269	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G1513A	p.A505T	GAGGCGGCAGACA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs115287948	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	44	461	0	0.161765	0	G|0.679;A|0.321	0.321	strong	SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	NM_001040022	exon3	c.G394A	p.V132M	GATGACGTGGAGT	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107979437	107979437	+	Silent	SNP	G	G	A	rs73253702	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	97	144	0	0.678322	0	G|0.942;A|0.058	0.058	strong	.	IRS4	253	.	NM_003604	exon1	c.C138T	p.T46T	CGACCCGGTCCCA	.	PASS	Atlas-SNP
PIP4K2A	5305	hgsc.bcm.edu	37	10	22830842	22830842	+	Silent	SNP	C	C	T	rs61731109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	41	109	0	0.418367	0	C|0.976;T|0.024	0.024	strong	.	PIP4K2A	59	.	NM_005028	exon8	c.G927A	p.P309P	TCCCACCGGGTGG	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30668374	30668374	+	Silent	SNP	G	G	A	rs9468812	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	107	0	0.490196	0	G|0.958;A|0.042	0.042	strong	.	MDC1	218	.	NM_014641	exon15	c.C6138T	p.F2046F	ATGAGGGAAGTCC	.	PASS	Atlas-SNP
SMPDL3B	27293	hgsc.bcm.edu	37	1	28285123	28285123	+	Missense_Mutation	SNP	G	G	A	rs34560878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	86	146	0	0.49711	0	G|0.986;A|0.014	0.014	strong	.	SMPDL3B	54	.	NM_014474	exon8	c.G1142A	p.R381H	TGGACCGCATCGC	.	PASS	Atlas-SNP
BPIFB1	92747	hgsc.bcm.edu	37	20	31877770	31877770	+	Missense_Mutation	SNP	C	C	T	rs114635109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	63	115	0	0.5625	0	C|0.988;T|0.012	0.012	strong	.	.	.	.	NM_033197	exon4	c.C337T	p.P113S	AAGATCCCCCTGG	.	PASS	Atlas-SNP
FAM107A	11170	hgsc.bcm.edu	37	3	58552329	58552329	+	Missense_Mutation	SNP	C	C	G	rs11539086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	23	102	0	0.338235	0	C|0.892;G|0.108	0.108	strong	.	FAM107A	33	.	NM_001076778	exon4	c.G421C	p.E141Q	CTCTCTCTTCGCT	.	PASS	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26107840	26107840	+	Silent	SNP	G	G	A	rs34719207	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	70	123	0	0.546875	0	G|0.996;A|0.004	0.004	strong	.	NOS2	113	.	NM_000625	exon9	c.C957T	p.F319F	GATTTCGAAGAGC	.	PASS	Atlas-SNP
DCDC2B	149069	hgsc.bcm.edu	37	1	32677370	32677370	+	Silent	SNP	C	C	T	rs182464428	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	36	85	0	0.473684	0	C|0.998;T|0.002	0.002	strong	.	DCDC2B	24	.	NM_001099434	exon3	c.C327T	p.P109P	TCCTCCCGTGACT	.	PASS	Atlas-SNP
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	32	114	0	0.323232	0	C|0.901;G|0.099	0.099	strong	.	ENPP4	44	.	NM_014936	exon3	c.C954G	p.A318A	GGTTGCCGATGAA	.	PASS	Atlas-SNP
CBL	867	hgsc.bcm.edu	37	11	119170362	119170362	+	Silent	SNP	C	C	T	rs1893177	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	47	113	0	0.594937	0	C|0.948;T|0.052	0.052	strong	.	CBL	408	.	NM_005188	exon16	c.C2592T	p.L864L	GAACCTCATGAGT	.	PASS	Atlas-SNP
LOXL1	4016	hgsc.bcm.edu	37	15	74219582	74219582	+	Missense_Mutation	SNP	G	G	A	rs3825942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	16	0	1	0	G|0.767;A|0.233	0.233	strong	.	LOXL1	25	.	NM_005576	exon1	c.G458A	p.G153D	ACGGGGGCTCCGC	.	PASS	Atlas-SNP
GGT5	2687	hgsc.bcm.edu	37	22	24622124	24622124	+	Silent	SNP	G	G	A	rs73879043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	54	122	0	0.534653	0	G|0.981;A|0.019	0.019	strong	.	GGT5	61	.	NM_001099781	exon8	c.C1149T	p.G383G	CCCGTGGCCCCAG	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10620386	10620386	+	Silent	SNP	A	A	G	rs1051419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	329	297	0	0.99697	0	G|0.694;C|0.000;A|0.306	0.694	strong	JAG1_ENST00000254958,NS,carcinoma,0,1	JAG1	213	1	NM_000214	exon26	c.T3417C	p.Y1139Y	GTTCTCATAATCC	.	PASS	Atlas-SNP
RASAL3	64926	hgsc.bcm.edu	37	19	15569378	15569378	+	Missense_Mutation	SNP	G	G	C	rs58123634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	65	118	0	0.451389	0	G|0.967;C|0.033	0.033	strong	.	RASAL3	49	.	NM_022904	exon7	c.C751G	p.L251V	GGTGCAGTGGCCA	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53680135	53680135	+	Silent	SNP	C	C	T	rs61741367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	32	48	0	0.438356	0	C|0.957;T|0.043	0.043	strong	.	ESPL1	158	.	NM_012291	exon18	c.C3615T	p.S1205S	AGCTTCCCTGAAT	.	PASS	Atlas-SNP
VTI1B	10490	hgsc.bcm.edu	37	14	68141105	68141105	+	Silent	SNP	C	C	T	rs2234510	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	32	24	0	0.507937	0	C|0.973;T|0.027	0.027	strong	.	VTI1B	15	.	NM_006370	exon1	c.G102A	p.G34G	CGCCGTCCCCAGC	.	PASS	Atlas-SNP
ZBED4	9889	hgsc.bcm.edu	37	22	50278588	50278588	+	Silent	SNP	C	C	T	rs61731526	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	19	42	0	0.345455	0	C|0.996;T|0.004	0.004	strong	.	ZBED4	102	.	NM_014838	exon2	c.C1278T	p.S426S	GGCGTCCTCTCCT	.	PASS	Atlas-SNP
IP6K3	117283	hgsc.bcm.edu	37	6	33694659	33694659	+	Silent	SNP	G	G	A	rs34252064	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	68	108	0	0.548387	0	G|0.901;A|0.099	0.099	strong	.	IP6K3	52	.	NM_001142883	exon5	c.C438T	p.S146S	GGGCTCGGACCTC	.	PASS	Atlas-SNP
OPRK1	4986	hgsc.bcm.edu	37	8	54147470	54147470	+	Silent	SNP	G	G	A	rs7815824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	55	110	0	0.466102	0	G|0.927;A|0.073	0.073	strong	.	OPRK1	90	.	NM_000912	exon3	c.C459T	p.S153S	GTCCACGCTCATC	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186611	12186611	+	Missense_Mutation	SNP	A	A	G	rs7259684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	62	0	0.493333	0	A|0.854;G|0.146	0.146	strong	.	ZNF844	69	.	NM_001136501	exon4	c.A676G	p.K226E	CCATATAAATGTA	.	PASS	Atlas-SNP
ZNF264	9422	hgsc.bcm.edu	37	19	57723182	57723182	+	Silent	SNP	C	C	T	rs61730346	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	47	65	0	0.580247	0	C|0.990;T|0.010	0.010	strong	.	ZNF264	65	.	NM_003417	exon4	c.C717T	p.T239T	GAAAACCTTTATT	.	PASS	Atlas-SNP
KIAA0141	9812	hgsc.bcm.edu	37	5	141309752	141309752	+	Missense_Mutation	SNP	A	A	G	rs76602789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	77	104	0	0.546099	0	A|0.980;G|0.020	0.020	strong	.	KIAA0141	44	.	NM_001142603	exon7	c.A667G	p.K223E	CAAGATAAATCAA	.	PASS	Atlas-SNP
GANAB	23193	hgsc.bcm.edu	37	11	62396263	62396263	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	3	144	0	0.0184049	0	.	.	none	GANAB_ENST00000346178,NS,carcinoma,+1,3	GANAB	110	3	NM_198335	exon18	c.C2224T	p.R742W	CTTCCCGATGGGC	.	scavenged	Atlas-SNP
PIAS4	51588	hgsc.bcm.edu	37	19	4012971	4012971	+	Silent	SNP	C	C	T	rs61729790	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	163	198	0	1	0	C|0.910;T|0.090	0.090	strong	.	PIAS4	40	.	NM_015897	exon2	c.C78T	p.F26F	GGGTTTCGTGGGC	.	PASS	Atlas-SNP
MXD3	83463	hgsc.bcm.edu	37	5	176734945	176734945	+	Missense_Mutation	SNP	C	C	A	rs35691394	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	22	23	0	0.564103	0	C|0.997;A|0.003	0.003	strong	.	MXD3	13	.	NM_001142935	exon5	c.G342T	p.Q114H	GGCCCGCTGCTCC	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	176011968	176011968	+	Missense_Mutation	SNP	G	G	A	rs114527399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	80	0	0.468354	0	G|0.996;A|0.004	0.004	strong	.	CDHR2	152	.	NM_017675	exon19	c.G2686A	p.A896T	GTGCGGGCCTGTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276889	152276889	+	Silent	SNP	A	A	G	rs3126067	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	413	406	417	2	0.983051	0.00479616	A|0.637;G|0.363	0.363	strong	.	FLG	900	.	NM_002016	exon3	c.T10473C	p.N3491N	TTCGTCATTACGA	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141130695	141130695	+	Silent	SNP	C	C	T	rs16843864	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	44	119	0	0.453608	0	C|0.863;T|0.137	0.137	strong	.	LRP1B	1315	.	NM_018557	exon69	c.G10650A	p.E3550E	ACTTGTCTCACAA	.	PASS	Atlas-SNP
CXorf30	645090	hgsc.bcm.edu	37	X	36385156	36385156	+	Silent	SNP	A	A	G	rs6632593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	71	148	0	0.533835	0	A|0.841;G|0.159	0.159	strong	.	CXorf30	76	.	NM_001098843	exon17	c.A1437G	p.E479E	TACTGAACCTGAT	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133682285	133682285	+	Silent	SNP	C	C	T	rs34608222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	56	106	0	0.478632	0	C|0.986;T|0.014	0.014	strong	.	EXOC4	118	.	NM_021807	exon15	c.C2247T	p.L749L	GGATCTCCCCCCA	.	PASS	Atlas-SNP
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	70	113	0	0.546875	0	G|0.765;A|0.235	0.235	strong	.	SPSB1	22	.	NM_025106	exon2	c.G201A	p.V67V	CTTTGTGAAGGAG	.	PASS	Atlas-SNP
MRPL19	9801	hgsc.bcm.edu	37	2	75874015	75874015	+	Missense_Mutation	SNP	C	C	G	rs11552948	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	134	211	0	0.503759	0	C|0.980;G|0.020	0.020	strong	.	MRPL19	21	.	NM_014763	exon1	c.C82G	p.P28A	CTCCCCCCGCCGG	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124135438	124135438	+	Missense_Mutation	SNP	G	G	A	rs2512167	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	238	244	1	1	0.00409836	G|0.522;N|0.001	.	strong	.	.	.	.	NM_001005198	exon1	c.G716A	p.G239E	TTAGTGGAATTAA	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102584104	102584104	+	Missense_Mutation	SNP	T	T	G	rs35866072	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	41	101	0	0.44086	0	T|0.907;G|0.093	0.093	strong	.	MMP8	68	.	NM_002424	exon10	c.A1379C	p.K460T	AGCCATTTATTGC	.	PASS	Atlas-SNP
ITIH4	3700	hgsc.bcm.edu	37	3	52853480	52853480	+	Missense_Mutation	SNP	T	T	A	rs2276814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	124	241	0	0.488189	0	T|0.888;A|0.112	0.112	strong	.	ITIH4	74	.	NM_002218	exon17	c.A2006T	p.Q669L	CCAAGTTGCCTGG	.	PASS	Atlas-SNP
SLC13A3	64849	hgsc.bcm.edu	37	20	45194904	45194904	+	Silent	SNP	C	C	G	rs202391	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	63	127	0	0.470149	0	C|0.801;G|0.199	0.199	strong	.	SLC13A3	88	.	NM_022829	exon11	c.G1458C	p.A486A	GATGGTCGCCGTG	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242062162	242062162	+	Silent	SNP	C	C	T	rs2302050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	55	104	0	0.474138	0	C|0.755;T|0.245	0.245	strong	.	PASK	230	.	NM_015148	exon12	c.G3057A	p.K1019K	TTTTTCCTTGTCC	.	PASS	Atlas-SNP
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs55900504		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	151	156	0	0.993421	0	.	.	weak	IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	NM_006435	exon1	c.T122C	p.M41T	CCCCGATGTCCAC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680438	100680438	+	Missense_Mutation	SNP	G	G	C	rs112926140	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	5	144	0	0.0367647	0	A|0.001;G|0.999	.	strong	MUC17,right_upper_lobe,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G5741C	p.S1914T	ACGGTAGCAGCAT	.	scavenged	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891126	44891126	+	Silent	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	2	85	2	0.0232558	0.0235294	.	.	none	ZNF285,NS,carcinoma,0,1	ZNF285	86	1	NM_152354	exon4	c.A1281T	p.P427P	CCTATATGGTTTC	.	scavenged	Atlas-SNP
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	153	272	0	0.472222	0	A|0.898;G|0.102	0.102	strong	.	ZRANB2	75	.	NM_203350	exon5	c.T342C	p.Y114Y	TTCTATATATTCA	.	PASS	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51738920	51738920	+	Missense_Mutation	SNP	T	T	C	rs61736475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	92	0	0.470588	0	T|0.895;C|0.105	0.105	strong	.	CD33	55	.	NM_001772	exon6	c.T913C	p.S305P	ACAGGGTCAGCCT	.	PASS	Atlas-SNP
MME	4311	hgsc.bcm.edu	37	3	154802114	154802114	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	3	89	0	0.0326087	0	.	.	none	MME,NS,carcinoma,+1,1	MME	133	1	NM_007287	exon2	c.A158G	p.D53G	CCTACGATGGTGA	.	scavenged	Atlas-SNP
RASGRF2	5924	hgsc.bcm.edu	37	5	80419576	80419576	+	Silent	SNP	A	A	C	rs34593336	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	60	139	0	0.487805	0	A|0.922;C|0.078	0.078	strong	.	RASGRF2	165	.	NM_006909	exon16	c.A2586C	p.R862R	CTATCGACAGCCT	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	120	0	1	0	A|0.690;G|0.310	0.310	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon11	c.T1456C	p.L486L	CTTCCAAGTCTTC	.	PASS	Atlas-SNP
MIB2	142678	hgsc.bcm.edu	37	1	1562536	1562536	+	Silent	SNP	G	G	A	rs11544452	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	67	99	0	0.567797	0	G|0.860;A|0.140	0.140	strong	.	MIB2	62	.	NM_080875	exon11	c.G1668A	p.A556A	GGTGGCGCTGGGT	.	PASS	Atlas-SNP
BLM	641	hgsc.bcm.edu	37	15	91346923	91346923	+	Silent	SNP	C	C	A	rs2227934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	36	84	0	0.418605	0	C|0.848;A|0.152	0.152	strong	.	BLM	122	.	NM_000057	exon18	c.C3531A	p.A1177A	TAAAGCCCAAACT	.	PASS	Atlas-SNP
SPAG7	9552	hgsc.bcm.edu	37	17	4863540	4863540	+	Missense_Mutation	SNP	T	T	C	rs73343382	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	95	197	0	0.519126	0	T|0.978;C|0.022	0.022	strong	.	SPAG7	22	.	NM_004890	exon4	c.A316G	p.I106V	TGAAGATCATGAC	.	PASS	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133327457	133327457	+	Silent	SNP	T	T	C	rs1051772	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	121	0	1	0	T|0.900;C|0.100	0.100	strong	.	TOPBP1	218	.	NM_007027	exon27	c.A4347G	p.S1449S	AACTCCTGAGTCA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47924233	47924233	+	Silent	SNP	G	G	A	rs79566365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	36	87	0	0.391304	0	G|0.951;A|0.049	0.049	strong	.	PKD1L1	328	.	NM_138295	exon19	c.C3228T	p.D1076D	TTGAATGTCACTG	.	PASS	Atlas-SNP
C6orf195	154386	hgsc.bcm.edu	37	6	2624053	2624053	+	Missense_Mutation	SNP	T	T	A	rs17135340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	59	126	0	0.556604	0	A|0.169;N|0.000	0.169	strong	.	C6orf195	10	.	NM_152554	exon3	c.A4T	p.I2F	GATAGATCATCAG	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2186100	2186100	+	Silent	SNP	C	C	T	rs749240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	274	283	0	0.992754	0	C|0.573;N|0.001	.	strong	.	SMG6	97	.	NM_017575	exon8	c.G2502A	p.Q834Q	CCGCCACTGGTCA	.	PASS	Atlas-SNP
DBNDD2	55861	hgsc.bcm.edu	37	20	44038574	44038574	+	Missense_Mutation	SNP	A	A	G	rs1127497	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	106	0	0.990291	0	A|0.252;G|0.748	0.748	strong	.	DBNDD2	30	.	NM_001048225	exon3	c.A586G	p.M196V	GCAGGGATGGACA	.	PASS	Atlas-SNP
ASB16	92591	hgsc.bcm.edu	37	17	42248205	42248205	+	Silent	SNP	C	C	T	rs56265171	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	103	180	0	0.542105	0	C|0.967;T|0.033	0.033	strong	.	ASB16	34	.	NM_080863	exon1	c.C48T	p.L16L	CTCTCTCCGCCTG	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14824088	14824088	+	Missense_Mutation	SNP	T	T	C	rs7864984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	44	91	0	0.478261	0	T|0.978;C|0.022	0.022	strong	.	FREM1	261	.	NM_144966	exon13	c.A2104G	p.M702V	CCACCATAAATAA	.	PASS	Atlas-SNP
NLN	57486	hgsc.bcm.edu	37	5	65054587	65054587	+	Missense_Mutation	SNP	G	G	A	rs34339013	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	70	127	0	0.542636	0	G|0.973;A|0.027	0.027	strong	.	NLN	51	.	NM_020726	exon2	c.G235A	p.G79S	ATGCTCGGTATTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1271321	1271321	+	Missense_Mutation	SNP	C	C	G	rs61732888	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	353	185	345	0	0.524079	0	C|0.633;G|0.367	0.367	strong	MUC5B,caecum,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon31	c.C13211G	p.A4404G	CTGCAGCCACTGG	.	PASS	Atlas-SNP
TEX38	374973	hgsc.bcm.edu	37	1	47138819	47138819	+	Missense_Mutation	SNP	T	T	G	rs614486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	50	72	0	0.561798	0	T|0.461;G|0.539	0.539	strong	.	.	.	.	NM_001145474	exon2	c.T312G	p.D104E	GTGGGATTTGGAC	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20898058	20898058	+	Silent	SNP	G	G	C	rs79604136	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	40	58	0	0.493827	0	G|0.970;C|0.030	0.030	strong	.	KLHL33	37	.	NM_001109997	exon2	c.C777G	p.P259P	GCGTCCGGGGGCA	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	200	225	0	0.990099	0	C|0.559;T|0.441	0.441	strong	.	EPHB1	519	.	NM_004441	exon3	c.C435T	p.S145S	TGAGAGCTTCTCC	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	37	15	70957106	70957106	+	Silent	SNP	A	A	G	rs78551559	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	101	203	0	0.497537	0	A|0.983;G|0.017	0.017	strong	.	UACA	235	.	NM_018003	exon17	c.T4008C	p.N1336N	AAGGCCATTGAGT	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107743664	107743664	+	Silent	SNP	A	A	G	rs402113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	24	39	0	0.648649	0	A|0.701;G|0.299	0.299	strong	.	LAMB4	253	.	NM_007356	exon10	c.T1005C	p.N335N	GTGGCTATTACAG	.	PASS	Atlas-SNP
C19orf21	126353	hgsc.bcm.edu	37	19	757483	757483	+	Silent	SNP	G	G	A	rs35484463	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	42	95	0	0.442105	0	G|0.982;A|0.018	0.018	strong	.	C19orf21	56	.	NM_173481	exon2	c.G537A	p.T179T	GTCCACGCCCCTG	.	PASS	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	44	128	0	0.369748	0	A|0.834;G|0.166	0.166	strong	RTN4IP1,NS,carcinoma,-2,1	RTN4IP1	31	1	NM_032730	exon9	c.T1182C	p.N394N	AACAACATTAATT	.	PASS	Atlas-SNP
LRCH1	23143	hgsc.bcm.edu	37	13	47127813	47127813	+	Silent	SNP	C	C	T	rs45540131	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	96	98	0	1	0	C|0.861;T|0.139	0.139	strong	.	LRCH1	104	.	NM_015116	exon1	c.C282T	p.H94H	CGGGCACGACCTC	.	PASS	Atlas-SNP
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630485	51630485	+	Missense_Mutation	SNP	C	C	A	rs273688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	58	121	0	0.552381	0	C|0.895;A|0.105	0.105	strong	SIGLEC9,NS,carcinoma,+1,1	SIGLEC9	85	1	NM_001198558	exon4	c.C947A	p.A316D	ATGCAGCTGAATT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801403	27801403	+	Missense_Mutation	SNP	C	C	G	rs1919125	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	301	326	0	1	0	C|0.375;G|0.625	0.625	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1964G	p.T655S	CATGTACTCAAGT	.	PASS	Atlas-SNP
SIAE	54414	hgsc.bcm.edu	37	11	124524627	124524627	+	Silent	SNP	A	A	G	rs1942663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	47	72	1	0.516484	0.0138889	A|0.804;G|0.196	0.196	strong	SIAE,scalp,malignant_melanoma,-1,2	SIAE	37	2	NM_170601	exon4	c.T468C	p.S156S	AGAGACAGAGAGG	.	scavenged	Atlas-SNP
SLC2A11	66035	hgsc.bcm.edu	37	22	24226890	24226890	+	Missense_Mutation	SNP	G	G	A	rs60699980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	109	269	0	0.465812	0	G|0.966;A|0.034	0.034	strong	.	SLC2A11	32	.	NM_030807	exon13	c.G1366A	p.A456T	TGTGGGGCCATCT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801739	27801739	+	Missense_Mutation	SNP	T	T	C	rs13416968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	104	156	0	0.474886	0	T|0.986;C|0.014	0.014	strong	.	C2orf16	357	.	NM_032266	exon1	c.T2300C	p.I767T	TGGATATAAAAAA	.	PASS	Atlas-SNP
EVL	51466	hgsc.bcm.edu	37	14	100563868	100563868	+	Silent	SNP	G	G	A	rs35006525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	51	77	0	0.548387	0	G|0.986;A|0.014	0.014	strong	.	EVL	42	.	NM_016337	exon3	c.G231A	p.T77T	GGCCACGCCAACC	.	PASS	Atlas-SNP
CES5A	221223	hgsc.bcm.edu	37	16	55880534	55880534	+	Silent	SNP	G	G	C	rs11860488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	92	153	0	0.571429	0	G|0.695;C|0.305	0.305	strong	.	CES5A	206	.	NM_001190158	exon14	c.C1644G	p.L548L	CAGCTGGAGGTAC	.	PASS	Atlas-SNP
CAMK2N2	94032	hgsc.bcm.edu	37	3	183978936	183978936	+	Silent	SNP	G	G	A	rs75699255	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	31	42	0	0.62	0	G|0.962;A|0.038	0.038	strong	.	CAMK2N2	2	.	NM_033259	exon1	c.C138T	p.P46P	CAGCTTGGGGGGT	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	10793	10793	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	6	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C34T	p.L12L	ATATTACTACCAC	.	PASS	Atlas-SNP
BCR	613	hgsc.bcm.edu	37	22	23651650	23651650	+	Missense_Mutation	SNP	A	A	G	rs71316760		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	108	330	0	0.367347	0	A|0.500;G|0.500	0.500	weak	BCR,NS,carcinoma,0,1	BCR	74	1	NM_004327	exon17	c.A3052G	p.T1018A	CAGCGCACCGTCA	.	scavenged	Atlas-SNP
CERS3	204219	hgsc.bcm.edu	37	15	101041921	101041921	+	Missense_Mutation	SNP	T	T	C	rs60405735	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	49	88	0	0.49	0	T|0.888;C|0.112	0.112	strong	.	.	.	.	NM_178842	exon4	c.A134G	p.Y45C	AAAGCATATGGAA	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	128	1	1	0.0078125	C|0.213;N|0.000	0.213	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon7	c.A880G	p.I294V	TACTGATGTTTGA	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38512956	38512956	+	Silent	SNP	A	A	G	rs1133001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	15	39	0	0.441176	0	A|0.475;G|0.525	0.525	strong	.	TTC3	182	.	NM_001001894	exon20	c.A1755G	p.V585V	AAAAGTATATTTG	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	14	12	0	0.388889	0	G|0.736;A|0.264	0.264	strong	KIF19,NS,carcinoma,0,1	KIF19	102	1	NM_153209	exon18	c.G2370A	p.S790S	GCGCTCGCGGGCC	.	PASS	Atlas-SNP
OXCT2	64064	hgsc.bcm.edu	37	1	40236074	40236074	+	Missense_Mutation	SNP	A	A	C	rs34458767	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	73	247	0	1	0	A|0.750;C|0.250	0.250	weak	.	OXCT2	12	.	NM_022120	exon1	c.T854G	p.L285R	TCTTTCAGGATCG	.	PASS	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19547357	19547357	+	Silent	SNP	A	A	G	rs10492785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	65	138	0	0.416667	0	A|0.802;G|0.198	0.198	strong	CCP110,NS,carcinoma,0,1	CCP110	57	1	NM_001199022	exon4	c.A366G	p.T122T	TGCTACATTTCCA	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73570718	73570718	+	Missense_Mutation	SNP	C	C	G	rs1126939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	59	100	0	0.5	0	C|0.621;G|0.379	0.379	strong	.	LLGL2	155	.	NM_004524	exon24	c.C2981G	p.P994R	TCGAGCCGCCGTG	.	PASS	Atlas-SNP
ARAP1	116985	hgsc.bcm.edu	37	11	72403832	72403832	+	Splice_Site	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	29	48	0	0.453125	0	.	.	none	.	ARAP1	168	.	NM_015242	exon29	c.3220-2A>G	.	TGGCTCTGTTTGA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17273893	17273893	+	Silent	SNP	G	G	T	rs7256689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	50	108	0	0.46729	0	G|0.238;T|0.762	0.762	strong	.	MYO9B	264	.	NM_001130065	exon10	c.G1632T	p.L544L	GCAGCTGCAGTAT	.	PASS	Atlas-SNP
GOLGA8B	440270	hgsc.bcm.edu	37	15	34825091	34825091	+	Missense_Mutation	SNP	T	T	A	rs200439797		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1873	467	1385	0	0.249333	0	T|0.998;A|0.002	0.002	weak	GOLGA8B_ENST00000267731,right_upper_lobe,carcinoma,+1,2	GOLGA8B	7	2	NM_001023567	exon3	c.A241T	p.R81W	TGGACCTCGAGTT	.	scavenged	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744183	54744183	+	Missense_Mutation	SNP	A	A	G	rs76090367	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	63	333	1	0.217241	0.003003	A|0.989;G|0.011	0.011	strong	LILRA6,nipple,malignant_melanoma,+1,1	LILRA6	75	1	NM_024318	exon6	c.T1225C	p.F409L	TGGGGAAAGACAG	.	scavenged	Atlas-SNP
TRH	7200	hgsc.bcm.edu	37	3	129694681	129694681	+	Missense_Mutation	SNP	C	C	G	rs5658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	102	223	0	0.485714	0	C|0.839;G|0.161	0.161	strong	.	TRH	30	.	NM_007117	exon2	c.C22G	p.L8V	TTGCTGCTCGCTC	.	PASS	Atlas-SNP
KLK8	11202	hgsc.bcm.edu	37	19	51504415	51504415	+	Silent	SNP	G	G	C	rs34542531	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	26	67	0	0.509804	0	G|0.975;C|0.025	0.025	strong	.	KLK8	46	.	NM_144505	exon2	c.C9G	p.R3R	TCGGGGGCGTCCC	.	PASS	Atlas-SNP
ZFP91	80829	hgsc.bcm.edu	37	11	58378424	58378424	+	Missense_Mutation	SNP	A	A	G	rs8373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	18	24	0	0.473684	0	A|0.780;G|0.220	0.220	strong	.	ZFP91	66	.	NM_053023	exon5	c.A619G	p.S207G	TTTAGTAGTGAAG	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101606084	101606084	+	Silent	SNP	G	G	A	rs116529941	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	75	111	0	0.551471	0	G|0.997;A|0.003	0.003	strong	.	LRRK1	310	.	NM_024652	exon32	c.G5442A	p.A1814A	CATCGCGGACGTG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	28	51	0	0.5	0	G|0.602;C|0.398	0.398	strong	.	.	.	.	NM_001080826	exon2	c.C1727G	p.S576C	CCGCCAGAGCTCC	.	PASS	Atlas-SNP
MAGEC3	139081	hgsc.bcm.edu	37	X	140967165	140967165	+	Missense_Mutation	SNP	T	T	C	rs11095909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	458	457	421	1	0.997817	0.0023753	T|0.639;C|0.361	0.361	strong	.	MAGEC3	228	.	NM_138702	exon3	c.T463C	p.S155P	ACCCTTTCCCTTC	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	31893307	31893307	+	Splice_Site	SNP	T	T	G	rs1800275	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	83	177	0	0.466292	0	T|0.809;0|0.003	.	strong	.	DMD	2127	.	NM_004009	exon49	c.7083+1A>C	.	CTACCTTAACGTC	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184550501	184550501	+	Missense_Mutation	SNP	A	A	G	rs9830734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	78	182	0	0.453488	0	A|0.480;G|0.520	0.520	strong	.	VPS8	109	.	NM_001009921	exon4	c.A247G	p.I83V	TCTTTTATTCTTG	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114397192	114397192	+	Silent	SNP	C	C	T	rs140397506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	63	115	0	0.557522	0	C|0.989;T|0.011	0.011	strong	.	RBM19	117	.	NM_001146699	exon5	c.G396A	p.E132E	CTGGAACTCTGTA	.	PASS	Atlas-SNP
SCN11A	11280	hgsc.bcm.edu	37	3	38945560	38945560	+	Silent	SNP	A	A	G	rs4073113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	139	188	1	0.992857	0.00531915	A|0.397;G|0.603	0.603	strong	.	SCN11A	296	.	NM_014139	exon12	c.T1638C	p.C546C	TTCTCCACAAGGG	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761957	130761957	+	Silent	SNP	A	A	G	rs3813359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	48	72	0	0.489796	0	A|0.770;G|0.230	0.230	strong	.	TMEM200A	108	.	NM_001258277	exon3	c.A390G	p.P130P	TGGCCCATTCACC	.	PASS	Atlas-SNP
PFN4	375189	hgsc.bcm.edu	37	2	24344060	24344060	+	Silent	SNP	T	T	G	rs33913065	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	62	139	0	0.512397	0	T|0.834;G|0.166	0.166	strong	.	PFN4	16	.	NM_199346	exon3	c.A228C	p.A76A	TTCATCTGCCCGG	.	PASS	Atlas-SNP
ZNF790	388536	hgsc.bcm.edu	37	19	37310344	37310344	+	Missense_Mutation	SNP	T	T	C	rs3745775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	28	55	0	0.538462	0	T|0.723;C|0.277	0.277	strong	.	ZNF790	89	.	NM_206894	exon5	c.A902G	p.Q301R	ATTCTCTGATGTC	.	PASS	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186195	39186195	+	Missense_Mutation	SNP	C	C	T	rs141392271	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	54	114	0	0.482143	0	C|0.898;T|0.102	0.102	strong	.	KRTAP1-4	4	.	NM_001257305	exon1	c.G136A	p.G46S	CATAGCCAATGCC	.	PASS	Atlas-SNP
FAM71A	149647	hgsc.bcm.edu	37	1	212798977	212798977	+	Missense_Mutation	SNP	A	A	G	rs3122712	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	59	0	0.509804	0	A|0.697;G|0.303	0.303	strong	.	FAM71A	87	.	NM_153606	exon1	c.A758G	p.N253S	CCACTAATGTGCT	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	37	12	53189446	53189446	+	Silent	SNP	C	C	T	rs117364830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	24	178	0	0.130435	0	C|0.971;T|0.029	0.029	strong	KRT3,NS,carcinoma,0,1	KRT3	65	1	NM_057088	exon1	c.G381A	p.G127G	ACCAGCCCCTCCA	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6174423	6174423	+	Silent	SNP	T	T	A	rs1800375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	85	0	1	0	T|0.770;A|0.230	0.230	strong	VWF,NS,carcinoma,0,1	VWF	338	1	NM_000552	exon11	c.A1173T	p.T391T	TTGACCTGTGACA	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7965669	7965669	+	Silent	SNP	C	C	T	rs3745385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	89	144	0	0.549383	0	C|0.956;T|0.044	0.044	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.C2262T	p.G754G	CAAAGGCAACCGC	.	PASS	Atlas-SNP
ACSS2	55902	hgsc.bcm.edu	37	20	33513983	33513983	+	Missense_Mutation	SNP	G	G	C	rs45486997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	95	185	0	0.521978	0	G|0.968;C|0.032	0.032	strong	.	ACSS2	75	.	NM_001076552	exon17	c.G1841C	p.G614A	TGGTGGGCCACCC	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187557863	187557863	+	Missense_Mutation	SNP	G	G	A	rs60068521	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	155	306	0	0.516667	0	G|0.999;A|0.001	0.001	strong	.	FAT1	500	.	NM_005245	exon5	c.C3848T	p.P1283L	GCATTGGGGCCCT	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24349482	24349482	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	57	130	0	0.587629	0	.	.	none	ADAM7,colon,carcinoma,-2,1	ADAM7	165	1	NM_003817	exon14	c.G1423A	p.G475S	TGCACTGGCCACT	.	PASS	Atlas-SNP
GBP4	115361	hgsc.bcm.edu	37	1	89655783	89655783	+	Missense_Mutation	SNP	T	T	C	rs41506251		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	145	251	0	0.516014	0	T|1.000;|0.000	.	weak	GBP4,colon,carcinoma,0,1	GBP4	89	1	NM_052941	exon7	c.A1135G	p.I379V	CTGCAATGGCTTC	.	PASS	Atlas-SNP
MUT	4594	hgsc.bcm.edu	37	6	49409599	49409599	+	Missense_Mutation	SNP	G	G	A	rs140727018	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	134	237	0	0.523438	0	G|0.999;A|0.001	0.001	strong	.	MUT	70	.	NM_000255	exon10	c.C1762T	p.R588C	CCTGGCGATATGC	.	PASS	Atlas-SNP
OR2T12	127064	hgsc.bcm.edu	37	1	248458718	248458718	+	Missense_Mutation	SNP	T	T	C	rs79635253	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	530	345	491	1	0.650943	0.00203666	T|0.961;C|0.039	0.039	strong	.	OR2T12	113	.	NM_001004692	exon1	c.A163G	p.R55G	TGGGCCTGTGGAG	.	PASS	Atlas-SNP
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747678	148747678	+	Missense_Mutation	SNP	G	G	A	rs35552800	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	144	0	0.441176	0	G|0.965;A|0.035	0.035	strong	.	PCYOX1L	32	.	NM_024028	exon6	c.G946A	p.A316T	ACCTTTGCAGGCT	.	PASS	Atlas-SNP
TATDN3	128387	hgsc.bcm.edu	37	1	212965284	212965284	+	Silent	SNP	C	C	G	rs61736926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	115	172	4	0.572139	0.0232558	C|0.772;G|0.228	0.228	strong	TATDN3,NS,carcinoma,0,1	TATDN3	23	1	NM_001146170	exon1	c.C21G	p.G7G	CGTAGGCTTGGTG	.	scavenged	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579801	55579801	+	Missense_Mutation	SNP	T	T	C	rs12790505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	79	129	0	0.451429	0	T|0.888;C|0.112	0.112	strong	OR5L1,NS,carcinoma,0,1	OR5L1	145	1	NM_001004738	exon1	c.T859C	p.S287P	CTGAACTCTGTGA	.	PASS	Atlas-SNP
FAM151A	338094	hgsc.bcm.edu	37	1	55075334	55075334	+	Silent	SNP	G	G	A	rs201640566	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	66	0	0.5	0	G|1.000;A|0.000	0.000	strong	.	FAM151A	58	.	NM_176782	exon8	c.C1365T	p.P455P	ATGGCCGGGGACC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	447	115	610	0	0.257271	0	C|0.891;G|0.109	0.109	strong	LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	NM_001081450	exon12	c.G1620C	p.Q540H	CACTGCCTGGGGG	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813421	248813421	+	Silent	SNP	G	G	A	rs200410497	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	69	163	0	0.448052	0	G|0.969;A|0.031	0.031	strong	.	OR2T27	52	.	NM_001001824	exon1	c.C765T	p.A255A	GTACATGGCAGCC	.	PASS	Atlas-SNP
IRF7	3665	hgsc.bcm.edu	37	11	614367	614367	+	Silent	SNP	T	T	C	rs11246214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	21	45	0	0.466667	0	T|0.956;C|0.044	0.044	strong	.	IRF7	23	.	NM_004031	exon4	c.A525G	p.T175T	AGCATGTGTGTGT	.	PASS	Atlas-SNP
SYNGAP1	8831	hgsc.bcm.edu	37	6	33393583	33393583	+	Silent	SNP	C	C	T	rs73402305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	77	183	0	0.458333	0	C|0.937;T|0.063	0.063	strong	SYNGAP1_ENST00000293748,NS,carcinoma,+2,2	SYNGAP1	202	2	NM_006772	exon3	c.C198T	p.P66P	ACACCCCCTACTG	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15358939	15358939	+	Missense_Mutation	SNP	A	A	C	rs114448506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	127	221	0	0.533613	0	A|0.997;C|0.003	0.003	strong	.	NBAS	246	.	NM_015909	exon48	c.T6390G	p.F2130L	AGTTCTAAAGAAC	.	PASS	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	37	5	35692775	35692775	+	Missense_Mutation	SNP	T	T	A	rs7710284	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	114	225	1	0.493506	0.00444444	T|0.679;A|0.321	0.321	strong	.	SPEF2	324	.	NM_024867	exon12	c.T1848A	p.N616K	GAAAAATGATGAA	.	PASS	Atlas-SNP
MASTL	84930	hgsc.bcm.edu	37	10	27459670	27459670	+	Silent	SNP	C	C	T	rs1981296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	37	77	0	0.506849	0	C|0.431;T|0.569	0.569	strong	.	MASTL	81	.	NM_032844	exon8	c.C1782T	p.I594I	AAGCATCAAAGAA	.	PASS	Atlas-SNP
ADH1B	125	hgsc.bcm.edu	37	4	100235053	100235053	+	Silent	SNP	A	A	G	rs1789882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	528	510	535	0	0.965909	0	A|0.177;G|0.823	0.823	strong	.	ADH1B	68	.	NM_000668	exon6	c.T753C	p.I251I	TTCCTGAATGGGT	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144952255	144952255	+	Missense_Mutation	SNP	G	G	C	rs61805377		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1786	461	1436	0	0.258119	0	.	.	weak	.	PDE4DIP	817	.	NM_022359	exon7	c.C875G	p.P292R	TCTCCTGGTACAT	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901946	129901946	+	Missense_Mutation	SNP	T	T	G	rs1050767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	111	231	2	0.435294	0.00865801	T|0.794;G|0.206	0.206	strong	MKI67,NS,carcinoma,+2,1	MKI67	363	1	NM_002417	exon13	c.A8158C	p.T2720P	TCTTTGTGCTTGC	.	scavenged	Atlas-SNP
ESD	2098	hgsc.bcm.edu	37	13	47354101	47354101	+	Missense_Mutation	SNP	C	C	T	rs9778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	31	67	0	0.3875	0	T|0.140;G|0.000;C|0.859	0.140	strong	.	ESD	23	.	NM_001984	exon8	c.G569A	p.G190E	AAATATCCACTAA	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18874720	18874720	+	Silent	SNP	C	C	G	rs916823	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	78	0	1	0	C|0.359;G|0.641	0.641	strong	.	FAM83G	51	.	NM_001039999	exon6	c.G2424C	p.S808S	AGAATCCGATGAG	.	PASS	Atlas-SNP
IFNAR1	3454	hgsc.bcm.edu	37	21	34713317	34713317	+	Silent	SNP	T	T	C	rs9981753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	42	140	0	0.42	0	T|0.986;C|0.014	0.014	strong	.	IFNAR1	44	.	NM_000629	exon3	c.T213C	p.D71D	GATGGATAATTGG	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31294773	31294773	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	38	74	0	0.431818	0	.	.	none	.	TRPM1	183	.	NM_001252020	exon27	c.G4181A	p.G1394D	TCTGGACCTAATT	.	PASS	Atlas-SNP
MCMBP	79892	hgsc.bcm.edu	37	10	121602830	121602830	+	Silent	SNP	G	G	A	rs34297798	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	111	190	0	0.518692	0	G|0.990;A|0.010	0.010	strong	.	MCMBP	49	.	NM_024834	exon9	c.C936T	p.A312A	CTTCTGGGCTAAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677816	100677816	+	Missense_Mutation	SNP	G	G	A	rs77671499	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	71	144	0	0.241497	0	G|0.981;A|0.019	0.019	strong	.	MUC17	804	.	NM_001040105	exon3	c.G3119A	p.G1040E	GTGAAGGAAGCAC	.	PASS	Atlas-SNP
LRRN4	164312	hgsc.bcm.edu	37	20	6032882	6032882	+	Silent	SNP	C	C	T	rs6053858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	9	21	0	0.473684	0	C|0.909;T|0.091	0.091	strong	.	LRRN4	54	.	NM_152611	exon2	c.G564A	p.G188G	GATGCCCCCCTGG	.	PASS	Atlas-SNP
SHPRH	257218	hgsc.bcm.edu	37	6	146276280	146276280	+	Missense_Mutation	SNP	C	C	T	rs182151362	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	52	86	0	0.452174	0	C|0.998;T|0.002	0.002	strong	.	SHPRH	169	.	NM_173082	exon2	c.G179A	p.S60N	TTTAGACTATCAC	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91739873	91739873	+	Missense_Mutation	SNP	A	A	G	rs7145583	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	72	183	0	0.48	0	A|0.997;G|0.003	0.003	strong	.	CCDC88C	192	.	NM_001080414	exon30	c.T5183C	p.F1728S	GCCACAAAGTTGG	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5965824	5965824	+	Missense_Mutation	SNP	G	G	C	rs12093500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	64	101	0	0.484848	0	G|0.980;C|0.020	0.020	strong	.	NPHP4	119	.	NM_015102	exon14	c.C1631G	p.A544G	ATACCGGCCTCCA	.	PASS	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	37	21	41455854	41455854	+	Silent	SNP	G	G	A	rs2297263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	62	105	0	0.455882	0	G|0.935;A|0.065	0.065	strong	.	DSCAM	347	.	NM_001271534	exon24	c.C4212T	p.N1404N	GCCCCCGTTGTCT	.	PASS	Atlas-SNP
OR5I1	10798	hgsc.bcm.edu	37	11	55703523	55703523	+	Silent	SNP	G	G	A	rs11231594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	44	86	0	0.458333	0	G|0.974;A|0.026	0.026	strong	.	OR5I1	110	.	NM_006637	exon1	c.C354T	p.A118A	CATGGCGGCCAGG	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs7671781	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	92	87	0	1	0	G|0.733;A|0.267	0.267	strong	.	PALLD	179	.	NM_001166108	exon2	c.G672A	p.M224I	CCCTATGGAAGAC	.	PASS	Atlas-SNP
SCO1	6341	hgsc.bcm.edu	37	17	10595250	10595250	+	Silent	SNP	T	T	C	rs2271228	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	59	124	1	0.412587	0.00806452	T|0.961;C|0.039	0.039	strong	SCO1,NS,carcinoma,-1,1	SCO1	24	1	NM_004589	exon4	c.A594G	p.P198P	GAAAAGTGGAGTT	.	scavenged	Atlas-SNP
LPCAT3	10162	hgsc.bcm.edu	37	12	7090193	7090193	+	Missense_Mutation	SNP	A	A	G	rs1984564	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	74	129	0	0.524823	0	A|0.759;G|0.241	0.241	strong	.	LPCAT3	33	.	NM_005768	exon6	c.T650C	p.I217T	ATGTCAATCAGCT	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	56	98	0	0.57732	0	G|0.910;A|0.090	0.090	strong	.	ZNF407	231	.	NM_001146190	exon1	c.G1534A	p.G512R	GACTCCGGGCTGC	.	PASS	Atlas-SNP
CCNB1	891	hgsc.bcm.edu	37	5	68471232	68471232	+	Silent	SNP	C	C	T	rs2069439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	47	137	0	0.376	0	C|0.998;T|0.002	0.002	strong	CCNB1,NS,carcinoma,+1,1	CCNB1	36	1	NM_031966	exon7	c.C951T	p.V317V	TGATGTCGAGCAA	.	PASS	Atlas-SNP
OR2H1	26716	hgsc.bcm.edu	37	6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A	rs61732185	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	143	257	0	0.471947	0	G|0.964;A|0.036	0.036	strong	.	OR2H1	38	.	NM_030883	exon3	c.G187A	p.D63N	CTCTCTGACCTCT	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893801	123893801	+	Missense_Mutation	SNP	A	A	G	rs74791330	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	394	52	526	1	0.13198	0.00190114	A|0.814;G|0.186	0.186	strong	OR10G9,NS,haematopoietic_neoplasm,0,3	OR10G9	80	3	NM_001001953	exon1	c.A82G	p.I28V	TTTGGAATCTTCC	.	scavenged	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76854463	76854463	+	Missense_Mutation	SNP	G	G	C	rs16931996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	35	81	0	0.625	0	G|0.956;C|0.044	0.044	strong	.	DUSP13	82	.	NM_001007273	exon6	c.C847G	p.R283G	CCAGTCGGTTGTC	.	PASS	Atlas-SNP
KIAA0141	9812	hgsc.bcm.edu	37	5	141307833	141307833	+	Missense_Mutation	SNP	T	T	C	rs10036567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	76	138	0	0.506667	0	T|0.836;C|0.164	0.164	strong	.	KIAA0141	44	.	NM_001142603	exon4	c.T382C	p.F128L	CGTTTCTTCTCAT	.	PASS	Atlas-SNP
TACR1	6869	hgsc.bcm.edu	37	2	75276649	75276649	+	Silent	SNP	C	C	T	rs34117315	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	108	192	0	0.490909	0	C|0.957;T|0.043	0.043	strong	TACR1,colon,carcinoma,-1,5	TACR1	62	5	NM_001058	exon5	c.G1134A	p.S378S	CAGGGACGAGGGT	.	PASS	Atlas-SNP
EGLN2	112398	hgsc.bcm.edu	37	19	41307170	41307170	+	Silent	SNP	G	G	A	rs2545763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	35	54	0	0.492958	0	G|0.911;A|0.089	0.089	strong	EGLN2,NS,carcinoma,0,1	EGLN2	31	1	NM_053046	exon2	c.G693A	p.P231P	GATCCCGCCGCGC	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408278	29408278	+	Silent	SNP	C	C	T	rs17184044	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	51	126	0	0.439655	0	C|0.956;T|0.044	0.044	strong	.	OR10C1	58	.	NM_013941	exon1	c.C486T	p.I162I	TTTCATCTTCTCT	.	PASS	Atlas-SNP
NLN	57486	hgsc.bcm.edu	37	5	65108215	65108215	+	Silent	SNP	A	A	G	rs2254485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	32	0	1	0	A|0.272;G|0.728	0.728	strong	.	NLN	51	.	NM_020726	exon12	c.A1977G	p.P659P	GAATCCAGAGGTA	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305774	+	Missense_Mutation	SNP	C	C	G	rs137947981	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	50	136	0	0.581395	0	.	.	weak	KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	NM_033188	exon1	c.G246C	p.Q82H	GGTGGTCTGGCAG	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49984879	49984879	+	Missense_Mutation	SNP	C	C	T	rs76547526	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	31	62	0	0.5	0	C|0.988;T|0.012	0.012	strong	.	WDFY4	205	.	NM_020945	exon16	c.C2948T	p.P983L	AGGCCCCGCAGCC	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157985149	157985149	+	Missense_Mutation	SNP	C	C	G	rs3800855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	59	81	0	0.572816	0	C|0.780;G|0.220	0.220	strong	.	PTPRN2	243	.	NM_130843	exon5	c.G419C	p.S140T	TCCCGACTGTACC	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26272270	26272270	+	Missense_Mutation	SNP	A	A	G	rs695633	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	99	0	0.990291	0	A|0.967;G|0.033	0.033	strong	.	MYO18B	322	.	NM_032608	exon24	c.A4195G	p.I1399V	GCCACCATTGGAA	.	PASS	Atlas-SNP
BBS12	166379	hgsc.bcm.edu	37	4	123664333	123664333	+	Missense_Mutation	SNP	G	G	C	rs7665271	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	43	78	0	0.409524	0	G|0.959;C|0.041	0.041	strong	.	BBS12	63	.	NM_001178007	exon3	c.G1286C	p.S429T	TAAACAGTAAGCG	.	PASS	Atlas-SNP
DYRK2	8445	hgsc.bcm.edu	37	12	68052166	68052166	+	Silent	SNP	C	C	T	rs56178357	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	85	163	0	0.5	0	C|0.909;T|0.091	0.091	strong	.	DYRK2	63	.	NM_006482	exon3	c.C1479T	p.S493S	GGAGAGCAGAGAG	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	20	51	0	0.454545	0	G|0.702;A|0.298	0.298	strong	.	PRR22	25	.	NM_001134316	exon3	c.C353T	p.P118L	GGCTGAGGCTCCA	.	PASS	Atlas-SNP
OR1J2	26740	hgsc.bcm.edu	37	9	125274015	125274015	+	Missense_Mutation	SNP	C	C	T	rs150890302	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	36	117	0	0.375	0	C|0.998;T|0.002	0.002	strong	.	OR1J2	64	.	NM_054107	exon1	c.C935T	p.S312F	TTTTCTCTTGGTG	.	PASS	Atlas-SNP
MAN1C1	57134	hgsc.bcm.edu	37	1	25944741	25944741	+	Silent	SNP	T	T	C	rs11247857	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	60	0	0.490566	0	T|0.815;C|0.185	0.185	strong	.	MAN1C1	48	.	NM_020379	exon1	c.T453C	p.R151R	GAGCCGTCTCCGC	.	PASS	Atlas-SNP
PPP2R3B	28227	hgsc.bcm.edu	37	X	295231	295231	+	Silent	SNP	A	A	G	rs1133523	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	17	0	1	0	A|0.446;G|0.554	0.554	strong	.	PPP2R3B	43	.	NM_013239	exon13	c.T1599C	p.P533P	CTCCACAGGGCTG	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169116304	169116304	+	Silent	SNP	T	T	A	rs189140579	bycluster;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	70	132	0	0.451613	0	T|1.000;C|0.000	.	alt	DOCK2,caecum,carcinoma,+2,1	DOCK2	389	1	NM_004946	exon9	c.T810A	p.I270I	GGAGATTGAGATG	.	PASS	Atlas-SNP
USP49	25862	hgsc.bcm.edu	37	6	41774340	41774340	+	Missense_Mutation	SNP	G	G	T	rs111948785	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	33	0	1	0	A|0.000;G|0.986;T|0.014	0.014	strong	.	USP49	58	.	NM_018561	exon4	c.C382A	p.L128M	GCGGCAGGACCAC	.	PASS	Atlas-SNP
WDR60	55112	hgsc.bcm.edu	37	7	158672619	158672619	+	Missense_Mutation	SNP	A	A	G	rs2788478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	93	181	0	0.556886	0	A|0.435;G|0.565	0.565	strong	.	WDR60	94	.	NM_018051	exon5	c.A818G	p.Q273R	GGCACCAAAGCAA	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	61	136	0	0.476562	0	C|0.766;T|0.234	0.234	strong	THBS1,NS,carcinoma,0,1	THBS1	106	1	NM_003246	exon9	c.C1410T	p.N470N	GATGAACGGGAAA	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17113083	17113083	+	Missense_Mutation	SNP	G	G	A	rs10426545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	52	148	1	0.40625	0.00675676	G|0.982;A|0.018	0.018	strong	CPAMD8,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CPAMD8	192	1	NM_015692	exon9	c.C892T	p.R298W	TGGCCCGCACAGT	.	scavenged	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31420143	31420143	+	Missense_Mutation	SNP	C	C	T	rs72797147	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	116	219	0	0.483333	0	C|0.982;T|0.018	0.018	strong	.	CAPN14	36	.	NM_001145122	exon8	c.G847A	p.V283M	ATTCCACCTTTCC	.	PASS	Atlas-SNP
RPL6	6128	hgsc.bcm.edu	37	12	112843105	112843105	+	Missense_Mutation	SNP	T	T	C	rs141161168	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	34	90	0	0.425	0	T|1.000;C|0.000	0.000	strong	.	RPL6	20	.	NM_001024662	exon7	c.A790G	p.I264V	GAGGAATAGCTTT	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448324	4448324	+	Silent	SNP	C	C	T	rs9910964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	31	62	0	0.5	0	C|0.916;T|0.084	0.084	strong	.	MYBBP1A	69	.	NM_014520	exon17	c.G2307A	p.A769A	CACCAGCGCCTTC	.	PASS	Atlas-SNP
CX3CR1	1524	hgsc.bcm.edu	37	3	39307256	39307256	+	Missense_Mutation	SNP	C	C	T	rs3732379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	76	148	0	0.447059	0	C|0.832;T|0.168	0.168	strong	.	CX3CR1	91	.	NM_001171174	exon2	c.G841A	p.V281I	TCATAACGTTGTA	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62197370	62197370	+	Silent	SNP	G	G	A	rs34830600	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	21	40	0	0.583333	0	G|0.827;A|0.173	0.173	strong	.	.	.	.	NM_001037335	exon9	c.C2805T	p.C935C	CTCCACGCACTCA	.	PASS	Atlas-SNP
GLTSCR1	29998	hgsc.bcm.edu	37	19	48182859	48182859	+	Silent	SNP	G	G	A	rs60219834	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	8	4	0	0.666667	0	G|0.943;A|0.057	0.057	strong	.	GLTSCR1	79	.	NM_015711	exon6	c.G432A	p.T144T	CCCGACGGGCGCT	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833145	82833145	+	Silent	SNP	G	G	A	rs2548541	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	85	0	0.486842	0	G|0.316;A|0.684	0.684	strong	.	VCAN	498	.	NM_004385	exon8	c.G4323A	p.Q1441Q	TTCTCAGAATTTC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134672609	134672609	+	Missense_Mutation	SNP	C	C	T	rs73391295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	78	120	0	0.549296	0	C|0.924;T|0.076	0.076	strong	.	TTC40	100	.	NM_001200049	exon38	c.G5341A	p.V1781I	CGTCAACACAATT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73676315	73676315	+	Silent	SNP	A	A	G	rs76266696	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	128	260	0	0.484848	0	A|0.994;G|0.006	0.006	strong	.	ALMS1	384	.	NM_015120	exon8	c.A2658G	p.V886V	GAAAGTATCAATT	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31256615	31256615	+	Missense_Mutation	SNP	C	C	A	rs3893680	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	10	235	0	0.0390625	0	.	.	weak	DDX11,lower_third,carcinoma,-2,1	DDX11	188	1	NM_030653	exon26	c.C2641A	p.R881S	CGAGCCCGTGTGG	.	scavenged	Atlas-SNP
ZNF536	9745	hgsc.bcm.edu	37	19	31039357	31039357	+	Missense_Mutation	SNP	C	C	A	rs61741995	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	18	27	0	0.6	0	C|0.982;A|0.018	0.018	strong	.	ZNF536	424	.	NM_014717	exon4	c.C2831A	p.P944H	CTGACCCCCCTTC	.	PASS	Atlas-SNP
SCAMP5	192683	hgsc.bcm.edu	37	15	75305040	75305040	+	Silent	SNP	A	A	G	rs7174129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	146	0	1	0	A|0.735;G|0.265	0.265	strong	.	SCAMP5	34	.	NM_001178111	exon4	c.A30G	p.P10P	CCCACCATTGCCC	.	PASS	Atlas-SNP
CACNG6	59285	hgsc.bcm.edu	37	19	54501527	54501527	+	Silent	SNP	G	G	A	rs34604090	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	18	66	0	0.310345	0	G|0.899;A|0.101	0.101	strong	CACNG6,colon,carcinoma,0,1	CACNG6	42	1	NM_145815	exon2	c.G366A	p.T122T	CACCACGGGGGAG	.	PASS	Atlas-SNP
TUBA1B	10376	hgsc.bcm.edu	37	12	49522238	49522238	+	Missense_Mutation	SNP	A	A	T	rs199895521	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	694	183	516	0	0.263689	0	A|0.998;T|0.002	0.002	weak	TUBA1B,bladder,carcinoma,0,1	TUBA1B	24	1	NM_006082	exon4	c.T859A	p.S287T	CTACAGAAAGCTG	.	scavenged	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239040343	239040343	+	Silent	SNP	G	G	A	rs73102311	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	36	62	0	0.521739	0	G|0.914;A|0.086	0.086	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2988A	p.K996K	GGAGAAGGAAGCT	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068137	5068137	+	Missense_Mutation	SNP	G	G	A	rs2500017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	130	223	0	0.483271	0	G|0.493;A|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.G382A	p.V128I	GTGGCCGTCTGTG	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91803567	91803567	+	Silent	SNP	A	A	G	rs16945475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	30	64	0	0.555556	0	A|0.900;G|0.100	0.100	strong	.	SV2B	98	.	NM_014848	exon7	c.A936G	p.E312E	TGATGAAGCCTGG	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443893	5443893	+	Missense_Mutation	SNP	G	G	A	rs10838094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	233	297	2	0.987288	0.00673401	G|0.611;A|0.389	0.389	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.G463A	p.V155I	TGCTGTGTTCTGG	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119043656	119043656	+	Missense_Mutation	SNP	C	C	T	rs643423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	28	78	0	0.466667	0	C|0.405;T|0.595	0.595	strong	.	NLRX1	128	.	NM_024618	exon4	c.C187T	p.P63S	CCCCCACCCGGGA	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	34	72	0	0.425	0	G|0.887;A|0.113	0.113	strong	.	DNHD1	198	.	NM_144666	exon24	c.G7120A	p.V2374M	TATGTGGTGGACC	.	PASS	Atlas-SNP
TAS2R41	259287	hgsc.bcm.edu	37	7	143175154	143175154	+	Silent	SNP	G	G	A	rs1404635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	81	185	0	0.413265	0	G|0.772;A|0.228	0.228	strong	.	TAS2R41	43	.	NM_176883	exon1	c.G189A	p.T63T	TGGGACGGTGCAC	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107591272	107591272	+	Silent	SNP	G	G	T	rs2853579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	77	106	0	0.641667	0	G|0.593;T|0.233	0.233	strong	ABCA1,NS,adenoma,0,1	ABCA1	244	1	NM_005502	exon15	c.C2040A	p.I680I	CCAGAGGATGCTG	.	PASS	Atlas-SNP
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712210	140712210	+	Silent	SNP	G	G	T	rs62378403	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	57	95	0	0.564356	0	G|0.826;T|0.174	0.174	strong	PCDHGA1_ENST00000517417,NS,carcinoma,0,2	PCDHGA1	397	2	NM_018912	exon1	c.G1959T	p.P653P	GCCCCCGCTCTCC	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22476717	22476717	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	51	92	0	0.476636	0	.	.	none	.	KIAA1967	72	.	NM_021174	exon20	c.C2576T	p.A859V	TGGCGGCAGAGAT	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151673589	151673589	+	Missense_Mutation	SNP	G	G	A	rs12201388	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	40	108	0	0.38835	0	G|0.902;A|0.098	0.098	strong	.	AKAP12	170	.	NM_005100	exon4	c.G4063A	p.E1355K	GTGAATGAAGAGA	.	PASS	Atlas-SNP
ALKBH7	84266	hgsc.bcm.edu	37	19	6374229	6374229	+	Silent	SNP	C	C	A	rs116186903	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	43	57	0	0.641791	0	C|0.994;A|0.006	0.006	strong	.	ALKBH7	18	.	NM_032306	exon2	c.C220A	p.R74R	GGCTTCCGAGAGA	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	32	80	0	0.484848	0	A|0.519;G|0.481	0.481	strong	.	RABEP1	59	.	NM_004703	exon17	c.A2385G	p.Q795Q	TGAACAACTAATG	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153036957	153036957	+	Silent	SNP	C	C	T	rs17091287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	63	149	0	0.379518	0	C|0.915;0|0.004	.	strong	.	PLXNB3	208	.	NM_001163257	exon15	c.C2433T	p.C811C	CGACTGCGCCATG	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119449165	119449165	+	Missense_Mutation	SNP	C	C	G	rs9819218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	63	108	0	0.496063	0	C|0.982;G|0.018	0.018	strong	.	.	.	.	NM_033364	exon8	c.C959G	p.S320C	GGTGGTCTAAACT	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982312	240982312	+	Missense_Mutation	SNP	G	G	A	rs115609219	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	47	132	1	0.382114	0.00757576	G|0.965;A|0.035	0.035	strong	PRR21,NS,carcinoma,0,2	PRR21	53	2	NM_001080835	exon1	c.C88T	p.H30Y	AGCCGTGGGGGAA	.	scavenged	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120378657	120378657	+	Silent	SNP	G	G	A	rs6684816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	96	164	0	0.475248	0	A|0.016;G|0.984	0.016	strong	.	NBPF7	46	.	NM_001047980	exon7	c.C1089T	p.S363S	GGAATTGGAGTGT	.	PASS	Atlas-SNP
TAL1	6886	hgsc.bcm.edu	37	1	47685569	47685569	+	Silent	SNP	G	G	A	rs144117146	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	61	108	0	0.559633	0	G|0.959;A|0.041	0.041	strong	.	TAL1	31	.	NM_003189	exon4	c.C819T	p.G273G	CGCGCCGCCCCCT	.	PASS	Atlas-SNP
FUT3	2525	hgsc.bcm.edu	37	19	5843784	5843784	+	Missense_Mutation	SNP	A	A	T	rs3894326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	91	194	0	0.464286	0	A|0.935;T|0.065	0.065	strong	.	FUT3	30	.	NM_001097640	exon3	c.T1067A	p.I356K	GCCGCTATGCTGC	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039183	239039183	+	Missense_Mutation	SNP	G	G	A	rs73102303	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	38	68	0	0.575758	0	G|0.871;A|0.129	0.129	strong	ESPNL,NS,carcinoma,0,1	ESPNL	63	1	NM_194312	exon9	c.G1828A	p.V610M	AAGGGCGTGCATG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230300	23230300	+	Missense_Mutation	SNP	C	C	T	rs382768	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	80	186	0	0.465116	0	C|0.947;T|0.053	0.053	strong	.	IGLL5	26	.	NM_001178126	exon1	c.C67T	p.R23C	AGGCAGCGCTGGC	.	PASS	Atlas-SNP
POLR3H	171568	hgsc.bcm.edu	37	22	41926757	41926757	+	Silent	SNP	G	G	A	rs35463585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	82	140	0	0.509317	0	G|0.976;A|0.024	0.024	strong	.	POLR3H	30	.	NM_001018050	exon5	c.C495T	p.P165P	TGAGCTGGGCCCT	.	PASS	Atlas-SNP
LETM1	3954	hgsc.bcm.edu	37	4	1843324	1843324	+	Missense_Mutation	SNP	C	C	T	rs116753949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	58	0	0.423077	0	C|0.957;T|0.043	0.043	strong	.	LETM1	48	.	NM_012318	exon3	c.G344A	p.R115H	TCATCGCGAACAG	.	PASS	Atlas-SNP
OR5H15	403274	hgsc.bcm.edu	37	3	97887902	97887902	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	481	16	467	4	0.033264	0.00856531	.	.	none	OR5H15,NS,carcinoma,0,1	OR5H15	70	1	NM_001005515	exon1	c.A359G	p.Y120C	TGGCATATGATCG	.	scavenged	Atlas-SNP
C12orf5	57103	hgsc.bcm.edu	37	12	4459032	4459032	+	Silent	SNP	G	G	A	rs7309402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	149	0	0.992308	0	G|0.742;A|0.258	0.258	strong	.	C12orf5	28	.	NM_020375	exon4	c.G240A	p.T80T	TATGACGGTAAAG	.	PASS	Atlas-SNP
OR1E2	8388	hgsc.bcm.edu	37	17	3336697	3336697	+	Missense_Mutation	SNP	G	G	A	rs77501388	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	98	221	0	0.426087	0	G|0.987;A|0.013	0.013	strong	OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	NM_003554	exon1	c.C439T	p.P147S	GCATGGGGCTCAT	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51173823	51173823	+	Silent	SNP	G	G	A	rs61740811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	114	221	0	0.5	0	G|0.957;A|0.043	0.043	strong	.	SALL1	301	.	NM_002968	exon2	c.C2310T	p.I770I	CTGGCAGATGGGG	.	PASS	Atlas-SNP
LIPF	8513	hgsc.bcm.edu	37	10	90433345	90433345	+	Missense_Mutation	SNP	T	T	A	rs6586145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	74	137	0	0.528571	0	T|0.872;A|0.128	0.128	strong	.	LIPF	62	.	NM_001198829	exon8	c.T700A	p.F234I	TTTCAGTTTATAT	.	PASS	Atlas-SNP
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	112	0	1	0	G|0.645;A|0.355	0.355	strong	.	HSD17B11	28	.	NM_016245	exon4	c.C531T	p.V177V	GACCGAGACATGT	.	PASS	Atlas-SNP
HCN4	10021	hgsc.bcm.edu	37	15	73617723	73617723	+	Silent	SNP	G	G	T	rs141966309	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	94	217	0	0.479592	0	G|0.998;T|0.002	0.002	strong	.	HCN4	150	.	NM_005477	exon5	c.C1653A	p.I551I	GTCGTGGATGCGC	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101591923	101591923	+	Silent	SNP	A	A	G	rs4965778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	50	86	0	0.526316	0	A|0.548;G|0.452	0.452	strong	.	LRRK1	310	.	NM_024652	exon24	c.A3447G	p.T1149T	CCTGACAGCCACA	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77407636	77407636	+	Silent	SNP	C	C	T	rs4145894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	56	152	0	0.388889	0	C|0.819;T|0.181	0.181	strong	.	TRPM6	377	.	NM_017662	exon19	c.G2442A	p.Q814Q	AAAATGCTGATTT	.	PASS	Atlas-SNP
ABTB2	25841	hgsc.bcm.edu	37	11	34176262	34176262	+	Missense_Mutation	SNP	T	T	C	rs2473928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	69	106	0	0.565574	0	T|0.973;C|0.027	0.027	strong	.	ABTB2	101	.	NM_145804	exon15	c.A2752G	p.T918A	TGTCAGTGGTGGG	.	PASS	Atlas-SNP
IL1RL1	9173	hgsc.bcm.edu	37	2	102957136	102957136	+	Missense_Mutation	SNP	C	C	T	rs114797672	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	128	301	0	0.477612	0	C|0.992;T|0.008	0.008	strong	.	IL1RL1	114	.	NM_016232	exon5	c.C458T	p.A153V	GTCAGGCTCTTCA	.	PASS	Atlas-SNP
STRN3	29966	hgsc.bcm.edu	37	14	31364948	31364948	+	Missense_Mutation	SNP	A	A	G	rs114922597	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	54	112	0	0.402985	0	A|0.990;G|0.010	0.010	strong	.	STRN3	117	.	NM_001083893	exon17	c.T2144C	p.M715T	TGGATCATTTTAC	.	PASS	Atlas-SNP
VNN1	8876	hgsc.bcm.edu	37	6	133004281	133004281	+	Missense_Mutation	SNP	A	A	G	rs61729583	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	36	71	0	0.413793	0	A|0.971;G|0.029	0.029	strong	.	VNN1	69	.	NM_004666	exon7	c.T1540C	p.X514Q	TATTCTACCAACT	.	PASS	Atlas-SNP
SLC16A6	9120	hgsc.bcm.edu	37	17	66270082	66270082	+	Missense_Mutation	SNP	A	A	G	rs35397826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	31	70	0	0.584906	0	A|0.883;G|0.117	0.117	strong	.	SLC16A6	56	.	NM_001174166	exon4	c.T362C	p.I121T	ATGCCGATGGCGA	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56369095	56369095	+	Silent	SNP	C	C	T	rs147356242	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	29	41	0	0.527273	0	C|0.994;T|0.006	0.006	strong	.	NLRP4	331	.	NM_134444	exon3	c.C336T	p.S112S	ATGGTCCAGCAAG	.	PASS	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	37	11	71941212	71941212	+	Silent	SNP	A	A	G	rs2276048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	81	0	1	0	G|0.306;A|0.694	0.306	strong	.	INPPL1	120	.	NM_001567	exon9	c.A987G	p.S329S	GAAGTCACAGAAG	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72358577	72358577	+	Silent	SNP	G	G	A	rs885822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	122	253	1	0.448529	0.00395257	G|0.316;A|0.684	0.684	strong	.	PRF1	64	.	NM_001083116	exon3	c.C900T	p.H300H	TTCCGAGTGGCGC	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	50	0	0.407407	0	A|0.774;G|0.226	0.226	strong	CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	NM_012099	exon3	c.A1117G	p.K373E	GGAGCGAAGCCTC	.	PASS	Atlas-SNP
PRKCA	5578	hgsc.bcm.edu	37	17	64785022	64785022	+	Silent	SNP	G	G	A	rs2228945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	25	73	0	0.431034	0	G|0.855;A|0.145	0.145	strong	PRKCA,colon,carcinoma,0,3	PRKCA	82	3	NM_002737	exon16	c.G1779A	p.E593E	GAGAGAGCATGCC	.	PASS	Atlas-SNP
DNASE2B	58511	hgsc.bcm.edu	37	1	84880380	84880380	+	Silent	SNP	T	T	C	rs3768250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	98	256	0	0.475728	0	T|0.679;C|0.321	0.321	strong	.	DNASE2B	40	.	NM_021233	exon6	c.T915C	p.H305H	AGATCATGCCAAG	.	PASS	Atlas-SNP
GIMAP6	474344	hgsc.bcm.edu	37	7	150324976	150324976	+	Missense_Mutation	SNP	T	T	C	rs11977216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	128	324	0	0.441379	0	T|0.964;C|0.036	0.036	strong	.	GIMAP6	60	.	NM_001244072	exon3	c.A920G	p.Q307R	GTATATTGGTAAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017945	1017945	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1212	49	1032	0	0.040429	0	.	.	none	.	MUC6	408	.	NM_005961	exon31	c.T4856C	p.F1619S	GTGGAGAAAGGTG	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20784910	20784910	+	Missense_Mutation	SNP	T	T	C	rs60197951	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	68	144	0	0.511278	0	T|0.981;C|0.019	0.019	strong	.	ABCB5	357	.	NM_001163941	exon26	c.T3278C	p.I1093T	CCCAAATAGCAAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417503	105417503	+	Missense_Mutation	SNP	G	G	T	rs146582718	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	406	389	0	0.987835	0	G|0.962;T|0.038	0.038	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4285A	p.P1429T	TTTCAGGGCCCTT	.	PASS	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155314034	155314034	+	Silent	SNP	A	A	G	rs359569	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	43	85	0	0.623188	0	A|0.426;G|0.574	0.574	strong	PLCH1,NS,carcinoma,0,1	PLCH1	406	1	NM_001130960	exon2	c.T177C	p.S59S	CTTCTCACTCTTC	.	PASS	Atlas-SNP
SLC7A9	11136	hgsc.bcm.edu	37	19	33333179	33333179	+	Silent	SNP	C	C	T	rs111630604	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	72	0	0.460526	0	C|0.987;T|0.013	0.013	strong	SLC7A9,NS,carcinoma,-1,3	SLC7A9	78	3	NM_001243036	exon11	c.G1119A	p.S373S	GACTAACGAGTTT	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140605078	140605078	+	Silent	SNP	C	C	T	rs2907322	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	29	36	0	0.537037	0	C|0.835;T|0.165	0.165	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C2001T	p.S667S	CTTCTCCCAGCCC	.	PASS	Atlas-SNP
TMEM223	79064	hgsc.bcm.edu	37	11	62559301	62559301	+	Missense_Mutation	SNP	C	C	T	rs2956139	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	58	125	0	0.453125	0	C|0.973;T|0.027	0.027	strong	.	TMEM223	22	.	NM_001080501	exon1	c.G166A	p.G56S	AGACGCCCTGGCC	.	PASS	Atlas-SNP
POPDC2	64091	hgsc.bcm.edu	37	3	119379186	119379186	+	Missense_Mutation	SNP	C	C	T	rs4688023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	96	0	0.486486	0	C|0.615;T|0.385	0.385	strong	.	POPDC2	36	.	NM_022135	exon1	c.G85A	p.V29I	GGTAGACAGCCCC	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207782889	207782889	+	Missense_Mutation	SNP	A	A	G	rs17047661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	77	131	0	0.506579	0	A|0.769;G|0.231	0.231	strong	.	CR1	354	.	NM_000651	exon37	c.A6151G	p.R2051G	GCAATTAGAGTAC	.	PASS	Atlas-SNP
CAPN3	825	hgsc.bcm.edu	37	15	42680058	42680058	+	Silent	SNP	T	T	C	rs17593	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	163	159	1	1	0.00628931	T|0.944;C|0.056	0.056	strong	.	CAPN3	172	.	NM_000070	exon4	c.T606C	p.S202S	CTGGAGTGCTCTG	.	PASS	Atlas-SNP
ZC4H2	55906	hgsc.bcm.edu	37	X	64139051	64139051	+	Silent	SNP	T	T	C	rs6524946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	62	154	0	0.48062	0	T|0.894;C|0.106	0.106	strong	.	ZC4H2	64	.	NM_018684	exon4	c.A432G	p.T144T	AGGTTCTGTCTGC	.	PASS	Atlas-SNP
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	97	157	1	0.989796	0.00636943	A|0.624;G|0.376	0.376	strong	.	ZNF155	30	.	NM_001260488	exon5	c.A252G	p.Q84Q	AACCCAAAGAGAA	.	PASS	Atlas-SNP
DLST	1743	hgsc.bcm.edu	37	14	75367807	75367807	+	Silent	SNP	C	C	T	rs20578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	117	230	0	0.554502	0	C|0.690;T|0.310	0.310	strong	.	DLST	42	.	NM_001933	exon14	c.C1098T	p.G366G	GGATGGCGGTACC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2088697	2088697	+	Missense_Mutation	SNP	G	G	C	rs34735757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	68	0	0.460526	0	G|0.986;C|0.014	0.014	strong	.	MYOM2	251	.	NM_003970	exon33	c.G3852C	p.E1284D	TGAAGAGATGGCT	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18775810	18775810	+	Missense_Mutation	SNP	C	C	A	rs934472	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	61	127	0	0.530435	0	C|0.566;A|0.434	0.434	strong	.	ADAMTSL1	306	.	NM_001040272	exon18	c.C2467A	p.L823I	ACCGGCCTCTCAA	.	PASS	Atlas-SNP
GPRASP2	114928	hgsc.bcm.edu	37	X	101971960	101971960	+	Silent	SNP	C	C	T	rs112000579	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	93	286	0	0.339416	0	C|0.981;T|0.019	0.019	strong	.	GPRASP2	89	.	NM_138437	exon4	c.C2163T	p.S721S	TATGTCCGGGTTT	.	PASS	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	63	120	0	0.446809	0	C|0.602;T|0.398	0.398	strong	C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	NM_001039706	exon11	c.C1116T	p.N372N	ATTCAACGTAATT	.	PASS	Atlas-SNP
ZNF556	80032	hgsc.bcm.edu	37	19	2877365	2877365	+	Missense_Mutation	SNP	C	C	T	rs10421121	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	52	92	0	0.536082	0	C|0.889;T|0.111	0.111	strong	.	ZNF556	73	.	NM_024967	exon4	c.C409T	p.R137C	CATCTGCGCAAGA	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	37	MT	3594	3594	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	5	0	1	0	.	.	none	.	.	.	.	ENST00000361390	exon1	c.C288T	p.V96V	CCTGGTCAACCTC	.	PASS	Atlas-SNP
ARHGEF16	27237	hgsc.bcm.edu	37	1	3397062	3397062	+	Missense_Mutation	SNP	G	G	A	rs56309807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	22	45	0	0.578947	0	G|0.974;A|0.026	0.026	strong	.	ARHGEF16	76	.	NM_014448	exon15	c.G2041A	p.E681K	TTCCCCGAGGACT	.	PASS	Atlas-SNP
SLC38A8	146167	hgsc.bcm.edu	37	16	84056442	84056442	+	Missense_Mutation	SNP	G	G	C	rs11861325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	71	0	0.468354	0	G|0.961;C|0.039	0.039	strong	.	SLC38A8	60	.	NM_001080442	exon6	c.C743G	p.S248C	CAGTGGGAGAGGC	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18649057	18649057	+	Missense_Mutation	SNP	C	C	T	rs12312266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	52	80	0	0.504854	0	C|0.665;N|0.000	.	strong	.	PIK3C2G	315	.	NM_004570	exon20	c.C2732T	p.P911L	CTAATCCGATGGG	.	PASS	Atlas-SNP
SLC44A4	80736	hgsc.bcm.edu	37	6	31838713	31838713	+	Silent	SNP	G	G	A	rs494620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	34	65	0	0.492754	0	G|0.559;A|0.441	0.441	strong	.	SLC44A4	67	.	NM_025257	exon10	c.C813T	p.Y271Y	GATGCCGTATGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515161	195515161	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	369	4	183	1	0.0108401	0.00546448	.	.	none	MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C3290A	p.A1097E	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
ZFP42	132625	hgsc.bcm.edu	37	4	188924450	188924450	+	Silent	SNP	A	A	G	rs61731386	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	37	59	0	0.616667	0	A|0.972;G|0.028	0.028	strong	.	ZFP42	87	.	NM_174900	exon4	c.A489G	p.S163S	CCTATCAGATCCT	.	PASS	Atlas-SNP
MRC1	4360	hgsc.bcm.edu	37	10	18122716	18122716	+	Silent	SNP	A	A	G	rs2985837	bycluster;bysubmitter	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	133	1	1	0.0075188	A|0.250;G|0.750	0.750	weak	.	MRC1	13	.	NM_002438	exon4	c.G726G	p.Q242Q	GCACCAAGCGAGG	.	PASS	Atlas-SNP
CLASP1	23332	hgsc.bcm.edu	37	2	122216419	122216419	+	Silent	SNP	A	A	G	rs2304560	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	81	0	1	0	A|0.779;G|0.221	0.221	strong	.	CLASP1	135	.	NM_001207051	exon13	c.T1311C	p.I437I	TACCCGAATAATT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280736	152280736	+	Missense_Mutation	SNP	T	T	C	rs78974621	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	657	218	451	0	0.331811	0	T|0.865;C|0.135	0.135	strong	.	FLG	900	.	NM_002016	exon3	c.A6626G	p.H2209R	TGATGATGCGACC	.	PASS	Atlas-SNP
WNK4	65266	hgsc.bcm.edu	37	17	40946913	40946913	+	Missense_Mutation	SNP	C	C	T	rs56226218	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	145	235	1	0.519713	0.00425532	C|0.974;T|0.026	0.026	strong	.	WNK4	182	.	NM_032387	exon14	c.C2474T	p.P825L	TTTCCCCAGGTCC	.	PASS	Atlas-SNP
CDC25C	995	hgsc.bcm.edu	37	5	137665323	137665323	+	Missense_Mutation	SNP	G	G	A	rs3734166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	49	136	0	0.418803	0	A|0.359;C|0.003	0.359	strong	.	CDC25C	37	.	NM_001790	exon3	c.C208T	p.R70C	GGCAACGTTTTGG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62198713	62198713	+	Silent	SNP	G	G	A	rs3810490	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	16	29	0	0.5	0	G|0.846;A|0.154	0.154	strong	.	.	.	.	NM_001037335	exon7	c.C1998T	p.I666I	CTCATCGATGAGA	.	PASS	Atlas-SNP
GABRR1	2569	hgsc.bcm.edu	37	6	89926962	89926962	+	Missense_Mutation	SNP	T	T	C	rs1186902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	113	206	0	0.545894	0	T|0.779;C|0.221	0.221	strong	GABRR1,NS,carcinoma,0,1	GABRR1	63	1	NM_001256703	exon1	c.A80G	p.H27R	GGCCAGTGCATTC	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20838318	20838318	+	Silent	SNP	G	G	A	rs3796064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	337	163	283	0	0.48368	0	G|0.702;A|0.298	0.298	strong	.	HS1BP3	33	.	NM_022460	exon4	c.C501T	p.F167F	AAAGTCGAAAGCC	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	98991223	98991223	+	Silent	SNP	A	A	G	rs1869608	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	49	91	0	0.521277	0	A|0.775;G|0.225	0.225	strong	.	MATN2	165	.	NM_002380	exon6	c.A1068G	p.K356K	AGATAAAAAAACG	.	PASS	Atlas-SNP
H6PD	9563	hgsc.bcm.edu	37	1	9324571	9324571	+	Silent	SNP	T	T	C	rs9434742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	151	139	0	1	0	T|0.603;C|0.397	0.397	strong	H6PD,NS,carcinoma,0,1	H6PD	71	1	NM_004285	exon5	c.T2019C	p.Y673Y	GATCTATGCCAGG	.	PASS	Atlas-SNP
RFPL4A	342931	hgsc.bcm.edu	37	19	56274214	56274214	+	Silent	SNP	G	G	T	rs114470138	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	547	213	321	0	0.389397	0	G|0.970;T|0.030	0.030	strong	.	RFPL4A	8	.	NM_001145014	exon3	c.G537T	p.V179V	GATTGTGCTTTCT	.	PASS	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	37	18	59821843	59821843	+	Missense_Mutation	SNP	T	T	C	rs17069506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	27	45	0	0.473684	0	T|0.938;C|0.062	0.062	strong	.	PIGN	62	.	NM_176787	exon7	c.A484G	p.K162E	CTCTTTTAGCATC	.	PASS	Atlas-SNP
HADHB	3032	hgsc.bcm.edu	37	2	26505745	26505745	+	Silent	SNP	G	G	A	rs7572240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	71	0	0.490566	0	G|0.982;A|0.018	0.018	strong	.	HADHB	50	.	NM_000183	exon11	c.G966A	p.A322A	CATGGCGGAGGAA	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	32	0	0.45614	0	A|0.771;C|0.229	0.229	strong	.	CD3EAP	27	.	NM_012099	exon3	c.A776C	p.K259T	AAGGGAAAGAAAC	.	PASS	Atlas-SNP
GOLM1	51280	hgsc.bcm.edu	37	9	88650332	88650332	+	Missense_Mutation	SNP	C	C	G	rs61741197	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	71	93	0	0.682692	0	C|0.947;G|0.053	0.053	strong	.	GOLM1	36	.	NM_016548	exon8	c.G966C	p.Q322H	GACAAGCTGGTCT	.	PASS	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53011955	53011955	+	Silent	SNP	G	G	A	rs61736102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	214	181	0	1	0	G|0.827;A|0.173	0.173	strong	.	KRT73	101	.	NM_175068	exon1	c.C354T	p.N118N	CTCCACGTTCAGG	.	PASS	Atlas-SNP
HDAC4	9759	hgsc.bcm.edu	37	2	240003873	240003873	+	Silent	SNP	G	G	A	rs10168964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	326	324	243	0	0.993865	0	G|0.924;A|0.076	0.076	strong	.	HDAC4	127	.	NM_006037	exon21	c.C2562T	p.D854D	GCTGGGGTCGCTG	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142222245	142222245	+	Silent	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	4	183	0	0.017094	0	.	.	none	ATR,colon,carcinoma,-1,1	ATR	285	1	NM_001184	exon30	c.G5247T	p.L1749L	AGTAGACAGCTGA	.	scavenged	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186254	39186254	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	68	135	0	0.49635	0	.	.	none	.	KRTAP1-4	4	.	NM_001257305	exon1	c.A77C	p.Q26P	CTTGGCTGGCAGC	.	PASS	Atlas-SNP
OR52H1	390067	hgsc.bcm.edu	37	11	5566460	5566460	+	Silent	SNP	G	G	A	rs115541630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	58	104	0	0.495726	0	G|0.983;A|0.017	0.017	strong	OR52H1,NS,carcinoma,0,1	OR52H1	46	1	NM_001005289	exon1	c.C294T	p.R98R	GATTTCGCGAGCC	.	PASS	Atlas-SNP
GUCA1C	9626	hgsc.bcm.edu	37	3	108639423	108639423	+	Missense_Mutation	SNP	C	C	T	rs2715687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	204	212	0	0.995122	0	C|0.337;T|0.662	0.662	strong	.	GUCA1C	39	.	NM_005459	exon2	c.G214A	p.V72I	AGTCAACAAATCC	.	PASS	Atlas-SNP
ADCY10	55811	hgsc.bcm.edu	37	1	167825485	167825485	+	Missense_Mutation	SNP	T	T	C	rs2071921	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	222	282	1	1	0.0035461	C|0.470;N|0.000	0.470	strong	.	ADCY10	175	.	NM_018417	exon17	c.A2089G	p.I697V	CACCAATGACAAT	.	PASS	Atlas-SNP
FAM117A	81558	hgsc.bcm.edu	37	17	47788755	47788755	+	Silent	SNP	G	G	A	rs34759387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	18	65	0	0.36	0	G|0.946;A|0.054	0.054	strong	.	FAM117A	45	.	NM_030802	exon8	c.C1224T	p.P408P	GGGAAGGGGAGAT	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95502303	95502303	+	Silent	SNP	G	G	A	rs11107896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	85	145	0	0.566667	0	G|0.906;A|0.094	0.094	strong	.	FGD6	127	.	NM_018351	exon10	c.C3168T	p.H1056H	ATTGGCGTGGTTG	.	PASS	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	37	4	9783971	9783971	+	Silent	SNP	C	C	T	rs113695344		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	10	133	5	0.0684932	0.037594	C|0.500;T|0.500	0.500	weak	DRD5,rectum,carcinoma,0,1	DRD5	119	1	NM_000798	exon1	c.C318T	p.Y106Y	CGGTTACTGGCCC	.	scavenged	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604641	140604641	+	Missense_Mutation	SNP	G	G	C	rs142548755	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	137	246	0	0.487544	0	G|0.994;C|0.006	0.006	strong	.	PCDHB14	132	.	NM_018934	exon1	c.G1564C	p.E522Q	GACTACGAGGCCC	.	PASS	Atlas-SNP
ACPL2	92370	hgsc.bcm.edu	37	3	141006162	141006162	+	Silent	SNP	G	G	A	rs34601454	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	41	115	0	0.42268	0	G|0.969;A|0.031	0.031	strong	.	ACPL2	50	.	NM_152282	exon7	c.G372A	p.P124P	GAAACCGTATCAC	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	48	78	0	0.494845	0	A|0.997;G|0.003	0.003	strong	.	PARVB	44	.	NM_001003828	exon4	c.A322G	p.M108V	CGCACGATGATTG	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21042391	21042391	+	Silent	SNP	G	G	A	rs114086288	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	55	114	0	0.533981	0	G|0.989;A|0.011	0.011	strong	.	DNAH3	1142	.	NM_017539	exon37	c.C5415T	p.N1805N	AACAGTGTTCATA	.	PASS	Atlas-SNP
CCDC105	126402	hgsc.bcm.edu	37	19	15133762	15133762	+	Missense_Mutation	SNP	G	G	C	rs8111625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	78	210	0	0.433333	0	G|0.132;C|0.868	0.868	strong	.	CCDC105	53	.	NM_173482	exon7	c.G1331C	p.S444T	ACCTCAGCTGGGG	.	PASS	Atlas-SNP
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357634	39357634	+	Silent	SNP	A	A	G	rs62230498		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	45	51	0	1	0	A|0.167;G|0.833	0.833	weak	.	APOBEC3A	20	.	NM_145699	exon3	c.A417G	p.A139A	GGAGGCACTGCAA	.	PASS	Atlas-SNP
CLDN8	9073	hgsc.bcm.edu	37	21	31587859	31587859	+	Missense_Mutation	SNP	T	T	C	rs685967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	49	110	0	0.49	0	T|0.908;C|0.092	0.092	strong	CLDN8,NS,adenocarcinoma,+2,1	CLDN8	40	1	NM_199328	exon1	c.A385G	p.T129A	TGCCCGTGATGAT	.	PASS	Atlas-SNP
MANBA	4126	hgsc.bcm.edu	37	4	103645082	103645082	+	Silent	SNP	C	C	T	rs6857760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	78	212	0	0.40625	0	C|0.893;T|0.107	0.107	strong	.	MANBA	78	.	NM_005908	exon3	c.G315A	p.T105T	TGAAACCGTATCC	.	PASS	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	37	19	36278470	36278470	+	Silent	SNP	C	C	G	rs231235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	49	0	1	0	C|0.531;G|0.469	0.469	strong	.	ARHGAP33	102	.	NM_052948	exon21	c.C2520G	p.A840A	CAGTGCCCAGCTC	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	82	0	0.504951	0	G|0.765;C|0.235	0.235	strong	ATAD5,NS,carcinoma,0,1	ATAD5	150	1	NM_024857	exon1	c.G39C	p.P13P	TGCTCCGCCTCCC	.	PASS	Atlas-SNP
C2orf53	339779	hgsc.bcm.edu	37	2	27361049	27361049	+	Missense_Mutation	SNP	G	G	C	rs61739485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	50	144	0	0.347222	0	G|0.972;C|0.028	0.028	strong	.	C2orf53	45	.	NM_178553	exon3	c.C149G	p.P50R	GAGAACGGTGGTT	.	PASS	Atlas-SNP
SPANXN4	441525	hgsc.bcm.edu	37	X	142121876	142121876	+	Missense_Mutation	SNP	A	A	T	rs10482390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	151	195	0	0.616327	0	A|0.920;0|0.042	.	strong	.	SPANXN4	10	.	NM_001009613	exon2	c.A144T	p.K48N	AGCAAAATATCCA	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88793156	88793156	+	Silent	SNP	G	G	A	rs376432833		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	22	51	0	0.392857	0	.	.	weak	.	PIEZO1	79	.	NM_001142864	exon25	c.C3666T	p.N1222N	GGTGACGTTGTAC	.	PASS	Atlas-SNP
KCNH1	3756	hgsc.bcm.edu	37	1	210857145	210857145	+	Silent	SNP	C	C	T	rs112047226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	32	56	0	0.432432	0	C|0.987;T|0.013	0.013	strong	KCNH1,colon,carcinoma,-1,1	KCNH1	199	1	NM_172362	exon11	c.G2448A	p.A816A	CCCTGGCGCCTGT	.	PASS	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196706659	196706659	+	Missense_Mutation	SNP	C	C	A	rs114743644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	46	103	0	0.5	0	C|0.999;A|0.001	0.001	strong	.	CFH	251	.	NM_000186	exon17	c.C2651A	p.S884Y	ATTCATCCAGGTC	.	PASS	Atlas-SNP
ZNF80	7634	hgsc.bcm.edu	37	3	113955890	113955890	+	Missense_Mutation	SNP	C	C	T	rs112412956	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	78	131	0	0.509804	0	C|0.987;T|0.013	0.013	strong	.	ZNF80	75	.	NM_007136	exon1	c.G32A	p.G11D	CCATCACCTGTCC	.	PASS	Atlas-SNP
CA9	768	hgsc.bcm.edu	37	9	35674101	35674101	+	Silent	SNP	T	T	C	rs12553173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	109	0	1	0	T|0.791;C|0.209	0.209	strong	.	CA9	48	.	NM_001216	exon1	c.T145C	p.L49L	TCCCCCTTGGGAG	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32740349	32740349	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	2	98	0	0.0224719	0	.	.	none	BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	2	NM_016252	exon55	c.G10861C	p.E3621Q	TCTCCTGAAGCTA	.	scavenged	Atlas-SNP
ZNF735	730291	hgsc.bcm.edu	37	7	63679733	63679733	+	Missense_Mutation	SNP	A	A	G	rs10270226	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	123	217	1	0.504098	0.00460829	A|0.311;G|0.689	0.689	strong	.	.	.	.	NM_001159524	exon4	c.A304G	p.S102G	GAGCAGAGCATAA	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	34	76	0	0.373626	0	C|0.562;T|0.438	0.438	strong	.	CDC16	50	.	NM_003903	exon5	c.C330T	p.D110D	GAAGGACGAAAGT	.	PASS	Atlas-SNP
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628411	60628411	+	Silent	SNP	G	G	T	rs75429795	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	55	94	0	0.478261	0	G|0.881;T|0.119	0.119	strong	.	ZSWIM6	51	.	NM_020928	exon1	c.G312T	p.P104P	GGAGCCGGTGCAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679809	100679809	+	Silent	SNP	C	C	T	rs4992074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	46	115	0	0.4	0	C|0.823;T|0.177	0.177	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5112T	p.S1704S	GGCCAGCTCTGCA	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113275878	113275878	+	Silent	SNP	C	C	T	rs16883323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	36	65	0	0.514286	0	C|0.969;T|0.031	0.031	strong	CSMD3_ENST00000343508,caecum,carcinoma,0,4	CSMD3	2325	4	NM_198123	exon61	c.G9852A	p.P3284P	GCACTGCGGTACT	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617311	183617311	+	Silent	SNP	T	T	A	rs10911392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	45	121	0	0.391304	0	T|0.917;A|0.083	0.083	strong	.	APOBEC4	45	.	NM_203454	exon2	c.A606T	p.I202I	ACCACTTATAAAG	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595012	55595012	+	Silent	SNP	A	A	T	rs35645945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	54	184	0	0.418605	0	A|0.934;T|0.066	0.066	strong	.	OR5L2	135	.	NM_001004739	exon1	c.A318T	p.T106T	TTGCACATGTGGA	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	709001	709001	+	Missense_Mutation	SNP	C	C	A	rs4984906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	132	0	0.491379	0	C|0.379;A|0.621	0.621	strong	.	WDR90	107	.	NM_145294	exon24	c.C3001A	p.P1001T	CTGGCCCCTACTG	.	PASS	Atlas-SNP
KIF9	64147	hgsc.bcm.edu	37	3	47286320	47286320	+	Missense_Mutation	SNP	T	T	C	rs115610071	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	84	216	0	0.48	0	T|0.992;C|0.008	0.008	strong	.	KIF9	59	.	NM_182902	exon15	c.A1475G	p.K492R	GCTTTCTTCCCAG	.	PASS	Atlas-SNP
THAP4	51078	hgsc.bcm.edu	37	2	242572693	242572693	+	Silent	SNP	C	C	T	rs147500721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	44	69	0	0.578947	0	C|0.985;T|0.015	0.015	strong	.	THAP4	27	.	NM_015963	exon2	c.G879A	p.P293P	CTTCTGCGGTGTC	.	PASS	Atlas-SNP
SPPL2A	84888	hgsc.bcm.edu	37	15	51023216	51023216	+	Silent	SNP	G	G	C	rs76947817	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	104	220	0	0.485981	0	G|0.977;C|0.023	0.023	strong	.	SPPL2A	26	.	NM_032802	exon10	c.C1035G	p.G345G	GAGAAGGCCTAGA	.	PASS	Atlas-SNP
SENP6	26054	hgsc.bcm.edu	37	6	76373002	76373002	+	Silent	SNP	G	G	A	rs16886792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	57	88	0	0.5	0	G|0.985;A|0.015	0.015	strong	.	SENP6	189	.	NM_015571	exon9	c.G762A	p.T254T	AAGAACGTCAATT	.	PASS	Atlas-SNP
ARL6IP4	51329	hgsc.bcm.edu	37	12	123466304	123466304	+	Missense_Mutation	SNP	A	A	G	rs74758272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	36	72	0	0.48	0	A|0.880;G|0.120	0.120	strong	.	ARL6IP4	14	.	NM_018694	exon3	c.A716G	p.K239R	AGAAGAAGAAGAG	.	PASS	Atlas-SNP
PREPL	9581	hgsc.bcm.edu	37	2	44571008	44571008	+	Silent	SNP	A	A	T	rs72875319	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	50	116	0	0.438596	0	A|0.966;T|0.034	0.034	strong	.	PREPL	69	.	NM_001171603	exon5	c.T492A	p.A164A	ATCTGGAGCAACT	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161139857	161139857	+	Silent	SNP	A	A	G	rs13231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	104	0	0.986667	0	A|0.787;G|0.213	0.213	strong	.	PLG	150	.	NM_000301	exon9	c.A1083G	p.Q361Q	GGAACAATTGGCT	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	839	152	658	1	0.181168	0.00151976	G|0.987;A|0.013	0.013	strong	OR2T3,NS,carcinoma,0,3	OR2T3	79	3	NM_001005495	exon1	c.G730A	p.A244T	GCCTTGGCCACCT	.	PASS	Atlas-SNP
ITIH4	3700	hgsc.bcm.edu	37	3	52860876	52860876	+	Silent	SNP	G	G	A	rs143427404	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	69	163	0	0.469388	0	G|0.995;A|0.005	0.005	strong	ITIH4,NS,carcinoma,-2,1	ITIH4	74	1	NM_001166449	exon4	c.C450T	p.L150L	CCGCTTGAGCAGC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	462	63	376	1	0.136364	0.00265957	T|0.944;G|0.056	0.056	strong	PSG2,NS,carcinoma,-1,2	PSG2	84	2	NM_031246	exon2	c.A129C	p.P43P	AACTTTTGGTGGC	.	scavenged	Atlas-SNP
BLM	641	hgsc.bcm.edu	37	15	91337479	91337479	+	Silent	SNP	G	G	A	rs2227933	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	90	197	0	0.382979	0	A|0.170;G|0.830	0.170	strong	.	BLM	122	.	NM_000057	exon16	c.G3102A	p.T1034T	TATAACGGAATGC	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76132805	76132805	+	Silent	SNP	C	C	G	rs73703182	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	95	183	0	0.549133	0	C|0.977;G|0.023	0.023	strong	.	DTX2	64	.	NM_001102594	exon9	c.C1452G	p.P484P	CCAGCCCCAGGGA	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11289307	11289307	+	Missense_Mutation	SNP	C	C	T	rs149142528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	29	66	0	0.42029	0	C|0.987;T|0.013	0.013	strong	.	KANK2	47	.	NM_015493	exon3	c.G1339A	p.V447M	TGGGCACTCGGCC	.	PASS	Atlas-SNP
NCKAP1	10787	hgsc.bcm.edu	37	2	183847598	183847598	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	4	221	0	0.0187793	0	.	.	none	NCKAP1,colon,carcinoma,+1,1	NCKAP1	105	1	NM_205842	exon13	c.C1177T	p.R393C	CATGACGAAGTAG	.	scavenged	Atlas-SNP
SLC22A20	440044	hgsc.bcm.edu	37	11	64981853	64981853	+	Missense_Mutation	SNP	G	G	T	rs239259	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	40	72	0	0.493827	0	G|0.667;T|0.333	0.333	strong	SLC22A20,NS,carcinoma,0,4	SLC22A20	36	4	NM_001004326	exon2	c.G438T	p.M146I	CTACATGGCCGGG	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3017138	3017138	+	Silent	SNP	C	C	T	rs1130428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	32	62	0	0.581818	0	C|0.960;T|0.040	0.040	strong	.	NQO2	21	.	NM_000904	exon6	c.C438T	p.S146S	CCTTTCCGTAACC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179435337	179435337	+	Silent	SNP	T	T	G	rs6732060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	72	135	0	0.428571	0	T|0.892;G|0.108	0.108	strong	.	TTN	18412	.	NM_001267550	exon326	c.A75522C	p.A25174A	ACGTACTGCATCT	.	PASS	Atlas-SNP
KIF3C	3797	hgsc.bcm.edu	37	2	26177198	26177198	+	Silent	SNP	A	A	G	rs17047211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	40	80	0	0.506329	0	A|0.828;G|0.172	0.172	strong	.	KIF3C	79	.	NM_002254	exon4	c.T1827C	p.Y609Y	GCGGATATACTCA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179605843	179605843	+	Silent	SNP	G	G	A	rs55895721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	53	0	0.45	0	G|0.981;A|0.019	0.019	strong	.	TTN	18412	.	NM_001267550	exon48	c.C12117T	p.P4039P	TTTGCAGGGGGTA	.	PASS	Atlas-SNP
ZPBP2	124626	hgsc.bcm.edu	37	17	38027824	38027824	+	Missense_Mutation	SNP	G	G	A	rs35829084	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	85	186	0	0.551948	0	G|0.968;A|0.032	0.032	strong	.	ZPBP2	33	.	NM_199321	exon4	c.G352A	p.A118T	GTTAAAGCAGAAA	.	PASS	Atlas-SNP
SLC27A5	10998	hgsc.bcm.edu	37	19	59023213	59023213	+	Missense_Mutation	SNP	A	A	C	rs146147877	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	37	58	0	0.5	0	A|0.995;C|0.005	0.005	strong	.	SLC27A5	58	.	NM_012254	exon1	c.T110G	p.L37R	TCCCCCAGGAGCC	.	PASS	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	37	10	12071397	12071397	+	Silent	SNP	G	G	A	rs11257490	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	113	153	0	1	0	G|0.765;A|0.235	0.235	strong	.	UPF2	111	.	NM_080599	exon3	c.C492T	p.L164L	TGAGTCGAGGCGG	.	PASS	Atlas-SNP
LMNA	4000	hgsc.bcm.edu	37	1	156106185	156106185	+	Silent	SNP	T	T	C	rs505058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	95	69	0	0.989583	0	T|0.729;G|0.001	.	strong	.	LMNA	31	.	NM_170707	exon7	c.T1338C	p.D446D	GGTGGATGAGGAG	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5444136	5444136	+	Nonsense_Mutation	SNP	C	C	T	rs2647574	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	136	154	0	0.992701	0	C|0.603;T|0.397	0.397	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.C706T	p.R236X	GCTGAGCGACTCC	.	PASS	Atlas-SNP
C17orf64	124773	hgsc.bcm.edu	37	17	58506748	58506748	+	Missense_Mutation	SNP	C	C	T	rs57928695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	75	108	0	0.510204	0	C|0.882;T|0.118	0.118	strong	.	C17orf64	19	.	NM_181707	exon5	c.C455T	p.P152L	ATGCGCCGGAGAG	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13260	13260	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	11	12	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.T924C	p.S308S	TTCAAGTCAACTA	.	PASS	Atlas-SNP
MAST2	23139	hgsc.bcm.edu	37	1	46496368	46496368	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	5	117	0	0.0420168	0	.	.	none	.	MAST2	136	.	NM_015112	exon22	c.C2643T	p.D881D	GGAGGACCATTCA	.	PASS	Atlas-SNP
PTCD3	55037	hgsc.bcm.edu	37	2	86344237	86344237	+	Silent	SNP	A	A	G	rs3764948	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	97	216	0	0.494898	0	A|0.939;G|0.061	0.061	strong	.	PTCD3	51	.	NM_017952	exon6	c.A369G	p.S123S	TAATTCATACCCC	.	PASS	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152082304	152082304	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	13	215	2	0.0449827	0.00930233	.	.	none	TCHH,NS,malignant_melanoma,0,1	TCHH	275	1	NM_007113	exon3	c.A3389C	p.K1130T	CTTCTCTTCTCCC	.	scavenged	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	81007527	81007527	+	Missense_Mutation	SNP	T	T	C	rs7963963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	80	141	0	0.481928	0	T|0.920;C|0.080	0.080	strong	PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	NM_001145026	exon26	c.T4559C	p.I1520T	TCCAGATTCACAA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536448	88536448	+	Silent	SNP	C	C	T	rs142168734		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	31	284	0	0.0928144	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.C2634T	p.D878D	CAGTGACAGCAGT	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326604	17326604	+	Missense_Mutation	SNP	C	C	T	rs7225976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	25	22	0	1	0	C|0.662;T|0.338	0.338	strong	.	.	.	.	NM_001243312	exon3	c.C419T	p.A140V	ATGGGGCAAATGC	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068661	5068661	+	Silent	SNP	A	A	G	rs2500019	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	48	83	0	0.551724	0	A|0.493;G|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.A906G	p.E302E	TCGAGAACGAGTG	.	PASS	Atlas-SNP
CHRDL2	25884	hgsc.bcm.edu	37	11	74413872	74413872	+	Silent	SNP	A	A	G	rs34528207	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	20	39	0	0.425532	0	A|0.791;G|0.209	0.209	strong	.	CHRDL2	47	.	NM_015424	exon9	c.T1087C	p.L363L	CCACCAAGTCCGA	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136587238	136587238	+	Silent	SNP	G	G	C	rs3816088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	25	64	0	0.390625	0	G|0.942;C|0.058	0.058	strong	.	LCT	309	.	NM_002299	exon3	c.C729G	p.V243V	GAAATCGACCGTG	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24848331	24848331	+	Silent	SNP	T	T	C	rs35698586	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	66	157	0	0.464789	0	T|0.985;C|0.015	0.015	strong	.	FAM65B	134	.	NM_015864	exon12	c.A999G	p.A333A	GGCTGCTGCCTTG	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	27	72	0	0.402985	0	T|0.697;C|0.303	0.303	strong	.	.	.	.	NM_019600	exon6	c.A1828G	p.T610A	AGGAAGTTGATAA	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	162929	162929	+	Silent	SNP	G	G	C	rs75342794	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	99	166	0	0.529412	0	G|0.941;C|0.059	0.059	strong	PLEKHG4B_ENST00000283426,NS,carcinoma,+2,1	PLEKHG4B	167	1	NM_052909	exon11	c.G1674C	p.S558S	TACCTCGGTGGCT	.	PASS	Atlas-SNP
OR14I1	401994	hgsc.bcm.edu	37	1	248844959	248844959	+	Missense_Mutation	SNP	T	T	C	rs55871516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	45	85	0	0.432692	0	T|0.871;C|0.129	0.129	strong	OR14I1,right_lower_lobe,carcinoma,-1,2	OR14I1	64	2	NM_001004734	exon1	c.A647G	p.Y216C	TGGAAATAGGAGA	.	PASS	Atlas-SNP
ELMSAN1	91748	hgsc.bcm.edu	37	14	74206658	74206658	+	Silent	SNP	G	G	A	rs758773	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	56	110	0	0.4375	0	G|0.859;A|0.141	0.141	strong	.	.	.	.	NM_194278	exon2	c.C54T	p.F18F	GCCCCCGAAGAGG	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41548003	41548003	+	Missense_Mutation	SNP	T	T	C	rs10093583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	33	51	0	0.589286	0	T|0.955;C|0.045	0.045	strong	.	ANK1	497	.	NM_001142446	exon33	c.A4096G	p.M1366V	CAGGCATGGCCAG	.	PASS	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183226213	183226213	+	Silent	SNP	A	A	G	rs16857710	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	88	116	0	0.590604	0	A|0.870;G|0.130	0.130	strong	KLHL6,NS,carcinoma,0,1	KLHL6	100	1	NM_130446	exon3	c.T543C	p.A181A	TGTGTCAGCCAGC	.	PASS	Atlas-SNP
KIF7	374654	hgsc.bcm.edu	37	15	90196113	90196113	+	Missense_Mutation	SNP	G	G	A	rs141865394	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	54	90	0	0.54	0	G|0.994;A|0.006	0.006	strong	.	KIF7	130	.	NM_198525	exon2	c.C49T	p.R17W	CAACCCGCACTGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	32	53	0	0.484848	0	C|0.687;T|0.313	0.313	strong	.	OBSCN	2142	.	NM_001271223	exon5	c.C1537T	p.L513L	CCTCCCCTGCAAC	.	PASS	Atlas-SNP
CPN1	1369	hgsc.bcm.edu	37	10	101835764	101835764	+	Silent	SNP	C	C	G	rs61754515	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	46	91	0	0.522727	0	C|0.959;G|0.041	0.041	strong	.	CPN1	62	.	NM_001308	exon2	c.G324C	p.R108R	CCTGTTCCGGAAC	.	PASS	Atlas-SNP
LPCAT3	10162	hgsc.bcm.edu	37	12	7091918	7091918	+	Silent	SNP	C	C	T	rs3764031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	69	170	0	0.463087	0	C|0.809;T|0.191	0.191	strong	.	LPCAT3	33	.	NM_005768	exon3	c.G285A	p.L95L	AATACACAGCAGG	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	118	0	1	0	G|0.762;A|0.238	0.238	strong	.	ATP13A4	154	.	NM_032279	exon13	c.C1482T	p.D494D	CAAGCCGTCCCTT	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77911224	77911224	+	Missense_Mutation	SNP	T	T	C	rs115848453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	71	152	0	0.39011	0	T|0.995;C|0.005	0.005	strong	.	USP35	179	.	NM_020798	exon5	c.T982C	p.S328P	GCCTTGTCTGTGC	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25963484	25963484	+	Missense_Mutation	SNP	C	C	T	rs116055743	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	65	136	0	0.515873	0	C|0.994;T|0.006	0.006	strong	.	ATP10A	270	.	NM_024490	exon8	c.G1426A	p.G476S	CCGAGCCCCCTCT	.	PASS	Atlas-SNP
MGARP	84709	hgsc.bcm.edu	37	4	140201259	140201259	+	Silent	SNP	G	G	A	rs28536098	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	96	0	0.467213	0	G|0.947;A|0.053	0.053	strong	.	.	.	.	NM_032623	exon1	c.C54T	p.P18P	GTTGGGGGGCGCC	.	PASS	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137263067	137263067	+	Silent	SNP	T	T	A	rs61751966	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	63	98	0	0.512195	0	T|0.987;A|0.013	0.013	strong	DGKI_ENST00000288490,NS,carcinoma,-2,2	DGKI	335	2	NM_004717	exon16	c.A1647T	p.A549A	TGGATTTGCTTCT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179613147	179613147	+	Missense_Mutation	SNP	G	G	C	rs75785339	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	317	147	282	0	0.463722	0	G|0.964;C|0.036	0.036	strong	.	TTN	18412	.	NM_133379	exon46	c.C13980G	p.H4660Q	GATATTGTGTGTG	.	PASS	Atlas-SNP
STPG1	90529	hgsc.bcm.edu	37	1	24710405	24710405	+	Missense_Mutation	SNP	A	A	G	rs11538189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	85	0	1	0	G|0.139;A|0.861	0.139	strong	.	.	.	.	NM_001199012	exon4	c.T278C	p.M93T	GGAAACATGCAAG	.	PASS	Atlas-SNP
EML1	2009	hgsc.bcm.edu	37	14	100331876	100331876	+	Silent	SNP	T	T	C	rs11160553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	125	0	0.490385	0	T|0.760;C|0.240	0.240	strong	.	EML1	97	.	NM_001008707	exon3	c.T276C	p.P92P	CCTGCCTTTAAGA	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1888193	1888193	+	Missense_Mutation	SNP	C	C	A	rs3820011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	76	125	0	0.510067	0	C|0.775;A|0.225	0.225	strong	.	KIAA1751	92	.	NM_001080484	exon17	c.G1882T	p.G628C	AGCTGCCGAAGTC	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41622189	41622189	+	Silent	SNP	G	G	A	rs305968	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	118	0	1	0	G|0.601;A|0.399	0.399	strong	.	CYP2F1	60	.	NM_000774	exon2	c.G96A	p.P32P	GCCTCCGGGACCC	.	PASS	Atlas-SNP
CAGE1	285782	hgsc.bcm.edu	37	6	7379031	7379031	+	Missense_Mutation	SNP	G	G	A	rs10223538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	72	169	0	0.483221	0	G|0.944;A|0.056	0.056	strong	.	CAGE1	165	.	NM_001170693	exon4	c.C506T	p.T169I	ACACTAGTTTCCA	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541035	12541035	+	Missense_Mutation	SNP	A	A	G	rs145053669	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	374	205	395	0	0.548128	0	A|0.993;G|0.007	0.007	strong	.	ZNF443	63	.	NM_005815	exon4	c.T1951C	p.C651R	CCTTACATTCATA	.	PASS	Atlas-SNP
KIF2C	11004	hgsc.bcm.edu	37	1	45218895	45218895	+	Silent	SNP	A	A	T	rs3795713	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	55	123	1	0.466102	0.00813008	A|0.741;T|0.259	0.259	strong	KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	NM_006845	exon6	c.A531T	p.R177R	CATCCGAGGCAGC	.	scavenged	Atlas-SNP
TP53INP1	94241	hgsc.bcm.edu	37	8	95942773	95942773	+	Silent	SNP	G	G	A	rs77630257	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	82	195	0	0.40796	0	A|0.010;G|0.990	0.010	strong	.	TP53INP1	22	.	NM_033285	exon4	c.C657T	p.H219H	CCGAGGGTGGCAA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552075	32552075	+	Missense_Mutation	SNP	A	A	G	rs1064664	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	23	33	0	0.319444	0	G|0.352;A|0.648	0.352	strong	.	HLA-DRB1	41	.	NM_002124	exon2	c.T181C	p.Y61H	GGTTATAGAAGTA	.	PASS	Atlas-SNP
RAPGEF6	51735	hgsc.bcm.edu	37	5	130840385	130840385	+	Silent	SNP	A	A	G	rs10063129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	78	144	0	0.46988	0	A|0.912;G|0.088	0.088	strong	.	RAPGEF6	361	.	NM_016340	exon11	c.T1188C	p.I396I	CATAACAATTTCT	.	PASS	Atlas-SNP
CYP27C1	339761	hgsc.bcm.edu	37	2	127953054	127953054	+	Silent	SNP	A	A	C	rs7568070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	85	139	0	0.534591	0	A|0.696;C|0.304	0.304	strong	CYP27C1,NS,carcinoma,0,1	CYP27C1	52	1	NM_001001665	exon5	c.T576G	p.T192T	GTACACAGTCCAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509076	195509076	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	24	161	0	0.0851064	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C9375A	p.D3125E	GGAAGTGTCGGTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678820	100678820	+	Missense_Mutation	SNP	T	T	C	rs4367469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	62	103	0	0.496	0	T|0.834;C|0.166	0.166	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4123C	p.C1375R	GAAGCCTGTTCAT	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220290674	220290674	+	Missense_Mutation	SNP	G	G	A	rs73991549	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	26	54	0	0.509804	0	G|0.989;A|0.011	0.011	strong	DES,brain,glioma,0,2	DES	53	2	NM_001927	exon9	c.G1375A	p.V459I	CAGGTCGTCAGTG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249605	71249605	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	32	174	0	0.164103	0	.	.	none	.	KRTAP5-8	28	.	NM_021046	exon1	c.C504T	p.C168C	CTGCTGCAAGCCC	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919878	30919878	+	Missense_Mutation	SNP	G	G	C	rs11970154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	53	64	0	1	0	G|0.816;C|0.184	0.184	strong	.	DPCR1	99	.	NM_080870	exon2	c.G3637C	p.G1213R	AACCTGGGGAACA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919081	12919081	+	Missense_Mutation	SNP	C	C	T	rs45443899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	342	177	267	0	0.517544	0	C|0.860;T|0.140	0.140	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.C217T	p.L73F	AAGACGCTTCATC	.	PASS	Atlas-SNP
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189602	50189602	+	Missense_Mutation	SNP	A	A	G	rs3813526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	25	54	0	0.520833	0	A|0.741;G|0.259	0.259	strong	.	NCKAP5L	142	.	NM_001037806	exon8	c.T2041C	p.S681P	TCTCTGAGCCCAG	.	PASS	Atlas-SNP
COG6	57511	hgsc.bcm.edu	37	13	40229891	40229891	+	Missense_Mutation	SNP	G	G	A	rs3812882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	57	53	0	0.678571	0	G|0.525;A|0.475	0.475	strong	.	COG6	49	.	NM_001145079	exon1	c.G28A	p.A10T	GTGGTCGCAGTGT	.	PASS	Atlas-SNP
ABL1	25	hgsc.bcm.edu	37	9	133760592	133760592	+	Missense_Mutation	SNP	C	C	T	rs2229067	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	60	95	0	0.625	0	C|0.971;T|0.029	0.029	strong	.	ABL1	1632	.	NM_007313	exon11	c.C2972T	p.S991L	AGCCGTCGGGGAC	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1418188	1418188	+	Missense_Mutation	SNP	C	C	T	rs151268825	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	65	144	0	0.507812	0	C|0.999;T|0.001	0.001	strong	TPO,NS,carcinoma,-1,1	TPO	224	1	NM_175719	exon2	c.C8T	p.A3V	TGAGAGCGCTCGC	.	PASS	Atlas-SNP
TNIK	23043	hgsc.bcm.edu	37	3	170824990	170824990	+	Silent	SNP	G	G	A	rs904617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	140	0	1	0	G|0.926;A|0.074	0.074	strong	.	TNIK	313	.	NM_015028	exon21	c.C2388T	p.Y796Y	TTTTTTGTAGCTC	.	PASS	Atlas-SNP
OGG1	4968	hgsc.bcm.edu	37	3	9796508	9796508	+	Missense_Mutation	SNP	G	G	A	rs1805373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	59	137	0	0.40411	0	G|0.969;A|0.031	0.031	strong	.	OGG1	57	.	NM_016819	exon4	c.G686A	p.R229Q	AGCTACGAGAGTC	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132237789	132237789	+	Silent	SNP	C	C	T	rs202066133	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	70	167	0	0.411765	0	C|1.000;T|0.000	0.000	strong	.	SFSWAP	69	.	NM_001261411	exon8	c.C1203T	p.T401T	CGTGACCGTGTCT	.	PASS	Atlas-SNP
PRUNE	58497	hgsc.bcm.edu	37	1	150999737	150999737	+	Silent	SNP	A	A	G	rs11204762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	55	104	0	0.482456	0	A|0.743;G|0.257	0.257	strong	.	PRUNE	40	.	NM_021222	exon6	c.A708G	p.K236K	GAGAAAAGACCAG	.	PASS	Atlas-SNP
KIAA1199	57214	hgsc.bcm.edu	37	15	81217024	81217024	+	Silent	SNP	G	G	A	rs28566789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	92	184	0	0.469388	0	G|0.973;A|0.027	0.027	strong	.	KIAA1199	118	.	NM_018689	exon17	c.G2265A	p.P755P	GCGGCCGTTCCTC	.	PASS	Atlas-SNP
SORL1	6653	hgsc.bcm.edu	37	11	121367626	121367626	+	Silent	SNP	T	T	C	rs12364988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	27	57	0	0.529412	0	T|0.511;C|0.489	0.489	strong	SORL1,NS,carcinoma,0,1	SORL1	218	1	NM_003105	exon6	c.T807C	p.H269H	ACGACATGAACCC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46787694	46787694	+	Missense_Mutation	SNP	A	A	G	rs6008794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	35	80	0	0.466667	0	A|0.696;G|0.304	0.304	strong	.	CELSR1	242	.	NM_014246	exon15	c.T5984C	p.L1995P	TGGGCTAGGAGCT	.	PASS	Atlas-SNP
IFI44L	10964	hgsc.bcm.edu	37	1	79095581	79095581	+	Missense_Mutation	SNP	T	T	C	rs987495	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	74	0	1	0	T|0.785;G|0.001	.	strong	IFI44L,NS,carcinoma,-1,1	IFI44L	93	1	NM_006820	exon4	c.T704C	p.I235T	CTGATATCACCAG	.	PASS	Atlas-SNP
SORBS1	10580	hgsc.bcm.edu	37	10	97154762	97154762	+	Silent	SNP	G	G	A	rs17110703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	108	228	0	0.504673	0	G|0.952;A|0.048	0.048	strong	.	SORBS1	185	.	NM_001034955	exon12	c.C1293T	p.S431S	ACCTTCGGAAGTT	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18715673	18715673	+	Silent	SNP	A	A	G	rs11044184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	181	0	0.442708	0	A|0.941;G|0.059	0.059	strong	.	PIK3C2G	315	.	NM_004570	exon26	c.A3504G	p.K1168K	TGTTAAATTGAAT	.	PASS	Atlas-SNP
DENND3	22898	hgsc.bcm.edu	37	8	142154291	142154291	+	Missense_Mutation	SNP	G	G	A	rs307761	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	72	124	0	0.489796	0	G|0.722;A|0.278	0.278	strong	.	DENND3	127	.	NM_014957	exon5	c.G428A	p.S143N	TGGACAGTCATAT	.	PASS	Atlas-SNP
CDC5L	988	hgsc.bcm.edu	37	6	44387305	44387305	+	Silent	SNP	T	T	C	rs11571982	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	61	144	0	0.484127	0	T|0.989;C|0.011	0.011	strong	.	CDC5L	86	.	NM_001253	exon9	c.T1212C	p.T404T	ACAGACTCCAAAC	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36349752	36349752	+	Missense_Mutation	SNP	G	G	A	rs404299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	203	244	0	0.995098	0	G|0.863;A|0.137	0.137	strong	.	KIRREL2	170	.	NM_199180	exon4	c.G508A	p.A170T	GATGGAGCCACCT	.	PASS	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100928421	100928421	+	Silent	SNP	C	C	T	rs74667145	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	35	70	0	0.479452	0	C|0.999;T|0.001	0.001	strong	.	CDC14A	65	.	NM_033313	exon9	c.C822T	p.I274I	GGCCATCGCCGTT	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149324153	149324153	+	Silent	SNP	G	G	A	rs34230349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	97	0	0.453333	0	G|0.984;A|0.016	0.016	strong	.	PDE6A	98	.	NM_000440	exon1	c.C84T	p.Y28Y	GGCCCGGTAGTGG	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16230427	16230427	+	Silent	SNP	C	C	T	rs34526519	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	54	88	0	0.457627	0	C|0.994;T|0.006	0.006	strong	.	ABCC1	156	.	NM_004996	exon29	c.C4218T	p.A1406A	GCTGGCCCACCTG	.	PASS	Atlas-SNP
SH2D3A	10045	hgsc.bcm.edu	37	19	6760974	6760974	+	Missense_Mutation	SNP	T	T	C	rs7258236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	33	79	0	0.423077	0	T|0.735;C|0.265	0.265	strong	.	SH2D3A	53	.	NM_005490	exon3	c.A94G	p.N32D	CGCCATTTTGCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515102	195515102	+	Missense_Mutation	SNP	G	G	C	rs199995135		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	19	181	1	0.0549133	0.00552486	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C3349G	p.H1117D	TGGTGTGACCTGT	.	scavenged	Atlas-SNP
PACS2	23241	hgsc.bcm.edu	37	14	105860919	105860919	+	Silent	SNP	C	C	T	rs201014934	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	2	65	0	0.0163934	0	C|1.000;T|0.000	0.000	strong	PACS2,NS,carcinoma,+2,1	PACS2	75	1	NM_001100913	exon25	c.C2625T	p.D875D	CAGCGACGTCAAG	.	scavenged	Atlas-SNP
DIRAS1	148252	hgsc.bcm.edu	37	19	2717256	2717256	+	Silent	SNP	C	C	G	rs3745812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	63	108	0	0.529412	0	C|0.851;G|0.149	0.149	strong	.	DIRAS1	26	.	NM_145173	exon2	c.G549C	p.G183G	CTGCTTCCCGGAG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	109	0	1	0	A|0.425;G|0.575	0.575	strong	HMCN1,NS,carcinoma,0,2	HMCN1	797	2	NM_031935	exon56	c.A8678G	p.E2893G	TGATAGAGTGTTT	.	PASS	Atlas-SNP
SCARB1	949	hgsc.bcm.edu	37	12	125263039	125263039	+	Missense_Mutation	SNP	C	C	T	rs701103	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	29	28	0	0.568627	0	C|0.956;T|0.044	0.044	strong	.	SCARB1	40	.	NM_001082959	exon12	c.G1495A	p.G499R	GCTGTCCGCTGGG	.	PASS	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Silent	SNP	T	T	C	rs2290906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	48	94	0	0.461538	0	T|0.737;C|0.263	0.263	strong	.	TNRC6C	173	.	NM_001142640	exon18	c.T4338C	p.S1446S	GCCTTCTTCGAGT	.	PASS	Atlas-SNP
KRT16	3868	hgsc.bcm.edu	37	17	39768756	39768756	+	Missense_Mutation	SNP	C	C	T	rs367990963		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	72	0	0.480519	0	.	.	weak	.	KRT16	45	.	NM_005557	exon1	c.G185A	p.C62Y	AGCCCGCAGGCTC	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	42	65	0	0.482759	0	A|0.950;G|0.050	0.050	strong	.	PARP14	242	.	NM_017554	exon6	c.A1891G	p.T631A	CCAAACACTGTAA	.	PASS	Atlas-SNP
C9orf50	375759	hgsc.bcm.edu	37	9	132377769	132377769	+	Missense_Mutation	SNP	G	G	A	rs117566704	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	35	62	0	0.555556	0	A|0.001;C|0.002;G|0.998	0.001	strong	.	C9orf50	25	.	NM_199350	exon4	c.C874T	p.R292C	CTGAGCGTCTGCG	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55534093	55534093	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	3	222	0	0.0121457	0	.	.	none	RP1,right_lower_lobe,carcinoma,+1,1	RP1	429	1	NM_006269	exon2	c.G567T	p.E189D	GACAGAGGTCATG	.	scavenged	Atlas-SNP
SSTR3	6753	hgsc.bcm.edu	37	22	37602611	37602611	+	Missense_Mutation	SNP	C	C	G	rs229568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	34	64	0	0.472222	0	C|0.934;G|0.066	0.066	strong	.	SSTR3	42	.	NM_001051	exon2	c.G1232C	p.S411T	ATCGTGCTGGACT	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531520	50531520	+	Silent	SNP	C	C	A	rs73307889	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	34	78	1	0.472222	0.0128205	C|0.984;A|0.016	0.016	strong	C10orf71_ENST00000374144,NS,carcinoma,+1,2	C10orf71	179	2	NM_001135196	exon3	c.C930A	p.T310T	CACGACCTTGCTA	.	scavenged	Atlas-SNP
ACOT12	134526	hgsc.bcm.edu	37	5	80655766	80655766	+	Missense_Mutation	SNP	T	T	G	rs147339997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	79	165	0	0.519737	0	T|0.996;G|0.004	0.004	strong	.	ACOT12	57	.	NM_130767	exon5	c.A452C	p.E151A	GTATCTTCATGTT	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	55	117	0	0.486726	0	C|0.660;T|0.340	0.340	strong	SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	NM_001235	exon3	c.C693T	p.T231T	CTATACCGTGGGT	.	PASS	Atlas-SNP
OPN3	23596	hgsc.bcm.edu	37	1	241803317	241803317	+	Silent	SNP	C	C	G	rs73139034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	52	109	0	0.553191	0	C|0.969;G|0.031	0.031	strong	.	OPN3	28	.	NM_014322	exon1	c.G240C	p.L80L	GTTGACCAGGAGG	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	190	230	0	0.989583	0	G|0.817;A|0.183	0.183	strong	.	MSH3	129	.	NM_002439	exon4	c.G693A	p.P231P	TACGCCGCTAGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510725	195510725	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	23	246	17	0.110048	0.0691057	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C7726T	p.P2576S	GAAGAGGGGTGGC	.	scavenged	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19422060	19422060	+	Silent	SNP	G	G	A	rs2236378	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	95	194	0	0.475	0	G|0.989;A|0.011	0.011	strong	.	UBR4	415	.	NM_020765	exon93	c.C13605T	p.V4535V	CAGCATGACGTTC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52375809	52375809	+	Silent	SNP	A	A	G	rs142094475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	26	67	0	0.464286	0	A|0.998;G|0.002	0.002	strong	.	ZNF577	63	.	NM_032679	exon7	c.T1434C	p.Y478Y	TGTAAGATACAAG	.	PASS	Atlas-SNP
C12orf68	387856	hgsc.bcm.edu	37	12	48577925	48577925	+	Missense_Mutation	SNP	A	A	G	rs140861476		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	22	49	0	0.468085	0	A|1.000;G|0.000	0.000	weak	.	C12orf68	11	.	NM_001013635	exon1	c.A20G	p.E7G	TGCTGGAGATCAT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149499284	149499284	+	Missense_Mutation	SNP	C	C	T	rs56163742	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	15	19	0	0.441176	0	C|0.873;T|0.127	0.127	strong	.	.	.	.	NM_198455	exon51	c.C7652T	p.A2551V	TGCAGGCCTGCCC	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	88	189	0	0.463158	0	T|0.003;G|0.006	.	strong	COL9A3,caecum,carcinoma,0,1	COL9A3	70	1	NM_001853	exon25	c.C1304A	p.A435E	GTGCCGCAGGCCC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73562744	73562744	+	Silent	SNP	G	G	A	rs10823849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	82	131	0	0.585714	0	G|0.681;A|0.319	0.319	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon52	c.G7572A	p.A2524A	GCCGGCGGGCACC	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371223	240371223	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	34	122	1	0.172589	0.00819672	.	.	none	FMN2,NS,carcinoma,0,3	FMN2	451	3	NM_020066	exon5	c.C3111T	p.P1037P	ACTTCCCGGAGCG	.	scavenged	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32109305	32109305	+	Missense_Mutation	SNP	T	T	C	rs112331962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	50	101	0	0.5	0	T|0.975;C|0.025	0.025	strong	.	PRR14L	198	.	NM_173566	exon4	c.A4520G	p.H1507R	GCACCATGTATTT	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51826921	51826921	+	Missense_Mutation	SNP	T	T	C	rs17567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	146	175	1	0.993197	0.00571429	T|0.702;C|0.298	0.298	strong	.	EPS15	72	.	NM_001981	exon24	c.A2466G	p.I822M	ACAAAATATTTCA	.	PASS	Atlas-SNP
FBXO10	26267	hgsc.bcm.edu	37	9	37537892	37537892	+	Missense_Mutation	SNP	G	G	T	rs7044561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	75	137	0	0.503356	0	G|0.983;T|0.017	0.017	strong	.	FBXO10	75	.	NM_012166	exon3	c.C634A	p.H212N	GGATGTGCCCGTT	.	PASS	Atlas-SNP
MBP	4155	hgsc.bcm.edu	37	18	74701936	74701936	+	Silent	SNP	G	G	A	rs76912958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	72	153	0	0.486486	0	G|0.977;A|0.023	0.023	strong	.	MBP	45	.	NM_001025101	exon5	c.C657T	p.P219P	GACTACGGGGTTT	.	PASS	Atlas-SNP
PWWP2B	170394	hgsc.bcm.edu	37	10	134219291	134219291	+	Silent	SNP	C	C	T	rs139452616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	12	19	0	0.705882	0	C|0.986;T|0.014	0.014	strong	.	PWWP2B	33	.	NM_001098637	exon2	c.C1287T	p.D429D	CCTGGACGAGGCC	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	74973926	74973926	+	Missense_Mutation	SNP	C	C	A	rs139481866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	339	178	310	0	0.525074	0	C|0.998;A|0.002	0.002	strong	.	LTBP2	158	.	NM_000428	exon26	c.G3863T	p.G1288V	TGGCAGCCCAGAA	.	PASS	Atlas-SNP
CAP2	10486	hgsc.bcm.edu	37	6	17541324	17541324	+	Missense_Mutation	SNP	A	A	G	rs34206659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	89	203	0	0.514451	0	A|0.971;G|0.029	0.029	strong	.	CAP2	61	.	NM_006366	exon9	c.A947G	p.Y316C	AATCTTATCCTTC	.	PASS	Atlas-SNP
RECQL	5965	hgsc.bcm.edu	37	12	21623179	21623179	+	Silent	SNP	T	T	C	rs61754415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	784	357	803	0	0.455357	0	T|0.893;C|0.107	0.107	strong	.	RECQL	45	.	NM_032941	exon16	c.A1899G	p.Q633Q	ACCAGATTGCTGA	.	PASS	Atlas-SNP
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	89	205	0	0.502825	0	A|0.805;G|0.195	0.195	strong	.	ITGB6	68	.	NM_000888	exon13	c.T2064C	p.N688N	CCCCTCATTATCT	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32134122	32134122	+	Missense_Mutation	SNP	T	T	C	rs75434030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	91	124	0	0.541667	0	T|0.995;C|0.005	0.005	strong	.	.	.	.	NM_018169	exon4	c.T233C	p.M78T	CTGATATGCATAA	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607758	84607758	+	Silent	SNP	T	T	A	rs10867826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	490	307	375	2	0.626531	0.00533333	T|0.426;A|0.574	0.574	strong	.	.	.	.	NM_001001670	exon4	c.T2373A	p.T791T	GGAGACTTCTTCA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46657798	46657798	+	Silent	SNP	A	A	G	rs6007748	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	60	77	0	0.6	0	A|0.737;G|0.263	0.263	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T1422C	p.D474D	AAATCTATCAGAG	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214787130	214787130	+	Silent	SNP	G	G	A	rs2070064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	89	270	1	0.465969	0.0037037	G|0.653;A|0.345	0.345	strong	CENPF,NS,carcinoma,0,1	CENPF	321	1	NM_016343	exon2	c.G33A	p.G11G	AGAAGGGCTGCCT	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56387581	56387581	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	27	79	0	0.284211	0	.	.	none	RFX7_ENST00000423270,NS,lymphoid_neoplasm,0,2	RFX7	170	2	NM_022841	exon9	c.G2345A	p.W782X	TGTTGCCATCCAT	.	PASS	Atlas-SNP
NUP35	129401	hgsc.bcm.edu	37	2	183993085	183993085	+	Silent	SNP	A	A	G	rs61743390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	44	90	0	0.444444	0	A|0.989;G|0.011	0.011	strong	.	NUP35	28	.	NM_138285	exon2	c.A111G	p.G37G	ACCTGGATTTTTA	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	133	0	1	0	C|0.698;T|0.302	0.302	strong	.	MICA	21	.	NM_001177519	exon4	c.C684T	p.S228S	GGCTTCCAGCTTC	.	PASS	Atlas-SNP
TMED7-TICAM2	100302736	hgsc.bcm.edu	37	5	114916351	114916351	+	Silent	SNP	T	T	G	rs7705473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	97	179	0	0.563953	0	T|0.989;G|0.011	0.011	strong	.	.	.	.	NM_001164468	exon4	c.A1110C	p.G370G	AGGAAATCCACGA	.	PASS	Atlas-SNP
ICAM1	3383	hgsc.bcm.edu	37	19	10385540	10385540	+	Missense_Mutation	SNP	A	A	T	rs5491	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	53	87	0	0.464912	0	A|0.924;T|0.076	0.076	strong	.	ICAM1	32	.	NM_000201	exon2	c.A167T	p.K56M	AGCCCAAGTTGTT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130150704	130150704	+	Missense_Mutation	SNP	A	A	G	rs61750883	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	33	68	0	0.485294	0	A|0.993;G|0.007	0.007	strong	.	COL6A5	205	.	NM_153264	exon33	c.A5644G	p.I1882V	TCATCCATCATCA	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38538319	38538319	+	Missense_Mutation	SNP	A	A	G	rs61998236	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	88	194	0	0.478261	0	A|0.974;G|0.026	0.026	strong	.	TTC3	182	.	NM_001001894	exon33	c.A3803G	p.D1268G	CTGAGGATGGGCA	.	PASS	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56919216	56919216	+	Missense_Mutation	SNP	A	A	G	rs61746763	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	20	70	0	0.4	0	A|0.981;G|0.019	0.019	strong	.	SLC12A3	99	.	NM_001126108	exon15	c.A1865G	p.N622S	CCTACAACCTGGC	.	PASS	Atlas-SNP
CSF2RA	1438	hgsc.bcm.edu	37	X	1428421	1428421	+	Missense_Mutation	SNP	G	G	T	rs28722602	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	111	272	0	0.451219	0	T|0.144;G|0.854;A|0.002	0.144	strong	.	CSF2RA	153	.	NM_172246	exon11	c.G1073T	p.R358L	CGACACGGGGGAA	.	PASS	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22059413	22059413	+	Silent	SNP	C	C	G	rs28710878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	64	0	0.443182	0	C|0.970;G|0.030	0.030	strong	.	BMP1	131	.	NM_006129	exon16	c.C2205G	p.L735L	CGTCCTCCATGAC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6966296	6966296	+	Silent	SNP	G	G	A	rs73390557	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	13	55	0	0.40625	0	G|0.950;A|0.050	0.050	strong	.	LAMA1	458	.	NM_005559	exon49	c.C6900T	p.S2300S	CTGGGAGCTGCAA	.	PASS	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5719649	5719649	+	Silent	SNP	T	T	C	rs78484876	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	116	217	1	0.485356	0.00460829	T|0.990;C|0.010	0.010	strong	.	TRIM22	66	.	NM_006074	exon4	c.T624C	p.G208G	GGAAGGTGAGGTG	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500189	90500189	+	Missense_Mutation	SNP	C	C	G	rs77127003	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	82	106	0	0.666667	0	C|0.948;G|0.052	0.052	strong	.	.	.	.	NM_178828	exon4	c.C787G	p.L263V	TCCAGCCTGGCTG	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13679335	13679335	+	Silent	SNP	C	C	T	rs1061376	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	81	144	0	0.55102	0	C|0.518;N|0.000	.	strong	.	FBLN2	137	.	NM_001004019	exon18	c.C3612T	p.D1204D	CCTGGACGTGGAG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79024915	79024915	+	Silent	SNP	G	G	C	rs16877111	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	149	1	1	0.00671141	G|0.893;C|0.107	0.107	strong	.	CMYA5	643	.	NM_153610	exon2	c.G327C	p.R109R	TAGTCGGGAAGGG	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	37	X	63412690	63412690	+	Missense_Mutation	SNP	A	A	C	rs34677493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	35	63	0	0.5	0	0|0.013;C|0.188	0.188	strong	.	.	.	.	NM_152424	exon2	c.T477G	p.F159L	AGAGGGAAACTTC	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11114174	11114174	+	Silent	SNP	A	A	G	rs61741309	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	60	74	0	0.517241	0	A|0.962;G|0.038	0.038	strong	.	CLEC16A	101	.	NM_015226	exon11	c.A1428G	p.Q476Q	CACGCAATGGAGC	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	73	0	0.467742	0	G|0.868;A|0.132	0.132	strong	PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	NM_001085382	exon1	c.C1413T	p.G471G	CCTGGGGCCGTGG	.	PASS	Atlas-SNP
GEN1	348654	hgsc.bcm.edu	37	2	17961321	17961321	+	Silent	SNP	A	A	G	rs16983864	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	26	52	0	0.490566	0	A|0.963;G|0.037	0.037	strong	.	GEN1	79	.	NM_182625	exon13	c.A1341G	p.A447A	TGAAGCAGCATAT	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77069474	77069474	+	Silent	SNP	G	G	A	rs35442986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	115	207	0	0.522727	0	G|0.914;A|0.086	0.086	strong	.	NUP54	48	.	NM_017426	exon1	c.C54T	p.T18T	GGCCGCGGTGGCT	.	PASS	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	37	5	57753149	57753149	+	Silent	SNP	A	A	G	rs17767072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	41	48	0	0.577465	0	A|0.871;G|0.129	0.129	strong	.	PLK2	71	.	NM_006622	exon7	c.T867C	p.Y289Y	GCACCTATAAGTT	.	PASS	Atlas-SNP
MGARP	84709	hgsc.bcm.edu	37	4	140187985	140187985	+	Missense_Mutation	SNP	G	G	A	rs6823412	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	98	206	0	0.518519	0	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_032623	exon4	c.C491T	p.A164V	CTCGCCGCTGCAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679316	100679316	+	Missense_Mutation	SNP	T	T	A	rs199509433	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	42	149	0	0.224599	0	T|0.906;A|0.094	0.094	strong	MUC17,right_upper_lobe,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.T4619A	p.V1540D	CTGCTGTCACCAG	.	PASS	Atlas-SNP
LRRIQ3	127255	hgsc.bcm.edu	37	1	74649119	74649119	+	Splice_Site	SNP	C	C	T	rs143858191	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	55	131	0	0.462185	0	C|0.998;T|0.002	0.002	strong	.	LRRIQ3	146	.	NM_001105659	exon3	c.249+1G>A	.	TGCTTACCTGATT	.	PASS	Atlas-SNP
TTLL2	83887	hgsc.bcm.edu	37	6	167755063	167755063	+	Missense_Mutation	SNP	G	G	A	rs34931196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	67	177	0	0.403614	0	G|0.970;A|0.030	0.030	strong	.	TTLL2	82	.	NM_031949	exon3	c.G1675A	p.V559I	GTTCTTGTTTTTC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105406238	105406238	+	Missense_Mutation	SNP	A	A	C	rs2819419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	30	34	0	1	0	A|0.417;C|0.583	0.583	strong	AHNAK2,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.T15550G	p.Y5184D	GCGAGTACTTGGT	.	PASS	Atlas-SNP
OR8S1	341568	hgsc.bcm.edu	37	12	48919793	48919793	+	Missense_Mutation	SNP	T	T	C	rs2705143	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	206	170	1	1	0.00588235	T|0.781;C|0.219	0.219	strong	.	OR8S1	47	.	NM_001005203	exon1	c.T379C	p.C127R	GCCATCTGCCGCC	.	PASS	Atlas-SNP
ZNF630	57232	hgsc.bcm.edu	37	X	47918205	47918205	+	Silent	SNP	G	G	A	rs501128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	44	100	0	0.295302	0	0|0.004;A|0.588	0.588	strong	.	ZNF630	71	.	NM_001037735	exon5	c.C1626T	p.P542P	CTCATAGGGTTTC	.	PASS	Atlas-SNP
ZP4	57829	hgsc.bcm.edu	37	1	238050136	238050136	+	Silent	SNP	T	T	C	rs520720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	62	127	0	0.484375	0	T|0.856;C|0.144	0.144	strong	ZP4,NS,carcinoma,-2,1	ZP4	161	1	NM_021186	exon6	c.A774G	p.E258E	CACCAGTTCATTT	.	PASS	Atlas-SNP
ZNF41	7592	hgsc.bcm.edu	37	X	47308509	47308509	+	Missense_Mutation	SNP	A	A	C	rs34301930	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	123	197	0	0.534783	0	A|0.966;C|0.034	0.034	strong	.	ZNF41	71	.	NM_007130	exon5	c.T660G	p.N220K	GTTACCATTTCCA	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141750613	141750613	+	Missense_Mutation	SNP	T	T	A	rs145430437	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	112	261	0	0.432432	0	T|0.988;A|0.012	0.012	strong	.	MGAM	767	.	NM_004668	exon24	c.T2754A	p.N918K	ACACAATGGTGTC	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45767455	45767455	+	Silent	SNP	A	A	G	rs136569	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	63	112	0	0.466667	0	A|0.380;G|0.620	0.620	strong	.	SMC1B	215	.	NM_148674	exon14	c.T2209C	p.L737L	TTTGTAACTGAGA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	10	386	3	0.037594	0.00777202	C|0.826;T|0.174	0.174	strong	PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon3	c.G985A	p.G329S	TGGCACCAGTCAC	.	scavenged	Atlas-SNP
OR52E4	390081	hgsc.bcm.edu	37	11	5906205	5906205	+	Missense_Mutation	SNP	G	G	A	rs4757987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	316	151	286	0	0.477848	0	G|0.588;A|0.412	0.412	strong	.	OR52E4	65	.	NM_001005165	exon1	c.G683A	p.R228H	TTTTTCGCCTTCC	.	PASS	Atlas-SNP
CYB5R2	51700	hgsc.bcm.edu	37	11	7687715	7687715	+	Missense_Mutation	SNP	T	T	C	rs12801394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	149	0	0.518519	0	T|0.205;C|0.795	0.795	strong	.	CYB5R2	23	.	NM_016229	exon8	c.A625G	p.N209D	ACAGGTTGAACTG	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782327	54782327	+	Missense_Mutation	SNP	G	G	C	rs7247025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	332	329	302	0	0.990964	0	A|0.000;C|0.121;G|0.878	0.121	strong	.	LILRB2	94	.	NM_005874	exon7	c.C1045G	p.R349G	ACTGCCGCCATGA	.	PASS	Atlas-SNP
APOBEC3B	9582	hgsc.bcm.edu	37	22	39380131	39380131	+	Silent	SNP	C	C	T	rs61730557	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	96	243	0	0.393443	0	C|0.974;T|0.026	0.026	strong	.	APOBEC3B	32	.	NM_004900	exon2	c.C69T	p.N23N	TGAAAACGAACCC	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21051209	21051209	+	Missense_Mutation	SNP	G	G	C	rs330150	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	71	155	0	0.486301	0	G|0.853;C|0.146	0.146	strong	DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	NM_017539	exon33	c.C4695G	p.I1565M	GAGGGAGATTTCT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186761	12186761	+	Missense_Mutation	SNP	A	A	G	rs7259845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	46	83	0	0.638889	0	A|0.715;G|0.285	0.285	strong	.	ZNF844	69	.	NM_001136501	exon4	c.A826G	p.T276A	ACTCACACTGGAG	.	PASS	Atlas-SNP
ACVR1C	130399	hgsc.bcm.edu	37	2	158390468	158390468	+	Missense_Mutation	SNP	T	T	C	rs7594480	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	63	0	1	0	T|0.843;C|0.157	0.157	strong	.	ACVR1C	85	.	NM_145259	exon9	c.A1444G	p.I482V	GAGATATAGTCTT	.	PASS	Atlas-SNP
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	88	0	0.5	0	T|0.587;C|0.413	0.413	strong	.	PARD3B	314	.	NM_152526	exon20	c.T2976C	p.S992S	GCCATCTGAGTAT	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108380740	108380740	+	Missense_Mutation	SNP	G	G	C	rs36005552	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	56	115	0	0.629214	0	G|0.990;C|0.010	0.010	strong	.	EXPH5	193	.	NM_015065	exon6	c.C5494G	p.R1832G	TCAGTCGACTCAG	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124154697	124154697	+	Splice_Site	SNP	G	G	T	rs10101626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	41	70	0	0.488095	0	G|0.784;T|0.216	0.216	strong	.	WDR67	97	.	NM_145647	exon19	c.2835+1G>T	.	AAGAAGGTAAAAA	.	PASS	Atlas-SNP
ARSF	416	hgsc.bcm.edu	37	X	3028289	3028289	+	Silent	SNP	C	C	T	rs5983011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	89	154	0	0.529762	0	C|0.874;0|0.003	.	strong	.	ARSF	97	.	NM_004042	exon10	c.C1386T	p.D462D	CAAGGACGACAGT	.	PASS	Atlas-SNP
CDC6	990	hgsc.bcm.edu	37	17	38457151	38457151	+	Missense_Mutation	SNP	G	G	A	rs13706	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	202	189	0	0.985366	0	G|0.734;A|0.266	0.266	strong	.	CDC6	53	.	NM_001254	exon10	c.G1321A	p.V441I	TCAGAAGTTGATG	.	PASS	Atlas-SNP
EFCAB11	90141	hgsc.bcm.edu	37	14	90398907	90398907	+	Silent	SNP	G	G	A	rs8778	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	26	78	0	0.419355	0	G|0.806;A|0.194	0.194	strong	.	EFCAB11	12	.	NM_145231	exon4	c.C282T	p.N94N	TACTTCGTTCCGA	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713821	32713821	+	Silent	SNP	C	C	A	rs34005994	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	645	24	593	0	0.0372093	0	C|0.778;A|0.222	0.222	strong	HLA-DQA2,NS,carcinoma,+2,1	HLA-DQA2	27	1	NM_020056	exon3	c.C585A	p.G195G	CTGGGGCCTGGAC	.	scavenged	Atlas-SNP
CROT	54677	hgsc.bcm.edu	37	7	86986863	86986863	+	Silent	SNP	T	T	C	rs75642989	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	37	59	0	0.513889	0	T|0.986;C|0.014	0.014	strong	.	CROT	81	.	NM_001143935	exon4	c.T156C	p.D52D	TCCAGATGCTAAG	.	PASS	Atlas-SNP
SFXN2	118980	hgsc.bcm.edu	37	10	104486822	104486822	+	Silent	SNP	C	C	T	rs35094483	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	190	192	0	0.994764	0	C|0.969;T|0.031	0.031	strong	.	SFXN2	40	.	NM_178858	exon3	c.C240T	p.P80P	CCACCCCGACACT	.	PASS	Atlas-SNP
FAAH	2166	hgsc.bcm.edu	37	1	46874246	46874246	+	Missense_Mutation	SNP	C	C	T	rs77101686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	43	59	1	0.632353	0.0169492	C|0.998;T|0.002	0.002	strong	FAAH,colon,carcinoma,-1,1	FAAH	36	1	NM_001441	exon8	c.C1067T	p.A356V	AGGCTGCGGGGCA	.	scavenged	Atlas-SNP
DCTN1	1639	hgsc.bcm.edu	37	2	74593482	74593482	+	Silent	SNP	G	G	A	rs140986485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	64	140	0	0.463768	0	G|0.997;A|0.003	0.003	strong	.	DCTN1	110	.	NM_004082	exon23	c.C2649T	p.S883S	GGGGCTGCTGGAG	.	PASS	Atlas-SNP
ZNF597	146434	hgsc.bcm.edu	37	16	3486736	3486736	+	Silent	SNP	G	G	A	rs34461484	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	43	0	0.48	0	G|0.985;A|0.015	0.015	strong	.	ZNF597	41	.	NM_152457	exon4	c.C963T	p.D321D	TTCAGAGTCCTCG	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813473	248813473	+	Missense_Mutation	SNP	A	A	C	rs78776291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	108	110	0	0.559586	0	A|0.941;C|0.059	0.059	strong	.	OR2T27	52	.	NM_001001824	exon1	c.T713G	p.V238G	GTGGCCACAGCCT	.	PASS	Atlas-SNP
ZNF839	55778	hgsc.bcm.edu	37	14	102807671	102807671	+	Missense_Mutation	SNP	C	C	T	rs9464	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	113	237	0	0.439689	0	T|0.080;G|0.001	0.080	strong	.	ZNF839	41	.	NM_018335	exon8	c.C1939T	p.P647S	TCCCCTCCAGTAA	.	PASS	Atlas-SNP
AARS2	57505	hgsc.bcm.edu	37	6	44279824	44279824	+	Silent	SNP	C	C	T	rs75506489	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	53	125	0	0.386861	0	C|0.980;T|0.020	0.020	strong	.	AARS2	77	.	NM_020745	exon2	c.G420A	p.G140G	TTCACCCCCAAAG	.	PASS	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32492529	32492529	+	Missense_Mutation	SNP	G	G	A	rs55789327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	108	208	0	0.53202	0	G|0.972;A|0.028	0.028	strong	.	DDX58	82	.	NM_014314	exon4	c.C431T	p.S144F	TTAGTAGAGCAAA	.	PASS	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	37	14	31578762	31578762	+	Silent	SNP	C	C	T	rs17097735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	67	149	0	0.432258	0	C|0.750;T|0.250	0.250	strong	.	HECTD1	159	.	NM_015382	exon36	c.G6321A	p.E2107E	CGTTCGCTCCACA	.	PASS	Atlas-SNP
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	111	205	0	0.5311	0	T|0.799;C|0.201	0.201	strong	EAF2,NS,carcinoma,0,1	EAF2	26	1	NM_018456	exon2	c.T162C	p.G54G	GGTTGGTGAAGGT	.	PASS	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17053499	17053499	+	Silent	SNP	A	A	G	rs4602367	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	73	147	0	0.532847	0	A|0.441;G|0.559	0.559	strong	.	PLCL2	145	.	NM_015184	exon2	c.A2283G	p.G761G	AGGAGGAAAGCCT	.	PASS	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	37	4	39306504	39306504	+	Silent	SNP	C	C	G	rs2066792	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	77	143	0	0.478261	0	C|0.922;G|0.078	0.078	strong	.	RFC1	114	.	NM_001204747	exon15	c.G2043C	p.R681R	CTTACTCCGGGTG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44890841	44890841	+	Silent	SNP	G	G	A	rs59953894	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	84	221	0	0.41791	0	G|0.962;A|0.038	0.038	strong	.	ZNF285	86	.	NM_152354	exon4	c.C1566T	p.S522S	ATTCCGGCTGAAG	.	PASS	Atlas-SNP
C9orf78	51759	hgsc.bcm.edu	37	9	132591509	132591509	+	Silent	SNP	A	A	G	rs3818553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	44	137	0	0.360656	0	A|0.766;G|0.234	0.234	strong	C9orf78,NS,carcinoma,0,1	C9orf78	26	1	NM_016520	exon8	c.T753C	p.G251G	CGTGTCACCTACT	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48517538	48517538	+	Missense_Mutation	SNP	G	G	A	rs62129078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	151	128	1	1	0.0078125	G|0.845;A|0.155	0.155	strong	.	ELSPBP1	29	.	NM_022142	exon3	c.G181A	p.G61S	TACAACGGCCAGT	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140603794	140603794	+	Silent	SNP	C	C	T	rs59600730	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	25	98	0	0.337838	0	C|0.977;T|0.023	0.023	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C717T	p.A239A	TAATGCCCCTGAG	.	PASS	Atlas-SNP
MX1	4599	hgsc.bcm.edu	37	21	42821113	42821113	+	Silent	SNP	T	T	C	rs2070229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	93	0	0.5	0	T|0.624;C|0.376	0.376	strong	MX1,NS,carcinoma,+1,1	MX1	58	1	NM_001144925	exon16	c.T1323C	p.R441R	GTATCGTGGTAGA	.	PASS	Atlas-SNP
CCDC144A	9720	hgsc.bcm.edu	37	17	16664991	16664991	+	Missense_Mutation	SNP	G	G	A	rs55685346		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	445	117	178	0	0.262921	0	.	.	weak	CCDC144B,NS,carcinoma,0,1	CCDC144A	53	1	NM_014695	exon13	c.G3625A	p.E1209K	AGGAAGGAGATAG	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	37	3	145794607	145794607	+	Missense_Mutation	SNP	A	A	G	rs115199093	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	78	154	0	0.5	0	A|0.998;G|0.002	0.002	strong	.	PLOD2	81	.	NM_182943	exon15	c.T1639C	p.Y547H	TGTTATAATGGGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417768	105417768	+	Silent	SNP	C	C	A	rs2396458	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	255	383	0	0.996094	0	C|0.809;A|0.191	0.191	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G4020T	p.V1340V	GGCAGACACCCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508385	195508385	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	352	26	413	0	0.0738636	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G10066C	p.G3356R	CGTGACCTGTGGA	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433444	169433444	+	Silent	SNP	C	C	T	rs72695199	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	77	115	0	0.616	0	C|0.907;T|0.093	0.093	strong	.	PALLD	179	.	NM_001166108	exon2	c.C789T	p.S263S	CCACAGCGCCCTC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152285541	152285541	+	Silent	SNP	T	T	C	rs116417983	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	542	253	535	0	0.46679	0	T|0.986;C|0.014	0.014	strong	.	FLG	900	.	NM_002016	exon3	c.A1821G	p.Q607Q	CGATGATTGTCCC	.	PASS	Atlas-SNP
CAPN6	827	hgsc.bcm.edu	37	X	110491865	110491865	+	Silent	SNP	G	G	A	rs17879776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	50	150	0	0.35461	0	G|0.991;A|0.009	0.009	strong	.	CAPN6	120	.	NM_014289	exon10	c.C1416T	p.T472T	GAACATGGTTGGG	.	PASS	Atlas-SNP
EIF4G1	1981	hgsc.bcm.edu	37	3	184039304	184039304	+	Missense_Mutation	SNP	A	A	G	rs16858632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	64	157	0	0.467153	0	A|0.976;G|0.024	0.024	strong	.	EIF4G1	151	.	NM_001194946	exon11	c.A953G	p.Y318C	AGCCATATCGCCT	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82835545	82835545	+	Silent	SNP	A	A	G	rs160279	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	35	78	0	0.538462	0	G|0.496;N|0.000	0.496	strong	VCAN,NS,carcinoma,+2,1	VCAN	498	1	NM_004385	exon8	c.A6723G	p.R2241R	CATGAGACCAACA	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1546805	1546805	+	Missense_Mutation	SNP	G	G	A	rs62623705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	30	93	0	0.410959	0	G|0.904;A|0.096	0.096	strong	SIRPB1,caecum,carcinoma,-1,1	SIRPB1	83	1	NM_006065	exon5	c.C1193T	p.A398V	AGTCAGGCCTTCT	.	PASS	Atlas-SNP
CLEC4C	170482	hgsc.bcm.edu	37	12	7890040	7890040	+	Missense_Mutation	SNP	G	G	T	rs77889141	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	27	67	0	0.5	0	G|0.981;T|0.019	0.019	strong	.	CLEC4C	44	.	NM_130441	exon5	c.C366A	p.N122K	CCTGGTGTTGATC	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179564885	179564885	+	Missense_Mutation	SNP	A	A	G	rs147268063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	72	113	0	0.483221	0	A|0.997;G|0.003	0.003	strong	.	TDRD5	149	.	NM_173533	exon4	c.A763G	p.M255V	ATGAGCATGGAAA	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506774	11506774	+	Missense_Mutation	SNP	C	C	T	rs202083397	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	445	109	114	1	0.244944	0.00877193	C|0.783;T|0.218	0.218	strong	PRB1,NS,malignant_melanoma,0,1	PRB1	33	1	NM_199353	exon3	c.G263A	p.R88Q	GGACTTCGGGACT	.	scavenged	Atlas-SNP
TXNDC11	51061	hgsc.bcm.edu	37	16	11773261	11773261	+	Silent	SNP	G	G	C	rs8191350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	53	101	0	0.445378	0	G|0.970;C|0.030	0.030	strong	.	TXNDC11	75	.	NM_015914	exon12	c.C2667G	p.T889T	GTTCTCGGTAAGG	.	PASS	Atlas-SNP
DBN1	1627	hgsc.bcm.edu	37	5	176885145	176885145	+	Missense_Mutation	SNP	A	A	C	rs139935466	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	43	117	0	0.401869	0	A|0.995;C|0.005	0.005	strong	.	DBN1	122	.	NM_080881	exon13	c.T1696G	p.S566A	GGGCTGAGGGCAG	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225373101	225373101	+	Missense_Mutation	SNP	G	G	T	rs6679852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	55	128	0	0.462185	0	G|0.994;T|0.006	0.006	strong	.	DNAH14	300	.	NM_001373	exon36	c.G5578T	p.V1860F	TTATCAGTTGCAG	.	PASS	Atlas-SNP
NMT1	4836	hgsc.bcm.edu	37	17	43181223	43181223	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	51	95	0	0.443478	0	.	.	none	.	NMT1	31	.	NM_021079	exon10	c.C1311T	p.D437D	GAGCGACGCCCTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105408827	105408827	+	Missense_Mutation	SNP	A	A	C	rs11850949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	113	269	1	0.444882	0.00371747	A|0.540;C|0.460	0.460	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T12961G	p.L4321V	CATCCAACGAGGC	.	PASS	Atlas-SNP
OAS1	4938	hgsc.bcm.edu	37	12	113357442	113357442	+	Missense_Mutation	SNP	G	G	A	rs2660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	119	0	1	0	G|0.225;A|0.775	0.775	strong	.	OAS1	128	.	NM_001032409	exon6	c.G1189A	p.G397R	CAGAGAGGACAAA	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Missense_Mutation	SNP	G	G	T	rs1135201	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	371	17	367	1	0.0458221	0.0027248	G|0.744;T|0.256	0.256	strong	SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.C316A	p.R106S	TGATGCGGATGGA	.	scavenged	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802782	57802782	+	Silent	SNP	C	C	T	rs80302225	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	27	76	0	0.428571	0	C|0.994;T|0.006	0.006	strong	.	ZNF460	59	.	NM_006635	exon3	c.C873T	p.Y291Y	TACCTACCGCTCC	.	PASS	Atlas-SNP
DYNLT3	6990	hgsc.bcm.edu	37	X	37701048	37701048	+	Silent	SNP	G	G	A	rs11771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	88	105	0	0.988764	0	G|0.663;0|0.004	.	strong	.	DYNLT3	9	.	NM_006520	exon3	c.C183T	p.A61A	TTTATAGGCTTTT	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	496	79	301	0	0.159274	0	G|0.970;A|0.030	0.030	strong	PCDHB11,NS,carcinoma,0,3	PCDHB11	162	3	NM_018931	exon1	c.G1594A	p.G532S	CGCGTGGGCGCCA	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32713706	32713706	+	Missense_Mutation	SNP	A	A	T	rs2366894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	204	277	0	1	0	A|0.424;T|0.576	0.576	strong	BIRC6_ENST00000421745,NS,carcinoma,0,3	BIRC6	838	3	NM_016252	exon42	c.A8020T	p.T2674S	AGTTCAACTGGAA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76522784	76522784	+	Silent	SNP	G	G	A	rs61744545	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	61	124	0	0.469231	0	G|0.933;A|0.067	0.067	strong	DNAH17,NS,carcinoma,-2,1	DNAH17	347	1	NM_173628	exon24	c.C3660T	p.R1220R	GGCCTCGCGCCTG	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87653594	87653594	+	Silent	SNP	A	A	G	rs201078979	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	31	87	0	0.402597	0	A|0.999;G|0.001	0.001	strong	.	PTPN13	203	.	NM_006264	exon11	c.A1650G	p.P550P	TGAACCATTTATA	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145741702	145741702	+	Missense_Mutation	SNP	C	C	G	rs4244612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	15	30	0	0.483871	0	C|0.586;G|0.414	0.414	strong	.	RECQL4	75	.	NM_004260	exon5	c.G801C	p.E267D	CCAGGGCTCCTCG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795636	29795636	+	Silent	SNP	G	G	A	rs1630223	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	91	194	0	0.452736	0	G|0.509;A|0.491	0.491	strong	.	HLA-G	90	.	NM_002127	exon2	c.G15A	p.A5A	CATGGCGCCCCGA	.	PASS	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282838	59282838	+	Silent	SNP	G	G	A	rs75125922	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	72	102	0	0.5	0	G|0.966;A|0.034	0.034	strong	.	OR4D9	47	.	NM_001004711	exon1	c.G453A	p.G151G	GGTGGGGGGCTTT	.	PASS	Atlas-SNP
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104382	26104382	+	Silent	SNP	C	C	T	rs2229767	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	81	97	0	0.473684	0	C|0.963;T|0.037	0.037	strong	.	HIST1H4C	14	.	NM_003542	exon1	c.C207T	p.D69D	TCGAGACGCCGTC	.	PASS	Atlas-SNP
SLC27A5	10998	hgsc.bcm.edu	37	19	59023166	59023166	+	Missense_Mutation	SNP	G	G	A	rs34415062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	49	72	0	0.5	0	G|0.817;A|0.183	0.183	strong	.	SLC27A5	58	.	NM_012254	exon1	c.C157T	p.R53W	AGGGCCGTGCTAA	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654993	247654993	+	Silent	SNP	T	T	C	rs10925061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	57	105	0	0.448819	0	T|0.645;C|0.355	0.355	strong	.	OR2W5	97	.	NM_001004698	exon1	c.T564C	p.S188S	CATGTCTTGTGAG	.	PASS	Atlas-SNP
SSMEM1	0	hgsc.bcm.edu	37	7	129855837	129855837	+	Missense_Mutation	SNP	C	C	T	rs4728190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	84	186	0	0.459016	0	C|0.758;T|0.242	0.242	strong	.	.	.	.	NM_145268	exon3	c.C262T	p.R88W	TGTAAGCGGCAAA	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11540079	11540079	+	Silent	SNP	C	C	T	rs8065057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	36	77	0	0.387097	0	C|0.984;T|0.016	0.016	strong	.	DNAH9	695	.	NM_001372	exon9	c.C1764T	p.H588H	TCAGCACGTCCAG	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22472473	22472473	+	Silent	SNP	G	G	A	rs112997942	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	52	86	0	0.485981	0	G|0.993;A|0.007	0.007	strong	.	KIAA1967	72	.	NM_021174	exon11	c.G1164A	p.A388A	CTGTGCGCAGGCC	.	PASS	Atlas-SNP
SLC24A5	283652	hgsc.bcm.edu	37	15	48426484	48426484	+	Missense_Mutation	SNP	A	A	G	rs1426654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	190	198	1	1	0.00505051	A|0.618;G|0.382	0.382	strong	.	SLC24A5	64	.	NM_205850	exon3	c.A331G	p.T111A	GCAGGCACAACTT	.	PASS	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	37	7	150068981	150068981	+	Silent	SNP	G	G	A	rs149624173	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	4	7	0	0.571429	0	G|0.994;A|0.006	0.006	strong	.	REPIN1	74	.	NM_001099695	exon3	c.G822A	p.R274R	GCCCAGGGGCCGC	.	PASS	Atlas-SNP
MTPN	136319	hgsc.bcm.edu	37	7	135614740	135614740	+	Silent	SNP	T	T	C	rs17168527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	31	49	0	0.534483	0	T|0.921;C|0.079	0.079	strong	.	MTPN	10	.	NM_145808	exon4	c.A291G	p.K97K	TGGGCCTTTCACA	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36482372	36482372	+	Silent	SNP	A	A	C	rs58740367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	72	0	1	0	A|0.955;C|0.045	0.045	strong	.	GPR179	170	.	NM_001004334	exon11	c.T7080G	p.T2360T	ATAGACAGTGGGA	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33769211	33769211	+	Missense_Mutation	SNP	C	C	T	rs77814846	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	76	158	0	0.490323	0	C|0.987;T|0.013	0.013	strong	.	SLFN13	79	.	NM_144682	exon5	c.G1293A	p.M431I	AGGTCGCATTTGC	.	PASS	Atlas-SNP
POLH	5429	hgsc.bcm.edu	37	6	43581586	43581586	+	Silent	SNP	G	G	A	rs3734690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	46	103	0	0.433962	0	G|0.939;A|0.061	0.061	strong	POLH,NS,carcinoma,+1,1	POLH	54	1	NM_006502	exon11	c.G1434A	p.T478T	AACCACGTCTCTG	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	67	128	0	0.462069	0	G|0.791;A|0.209	0.209	strong	.	REST	104	.	NM_001193508	exon4	c.G3165A	p.A1055A	CAAAGCGGCTAAG	.	PASS	Atlas-SNP
ARNTL2	56938	hgsc.bcm.edu	37	12	27553566	27553566	+	Missense_Mutation	SNP	A	A	G	rs1037921	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	114	0	0.504951	0	A|0.963;G|0.037	0.037	strong	.	ARNTL2	54	.	NM_020183	exon10	c.A1019G	p.N340S	AAGACAACAGTAA	.	PASS	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172835125	172835125	+	Missense_Mutation	SNP	T	T	C	rs1515442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	137	219	1	0.524904	0.00456621	T|0.604;C|0.396	0.396	strong	SPATA16,NS,carcinoma,+2,1	SPATA16	111	1	NM_031955	exon2	c.A397G	p.M133V	CACCCATTTCATC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	86	99	0	0.671875	0	G|0.668;A|0.332	0.332	strong	.	PCSK5	329	.	NM_001190482	exon31	c.G4097A	p.R1366H	ACTCGCGCCACTG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140627184	140627184	+	Missense_Mutation	SNP	C	C	G	rs79326925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	63	117	0	0.577982	0	C|0.979;G|0.021	0.021	strong	.	PCDHB15	138	.	NM_018935	exon1	c.C2038G	p.Q680E	CCGGCCCAAGCCC	.	PASS	Atlas-SNP
NCLN	56926	hgsc.bcm.edu	37	19	3207398	3207398	+	Silent	SNP	G	G	A	rs76473246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	46	117	0	0.489362	0	G|0.967;A|0.033	0.033	strong	.	NCLN	27	.	NM_020170	exon14	c.G1563A	p.P521P	CAAGCCGGCCGTC	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5037241	5037241	+	Silent	SNP	G	G	A	rs117611547		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	4	92	3	0.0380952	0.0326087	.	.	weak	USP6_ENST00000250066,NS,carcinoma,0,3	USP6	213	3	NM_004505	exon7	c.G444A	p.V148V	GGACGTGAGGACG	.	scavenged	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2039779	2039779	+	Silent	SNP	G	G	A	rs62639301	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	51	66	1	0.520408	0.0151515	G|0.889;A|0.111	0.111	strong	SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	NM_139045	exon4	c.G669A	p.Q223Q	GCAACAGCAGCAG	.	scavenged	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150554553	150554553	+	Missense_Mutation	SNP	C	C	T	rs1049742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	55	63	0	0.528846	0	C|0.946;T|0.054	0.054	strong	.	ABP1	92	.	NM_001091	exon2	c.C995T	p.S332F	CCTCCTCCGGGCT	.	PASS	Atlas-SNP
FAM86B1	85002	hgsc.bcm.edu	37	8	12044042	12044042	+	Silent	SNP	G	G	A	rs76431111	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	474	49	255	0	0.103376	0	G|0.500;A|0.500	0.500	strong	FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	NM_001083537	exon5	c.C459T	p.S153S	AGGGTCGCTGAAG	.	scavenged	Atlas-SNP
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	108	1	1	0.00925926	G|0.424;A|0.576	0.576	strong	.	TMEM60	24	.	NM_032936	exon2	c.C117T	p.F39F	TGGAATGAATATG	.	PASS	Atlas-SNP
THOP1	7064	hgsc.bcm.edu	37	19	2790508	2790508	+	Missense_Mutation	SNP	C	C	T	rs76198851	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	27	50	0	0.586957	0	C|0.998;T|0.002	0.002	strong	.	THOP1	49	.	NM_003249	exon2	c.C106T	p.R36C	GAGGAGCGCACCA	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3656557	3656557	+	Silent	SNP	G	G	A	rs28516461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	121	242	0	0.467181	0	G|0.891;A|0.109	0.109	strong	.	SLX4	173	.	NM_032444	exon3	c.C678T	p.H226H	TGAAGCGTGTCTC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501999	88501999	+	Silent	SNP	G	G	A	rs116696830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	38	61	0	0.475	0	G|0.992;A|0.008	0.008	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G8037A	p.A2679A	TGCAGCGGAGACT	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61512185	61512185	+	Missense_Mutation	SNP	G	G	C	rs41282984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	63	100	0	0.525	0	G|0.921;C|0.079	0.079	strong	.	DIDO1	321	.	NM_001193369	exon16	c.C5123G	p.S1708C	CCAGCAGAATGAA	.	PASS	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77757845	77757845	+	Silent	SNP	C	C	T	rs8080971	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	49	80	0	0.720588	0	C|0.948;T|0.052	0.052	strong	.	CBX2	50	.	NM_005189	exon5	c.C603T	p.P201P	GCTGCCCCCTCCA	.	PASS	Atlas-SNP
MAPK1	5594	hgsc.bcm.edu	37	22	22162126	22162126	+	Silent	SNP	A	A	G	rs3729910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	37	82	0	0.536232	0	A|0.955;G|0.045	0.045	strong	.	MAPK1	38	.	NM_002745	exon2	c.T129C	p.Y43Y	ATTATCATAAGCA	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106814695	106814695	+	Silent	SNP	C	C	G	rs35998713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	83	171	0	0.482558	0	C|0.952;G|0.048	0.048	strong	.	ZFPM2	219	.	NM_012082	exon8	c.C2385G	p.V795V	AATTGTCTCTAAA	.	PASS	Atlas-SNP
BHLHE41	79365	hgsc.bcm.edu	37	12	26275297	26275297	+	Missense_Mutation	SNP	G	G	T	rs121912617	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	4	4	0	0.8	0	.	.	alt	.	BHLHE41	20	.	NM_030762	exon5	c.C1151A	p.P384Q	GGGAACGGGGCGG	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595114	55595114	+	Silent	SNP	G	G	T	rs34929168	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	126	290	0	0.45	0	G|0.913;T|0.087	0.087	strong	.	OR5L2	135	.	NM_001004739	exon1	c.G420T	p.L140L	GAAGCTGCGTGTG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	86	186	0	0.49711	0	C|0.643;T|0.357	0.357	strong	.	MLL3	1564	.	NM_170606	exon38	c.G8685A	p.Q2895Q	GGATGCCTGAATG	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	62	81	0	0.666667	0	G|0.884;A|0.116	0.116	strong	.	RGS3	251	.	NM_144488	exon21	c.G2426A	p.R809Q	CCACCCGGGACCT	.	PASS	Atlas-SNP
ZNF554	115196	hgsc.bcm.edu	37	19	2834595	2834595	+	Silent	SNP	C	C	T	rs61744481	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	73	121	0	0.544776	0	C|0.961;T|0.039	0.039	strong	.	ZNF554	47	.	NM_001102651	exon5	c.C1362T	p.H454H	CCAGCACGAGCGA	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117804544	117804544	+	Silent	SNP	T	T	C	rs1061495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	25	123	0	0.265957	0	T|0.688;C|0.312	0.312	strong	.	TNC	282	.	NM_002160	exon18	c.A5202G	p.T1734T	TTGGGCTGTGGGT	.	PASS	Atlas-SNP
APC2	10297	hgsc.bcm.edu	37	19	1469030	1469030	+	Silent	SNP	A	A	G	rs265278	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	17	10	0	0.73913	0	A|0.833;G|0.167	0.167	strong	.	APC2	50	.	NM_005883	exon15	c.A5730G	p.K1910K	GCCCAAAACGCCG	.	PASS	Atlas-SNP
FUK	197258	hgsc.bcm.edu	37	16	70508544	70508544	+	Missense_Mutation	SNP	C	C	T	rs17883716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	93	0	0.489583	0	C|0.995;T|0.005	0.005	strong	.	FUK	72	.	NM_145059	exon17	c.C2102T	p.P701L	AACTGCCGGGACC	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	168833976	168833976	+	Missense_Mutation	SNP	C	C	T	rs149928659	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	90	240	0	0.481283	0	C|0.999;T|0.001	0.001	strong	.	MECOM	216	.	NM_004991	exon8	c.G1684A	p.E562K	ACCTCTCGGGCTG	.	PASS	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238725833	238725833	+	Missense_Mutation	SNP	A	A	G	rs73086770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	85	185	0	0.399061	0	A|0.967;G|0.033	0.033	strong	.	RBM44	167	.	NM_001080504	exon3	c.A274G	p.S92G	ACAGAGAGTACTC	.	PASS	Atlas-SNP
CABP5	56344	hgsc.bcm.edu	37	19	48543923	48543923	+	Silent	SNP	C	C	A	rs12982629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	129	0	1	0	C|0.798;A|0.202	0.202	strong	.	CABP5	28	.	NM_019855	exon3	c.G177T	p.T59T	ACCCATCGTCCTC	.	PASS	Atlas-SNP
SYTL3	94120	hgsc.bcm.edu	37	6	159184507	159184507	+	Silent	SNP	C	C	T	rs2291386	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	44	74	0	0.54321	0	C|0.879;T|0.121	0.121	strong	.	SYTL3	49	.	NM_001242384	exon18	c.C1689T	p.N563N	AATGAACGACCGC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216258194	216258194	+	Silent	SNP	G	G	T	rs56110889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	118	0	1	0	G|0.844;T|0.156	0.156	strong	.	USH2A	1168	.	NM_206933	exon25	c.C5013A	p.G1671G	GAGACAGCCCACA	.	PASS	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	37	1	247587408	247587408	+	Silent	SNP	C	C	T	rs7525979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	109	198	0	0.471861	0	C|0.877;T|0.123	0.123	strong	.	NLRP3	286	.	NM_183395	exon3	c.C663T	p.T221T	GCACACCGTGGTG	.	PASS	Atlas-SNP
TNFSF15	9966	hgsc.bcm.edu	37	9	117568219	117568219	+	Missense_Mutation	SNP	C	C	T	rs150191342	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	75	104	0	0.694444	0	C|0.996;T|0.004	0.004	strong	.	TNFSF15	23	.	NM_005118	exon1	c.G74A	p.R25K	TTGGGCCTGCAGC	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31767717	31767717	+	Silent	SNP	G	G	A	rs61744745	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	86	155	0	0.51497	0	G|0.961;A|0.039	0.039	strong	.	TSHZ3	549	.	NM_020856	exon2	c.C2982T	p.H994H	CTCTAGGTGACTG	.	PASS	Atlas-SNP
ARHGEF26	26084	hgsc.bcm.edu	37	3	153840389	153840389	+	Missense_Mutation	SNP	T	T	C	rs13096373	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	89	0	0.419753	0	T|0.706;C|0.294	0.294	strong	.	ARHGEF26	158	.	NM_001251962	exon2	c.T608C	p.F203S	GGCTCTTTCCTGG	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95056407	95056407	+	Missense_Mutation	SNP	G	G	C	rs6114	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	50	141	0	0.413223	0	G|0.974;C|0.026	0.026	strong	.	SERPINA5	69	.	NM_000624	exon4	c.G649C	p.G217R	CACAAAGGCACCC	.	PASS	Atlas-SNP
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	63	142	0	0.403846	0	C|0.492;G|0.508	0.508	strong	.	C15orf41	24	.	NM_001130010	exon4	c.C217G	p.L73V	AGGTACCTGAATG	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85447611	85447611	+	Silent	SNP	T	T	C	rs680498	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	108	1	1	0.00925926	C|0.687;T|0.313	0.687	strong	SYTL2_ENST00000316356,bladder,carcinoma,-1,1	SYTL2	231	1	NM_001162953	exon5	c.A519G	p.S173S	TTGTGATGAGTGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152279841	152279841	+	Missense_Mutation	SNP	G	G	C	rs3126074	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	476	476	368	0	1	0	G|0.693;C|0.307	0.307	strong	.	FLG	900	.	NM_002016	exon3	c.C7521G	p.H2507Q	TCCTGAGTGCCCA	.	PASS	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	37	1	55073630	55073630	+	Silent	SNP	C	C	T	rs78753605	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	87	165	0	0.55414	0	C|0.984;T|0.016	0.016	strong	.	ACOT11	105	.	NM_147161	exon15	c.C1518T	p.I506I	TGTCATCGCGCTG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31380153	31380153	+	Missense_Mutation	SNP	T	T	C	rs199843678	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	17	140	0	0.165049	0	T|0.973;C|0.027	0.027	strong	MICA,uveal_tract,malignant_melanoma,0,1	MICA	21	1	NM_001177519	exon5	c.T944C	p.V315A	CTGCTGTTGCTGC	.	PASS	Atlas-SNP
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	28	0	0.470588	0	T|0.711;C|0.289	0.289	strong	.	COG8	32	.	NM_032382	exon1	c.A42G	p.T14T	CGCTGCTGTGGCC	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3245054	3245054	+	Missense_Mutation	SNP	C	C	T	rs73657835	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	42	86	0	0.5	0	C|0.966;T|0.034	0.034	strong	CSMD1_ENST00000537824,NS,carcinoma,+1,2	CSMD1	1469	2	NM_033225	exon18	c.G2744A	p.R915K	TGGTTCCTCTCAC	.	PASS	Atlas-SNP
CAPN9	10753	hgsc.bcm.edu	37	1	230914729	230914729	+	Missense_Mutation	SNP	A	A	C	rs1933631	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	26	68	0	0.38806	0	A|0.692;C|0.308	0.308	strong	.	CAPN9	116	.	NM_006615	exon9	c.A964C	p.K322Q	GCATTTAAGGACT	.	PASS	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64677270	64677270	+	Missense_Mutation	SNP	C	C	T	rs61746812	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	32	30	0	0.571429	0	C|0.978;T|0.022	0.022	strong	ATG2A,NS,carcinoma,0,1	ATG2A	133	1	NM_015104	exon14	c.G1990A	p.V664M	CCCGCACGGCCTG	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	111	0	0.485437	0	G|0.739;C|0.261	0.261	strong	.	ZNF844	69	.	NM_001136501	exon4	c.G922C	p.A308P	GAGAAGGCTTATG	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6897464	6897464	+	Missense_Mutation	SNP	C	C	G	rs330880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	114	208	0	0.467213	0	C|0.551;G|0.449	0.449	strong	.	EMR1	153	.	NM_001256253	exon5	c.C420G	p.S140R	CAGCAGCGTCTGC	.	PASS	Atlas-SNP
ITGAX	3687	hgsc.bcm.edu	37	16	31371674	31371674	+	Missense_Mutation	SNP	G	G	A	rs2230428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	82	182	0	0.450549	0	G|0.860;A|0.140	0.140	strong	ITGAX,colon,carcinoma,0,1	ITGAX	198	1	NM_000887	exon8	c.G751A	p.A251T	GATGCCGCCAAAA	.	PASS	Atlas-SNP
PDIA6	10130	hgsc.bcm.edu	37	2	10933294	10933294	+	Silent	SNP	C	C	T	rs114716918	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	83	153	0	0.515528	0	C|0.990;T|0.010	0.010	strong	PDIA6,NS,carcinoma,-1,1	PDIA6	31	1	NM_005742	exon5	c.G381A	p.A127A	ACTCAGCGCAGCA	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	124987404	124987404	+	Missense_Mutation	SNP	A	A	G	rs77810887	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	150	252	0	0.520833	0	A|0.988;G|0.012	0.012	strong	.	FER1L6	268	.	NM_001039112	exon8	c.A541G	p.N181D	TTCTGCAACAAGT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123970173	123970173	+	Missense_Mutation	SNP	T	T	C	rs7083331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	93	0	0.479167	0	T|0.899;C|0.101	0.101	strong	.	TACC2	271	.	NM_206862	exon9	c.T6233C	p.I2078T	TCCCCATCTCTAA	.	PASS	Atlas-SNP
SLC30A8	169026	hgsc.bcm.edu	37	8	118184784	118184784	+	Missense_Mutation	SNP	G	G	A	rs16889462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	72	79	0	0.576	0	A|0.044;G|0.956	0.044	strong	.	SLC30A8	102	.	NM_173851	exon8	c.G974A	p.R325Q	CCAGCCGGGACAG	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47603338	47603338	+	Missense_Mutation	SNP	G	G	A	rs112604161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	82	110	0	0.479532	0	G|0.987;A|0.013	0.013	strong	.	CYP4A22	60	.	NM_001010969	exon1	c.G181A	p.G61R	CTCTTCGGGCACA	.	PASS	Atlas-SNP
ELL	8178	hgsc.bcm.edu	37	19	18561473	18561473	+	Silent	SNP	G	G	A	rs34868531	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	58	50	0	0.54717	0	G|0.980;A|0.020	0.020	strong	.	ELL	52	.	NM_006532	exon8	c.C1279T	p.L427L	GGGGCAGGCCGAG	.	PASS	Atlas-SNP
CNTNAP1	8506	hgsc.bcm.edu	37	17	40841001	40841001	+	Missense_Mutation	SNP	G	G	C	rs35437096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	53	118	1	0.486239	0.00847458	G|0.961;C|0.039	0.039	strong	CNTNAP1,uveal_tract,malignant_melanoma,-1,1	CNTNAP1	116	1	NM_003632	exon10	c.G1564C	p.V522L	ACTCTGGTGGAGG	.	scavenged	Atlas-SNP
ABLIM1	3983	hgsc.bcm.edu	37	10	116203801	116203801	+	Silent	SNP	A	A	C	rs74158004	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	57	112	0	0.459677	0	A|0.963;C|0.037	0.037	strong	.	ABLIM1	131	.	NM_002313	exon17	c.T1920G	p.S640S	GATGGGAGAATCG	.	PASS	Atlas-SNP
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	41	53	0	0.445652	0	G|0.964;A|0.036	0.036	strong	.	CTC1	75	.	NM_025099	exon13	c.C2160T	p.T720T	TGGGCCGGTGGGA	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	53	97	0	0.576087	0	G|0.598;A|0.402	0.402	strong	.	CD109	170	.	NM_133493	exon21	c.G2533A	p.V845I	GATGCTGTCACCC	.	PASS	Atlas-SNP
CNPY4	245812	hgsc.bcm.edu	37	7	99722173	99722173	+	Missense_Mutation	SNP	G	G	A	rs60551236	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	100	0	0.479167	0	G|0.979;A|0.021	0.021	strong	.	CNPY4	18	.	NM_152755	exon5	c.G502A	p.G168R	ATTGTGGGAGACT	.	PASS	Atlas-SNP
NPR1	4881	hgsc.bcm.edu	37	1	153662340	153662340	+	Missense_Mutation	SNP	G	G	A	rs35240348	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	85	141	0	0.53125	0	G|0.890;A|0.110	0.110	strong	.	NPR1	104	.	NM_000906	exon19	c.G2816A	p.R939Q	ACGGGCGGCTACA	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39736693	39736693	+	Silent	SNP	G	G	T	rs34909359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	33	74	0	0.452055	0	G|0.979;T|0.021	0.021	strong	.	CTAGE5	75	.	NM_001247989	exon1	c.G30T	p.P10P	TCAACCGTATTTG	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101177848	101177848	+	Missense_Mutation	SNP	T	T	G	rs6809436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	68	110	0	0.544	0	T|0.902;G|0.098	0.098	strong	.	SENP7	170	.	NM_020654	exon4	c.A235C	p.K79Q	GTTTTTTATTTTT	.	PASS	Atlas-SNP
TRIM39-RPP21	202658	hgsc.bcm.edu	37	6	30314566	30314566	+	Silent	SNP	T	T	G	rs35287137	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	76	136	0	0.496732	0	.	.	alt	.	.	.	.	NM_001199119	exon10	c.T1491G	p.T497T	GCAGACTCAGGGT	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262047	39262047	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	16	128	3	0.0981595	0.0234375	.	.	none	KRTAP4-9_ENST00000377734,NS,carcinoma,0,6	KRTAP4-9	110	6	NM_001146041	exon1	c.A407G	p.K136R	GCTGCAAGCCCCA	.	scavenged	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	66	137	0	0.515625	0	C|0.865;G|0.135	0.135	strong	.	UTP20	222	.	NM_014503	exon13	c.C1505G	p.S502C	TTTTATCTATAAT	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084470	+	Missense_Mutation	SNP	C	C	T	rs140846339	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1052	191	718	2	0.181559	0.00278552	.	.	weak	OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	NM_001005522	exon1	c.C151T	p.H51Y	TGGGACCACCGGC	.	scavenged	Atlas-SNP
CACNB2	783	hgsc.bcm.edu	37	10	18828635	18828635	+	Missense_Mutation	SNP	T	T	G	rs58225473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	36	73	0	0.610169	0	T|0.858;G|0.142	0.142	strong	.	CACNB2	220	.	NM_201596	exon14	c.T1965G	p.D655E	CAGGGATGTTTAC	.	PASS	Atlas-SNP
CLU	1191	hgsc.bcm.edu	37	8	27457512	27457512	+	Missense_Mutation	SNP	T	T	G	rs9331936	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	45	78	0	0.555556	0	T|0.922;G|0.078	0.078	strong	.	CLU	54	.	NM_001831	exon7	c.A949C	p.N317H	AGGGGTTGTTGGT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155219318	155219318	+	Missense_Mutation	SNP	C	C	G	rs28561984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	94	212	0	0.456311	0	C|0.867;G|0.027;T|0.106	0.027	strong	.	DCHS2	594	.	NM_017639	exon18	c.G4783C	p.E1595Q	GCGACTCGGGGGA	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	217	252	0	0.806691	0	C|0.575;T|0.425	0.425	strong	TLR1,NS,carcinoma,-1,1	TLR1	70	1	NM_003263	exon4	c.G1518A	p.S506S	ATCAGCCGATGGG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31237275	31237275	+	Missense_Mutation	SNP	G	G	A	rs41559915	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	81	157	0	0.522581	0	G|0.981;A|0.019	0.019	strong	HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	NM_002117	exon6	c.C1043T	p.A348V	CACGCAGCCTGAG	.	PASS	Atlas-SNP
SLC26A10	65012	hgsc.bcm.edu	37	12	58017665	58017665	+	Nonsense_Mutation	SNP	G	G	A	rs115563091	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	40	70	0	0.56338	0	G|0.999;A|0.001	0.001	strong	.	SLC26A10	89	.	NM_133489	exon8	c.G1100A	p.W367X	TGCTGTGGCTGGG	.	PASS	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49437753	49437753	+	Silent	SNP	G	G	A	rs111924728	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	42	123	0	0.43299	0	G|0.986;A|0.014	0.014	strong	.	MLL2	1173	.	NM_003482	exon22	c.C5217T	p.G1739G	CACGGCGCCCTCT	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	235364	235364	+	Silent	SNP	C	C	T	rs35277230	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	321	161	301	0	0.501558	0	C|0.899;T|0.101	0.101	strong	.	SDHA	80	.	NM_004168	exon9	c.C1170T	p.F390F	GATCTTCGCTGGC	.	PASS	Atlas-SNP
DLGAP1	9229	hgsc.bcm.edu	37	18	3814148	3814148	+	Silent	SNP	C	C	G	rs3786431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	107	0	1	0	C|0.896;G|0.104	0.104	strong	.	DLGAP1	201	.	NM_001242761	exon5	c.G1083C	p.T361T	AGGACTCGTGTCT	.	PASS	Atlas-SNP
KLHL36	79786	hgsc.bcm.edu	37	16	84691256	84691256	+	Silent	SNP	C	C	T	rs12102528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	23	45	0	0.38983	0	C|0.984;T|0.016	0.016	strong	.	KLHL36	51	.	NM_024731	exon3	c.C843T	p.P281P	CCAGCCCGTCATG	.	PASS	Atlas-SNP
TMEM8B	51754	hgsc.bcm.edu	37	9	35842480	35842480	+	Silent	SNP	A	A	G	rs7037450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	52	115	0	0.495238	0	A|0.962;G|0.038	0.038	strong	.	TMEM8B	53	.	NM_001042590	exon6	c.A45G	p.E15E	CCCAGAACCGCCA	.	PASS	Atlas-SNP
CEP85L	387119	hgsc.bcm.edu	37	6	118887215	118887215	+	Missense_Mutation	SNP	T	T	A	rs9489444	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	114	175	0	0.564356	0	T|0.964;A|0.036	0.036	strong	.	CEP85L	26	.	NM_001178035	exon4	c.A506T	p.D169V	CAGTTATCCGGGG	.	PASS	Atlas-SNP
ARSH	347527	hgsc.bcm.edu	37	X	2933311	2933311	+	Missense_Mutation	SNP	G	G	A	rs61995728	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	132	314	1	0.425806	0.00318471	G|0.952;A|0.048	0.048	strong	.	ARSH	72	.	NM_001011719	exon4	c.G641A	p.S214N	ACTCTAGTTATGG	.	PASS	Atlas-SNP
RIC3	79608	hgsc.bcm.edu	37	11	8159843	8159843	+	Missense_Mutation	SNP	G	G	A	rs73411617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	168	0	0.439024	0	G|0.958;A|0.042	0.042	strong	.	RIC3	42	.	NM_001206672	exon3	c.C403T	p.P135S	TTCCAGGCATGGC	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108780895	108780895	+	Silent	SNP	T	T	A	rs79817474	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	68	128	0	0.561983	0	T|0.989;A|0.011	0.011	strong	.	MORC1	211	.	NM_014429	exon11	c.A906T	p.I302I	TTTCAATATGGAT	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	14000	14000	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	8	8	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.T1664A	p.L555Q	TAGACCTAACCTG	.	PASS	Atlas-SNP
SLC26A8	116369	hgsc.bcm.edu	37	6	35987425	35987425	+	Silent	SNP	T	T	C	rs61743377	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	89	227	0	0.434146	0	T|0.986;C|0.014	0.014	strong	.	SLC26A8	95	.	NM_052961	exon2	c.A60G	p.S20S	TGCGAATGAGTTT	.	PASS	Atlas-SNP
OR13F1	138805	hgsc.bcm.edu	37	9	107266813	107266813	+	Silent	SNP	C	C	T	rs61754949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	47	196	0	0.279762	0	C|0.987;T|0.013	0.013	strong	.	OR13F1	75	.	NM_001004485	exon1	c.C270T	p.N90N	GAGAAACACTATT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186372	12186372	+	Missense_Mutation	SNP	G	G	A	rs56481038		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	57	86	0	0.518182	0	.	.	weak	.	ZNF844	69	.	NM_001136501	exon4	c.G437A	p.R146H	AACAACGTAAGAA	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269686	43269686	+	Silent	SNP	C	C	T	rs61393109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	20	31	0	0.465116	0	C|0.988;T|0.012	0.012	strong	.	PSG8	101	.	NM_001130168	exon1	c.G48A	p.K16K	GAGCCCCTTCCAG	.	PASS	Atlas-SNP
ZSCAN25	221785	hgsc.bcm.edu	37	7	99217424	99217424	+	Silent	SNP	G	G	A	rs10282706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	118	119	0	0.991597	0	G|0.735;A|0.265	0.265	strong	.	.	.	.	NM_145115	exon4	c.G195A	p.E65E	CCAGGAGCTCTGT	.	PASS	Atlas-SNP
PPP1R3F	89801	hgsc.bcm.edu	37	X	49137916	49137916	+	Missense_Mutation	SNP	T	T	C	rs17148347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	59	115	0	0.460938	0	0|0.016;C|0.097	0.097	strong	.	PPP1R3F	56	.	NM_033215	exon2	c.T1052C	p.F351S	ACACCTTTGCCAT	.	PASS	Atlas-SNP
CDC42EP2	10435	hgsc.bcm.edu	37	11	65088498	65088498	+	Silent	SNP	T	T	C	rs4149835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	57	133	0	0.445312	0	T|0.914;C|0.086	0.086	strong	.	CDC42EP2	13	.	NM_006779	exon2	c.T129C	p.I43I	TCATATTGGCAGT	.	PASS	Atlas-SNP
ARHGDIB	397	hgsc.bcm.edu	37	12	15095558	15095558	+	Silent	SNP	C	C	G	rs4703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	42	84	0	0.538462	0	C|0.500;G|0.500	0.500	strong	.	ARHGDIB	33	.	NM_001175	exon6	c.G504C	p.A168A	GCCTCGCGCCAGC	.	PASS	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17051328	17051328	+	Silent	SNP	T	T	C	rs7653834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	67	148	0	0.429487	0	C|0.402;N|0.000	0.402	strong	.	PLCL2	145	.	NM_015184	exon2	c.T112C	p.L38L	TACTTTTTACTGG	.	PASS	Atlas-SNP
CEACAM4	1089	hgsc.bcm.edu	37	19	42125710	42125710	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	55	103	0	0.474138	0	.	.	none	CEACAM4,NS,neuroblastoma,+1,1	CEACAM4	42	1	NM_001817	exon7	c.T728C	p.V243A	TAAGAGACCACAT	.	PASS	Atlas-SNP
CCNL1	57018	hgsc.bcm.edu	37	3	156877707	156877707	+	Silent	SNP	A	A	T	rs9814142	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	80	94	1	0.529801	0.0106383	A|0.954;T|0.046	0.046	strong	CCNL1,NS,carcinoma,0,1	CCNL1	53	1	NM_020307	exon1	c.T177A	p.I59I	CTCCGGAATCAGA	.	scavenged	Atlas-SNP
FAH	2184	hgsc.bcm.edu	37	15	80460421	80460421	+	Silent	SNP	C	C	T	rs116272698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	105	215	0	0.477273	0	C|0.990;T|0.010	0.010	strong	.	FAH	36	.	NM_000137	exon6	c.C483T	p.G161G	CCATGGCCGTGCC	.	PASS	Atlas-SNP
ACE2	59272	hgsc.bcm.edu	37	X	15582298	15582298	+	Missense_Mutation	SNP	T	T	C	rs41303171	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	87	225	0	0.410377	0	T|0.986;C|0.014	0.014	strong	.	ACE2	87	.	NM_021804	exon18	c.A2158G	p.N720D	GGCTGTTGTCATT	.	PASS	Atlas-SNP
OSBP2	23762	hgsc.bcm.edu	37	22	31091139	31091139	+	Silent	SNP	A	A	G	rs13053290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	135	0	1	0	A|0.726;G|0.274	0.274	strong	OSBP2,NS,carcinoma,0,1	OSBP2	52	1	NM_030758	exon1	c.A243G	p.E81E	ATCGGAACCTGTG	.	PASS	Atlas-SNP
FAAH	2166	hgsc.bcm.edu	37	1	46877885	46877885	+	Missense_Mutation	SNP	C	C	G	rs75429705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	107	207	1	0.545918	0.00483092	C|0.997;G|0.003	0.003	strong	.	FAAH	36	.	NM_001441	exon13	c.C1427G	p.A476G	TGCTGGCCCCTGC	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54410099	54410099	+	Missense_Mutation	SNP	G	G	A	rs444527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	104	222	1	0.495238	0.0045045	G|0.861;A|0.139	0.139	strong	CDC20B,bladder,carcinoma,+2,2	CDC20B	61	2	NM_001170402	exon12	c.C1507T	p.R503W	ACACCCGGGTCTG	.	PASS	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156621252	156621252	+	Silent	SNP	G	G	A	rs146863260	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	35	0	0.470588	0	G|0.994;A|0.006	0.006	strong	.	BCAN	174	.	NM_198427	exon7	c.G1068A	p.S356S	AGACTCGGCCCAG	.	PASS	Atlas-SNP
CYP8B1	1582	hgsc.bcm.edu	37	3	42916596	42916596	+	Missense_Mutation	SNP	T	T	C	rs35764459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	46	98	0	0.469388	0	T|0.977;C|0.023	0.023	strong	.	CYP8B1	59	.	NM_004391	exon1	c.A713G	p.K238R	AGCATCTTGTGAA	.	PASS	Atlas-SNP
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	32	86	0	0.432432	0	C|0.647;T|0.353	0.353	strong	.	JAK2	35466	.	NM_004972	exon6	c.C489T	p.H163H	TGTGCACGGATGG	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	19	41	0	0.422222	0	G|0.662;A|0.338	0.338	strong	.	SERPINH1	33	.	NM_001235	exon5	c.G1011A	p.L337L	CGACTTGTCACGC	.	PASS	Atlas-SNP
LY6G6C	80740	hgsc.bcm.edu	37	6	31687008	31687008	+	Silent	SNP	G	G	A	rs1065356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	87	176	0	0.480663	0	G|0.690;A|0.310	0.310	strong	LY6G6C,NS,adenocarcinoma,-1,1	LY6G6C	9	1	NM_025261	exon3	c.C243T	p.R81R	CAGCTTGCGGTTG	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444697	61444697	+	Missense_Mutation	SNP	G	G	C	rs6122315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	13	8	0	1	0	G|0.636;C|0.364	0.364	strong	OGFR,colon,carcinoma,0,3	OGFR	63	3	NM_007346	exon7	c.G1730C	p.S577T	CCGAGAGCCCATC	.	PASS	Atlas-SNP
FKBP8	23770	hgsc.bcm.edu	37	19	18652521	18652521	+	Missense_Mutation	SNP	G	G	A	rs11574806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	103	194	0	0.522843	0	G|0.907;A|0.093	0.093	strong	.	FKBP8	69	.	NM_012181	exon2	c.C260T	p.A87V	GCCGGGGCTGGGG	.	PASS	Atlas-SNP
WDR35	57539	hgsc.bcm.edu	37	2	20135283	20135283	+	Silent	SNP	T	T	C	rs6741091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	39	85	0	0.397959	0	T|0.533;C|0.467	0.467	strong	.	WDR35	92	.	NM_001006657	exon22	c.A2529G	p.E843E	TAACCCTTCATAA	.	PASS	Atlas-SNP
SYCP1	6847	hgsc.bcm.edu	37	1	115537343	115537343	+	Silent	SNP	T	T	C	rs17033011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	53	93	0	0.490741	0	T|0.954;C|0.046	0.046	strong	.	SYCP1	149	.	NM_003176	exon31	c.T2728C	p.L910L	GAGACATTGAAAA	.	PASS	Atlas-SNP
FAM110A	83541	hgsc.bcm.edu	37	20	825579	825579	+	Silent	SNP	G	G	A	rs8124809	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	86	87	0	0.547771	0	A|0.020;C|0.000;G|0.979	0.020	strong	.	FAM110A	18	.	NM_207121	exon2	c.G132A	p.E44E	TGTGGAGCGCCTG	.	PASS	Atlas-SNP
ZNF250	58500	hgsc.bcm.edu	37	8	146115367	146115367	+	Silent	SNP	A	A	G	rs2735906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	78	147	0	0.464286	0	A|0.155;G|0.845	0.845	strong	.	ZNF250	37	.	NM_021061	exon3	c.T135C	p.G45G	GTAGAGACCCCTC	.	PASS	Atlas-SNP
CCDC164	92749	hgsc.bcm.edu	37	2	26678040	26678040	+	Missense_Mutation	SNP	G	G	T	rs3172008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	52	125	0	0.40625	0	G|0.870;N|0.001	.	strong	CCDC164,NS,carcinoma,+1,2	CCDC164	84	2	NM_145038	exon16	c.G2105T	p.S702I	AAAACAGTTCTCT	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48174766	48174766	+	Silent	SNP	A	A	G	rs16945872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	94	0	0.456311	0	A|0.955;G|0.045	0.045	strong	.	ABCC12	190	.	NM_033226	exon4	c.T489C	p.I163I	CAGTCCAATGCCA	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	37	17	80828203	80828203	+	Silent	SNP	C	C	T	rs36018199	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	53	94	0	0.424	0	C|0.977;T|0.023	0.023	strong	.	TBCD	94	.	NM_005993	exon14	c.C1422T	p.F474F	GGCCTTCGCGCGT	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39619186	39619186	+	Missense_Mutation	SNP	G	G	C	rs2604956	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	73	144	0	0.474026	0	G|0.927;C|0.073	0.073	strong	KRT32,brain,glioma,0,2	KRT32	57	2	NM_002278	exon6	c.C1113G	p.D371E	CTCCAGGTCAGCC	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274343	39274343	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	14	175	4	0.0933333	0.0228571	.	.	none	KRTAP4-11,NS,malignant_melanoma,0,2	KRTAP4-11	94	2	NM_033059	exon1	c.T225C	p.C75C	GGGGCGACAGCAG	.	scavenged	Atlas-SNP
ACOX3	8310	hgsc.bcm.edu	37	4	8394094	8394094	+	Silent	SNP	G	G	A	rs28627156	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	84	0	0.527027	0	G|0.872;A|0.128	0.128	strong	.	ACOX3	70	.	NM_001101667	exon11	c.C1266T	p.C422C	CTCCCGGCATTCC	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs3198831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	286	303	1	0.996516	0.00330033	G|0.625;C|0.375	0.375	strong	.	PSG6	89	.	NM_001031850	exon2	c.C253G	p.H85D	GACCGTGTACTAC	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37451768	37451768	+	Missense_Mutation	SNP	T	T	G	rs41276130	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	105	211	0	0.475113	0	T|0.930;G|0.070	0.070	strong	.	ANKRD30A	448	.	NM_052997	exon17	c.T1826G	p.L609W	AAACATTGAGAGC	.	PASS	Atlas-SNP
CCDC18	343099	hgsc.bcm.edu	37	1	93720153	93720153	+	Missense_Mutation	SNP	G	G	T	rs61729705	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	90	217	0	0.45	0	A|0.000;G|0.947;T|0.053	0.053	strong	.	CCDC18	93	.	NM_206886	exon24	c.G3324T	p.R1108S	ACAAAGGATGAAA	.	PASS	Atlas-SNP
CSNK2B	1460	hgsc.bcm.edu	37	6	31635710	31635710	+	Silent	SNP	T	T	C	rs14365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	91	0	0.431193	0	T|0.720;C|0.280	0.280	strong	.	CSNK2B	15	.	NM_001320	exon3	c.T138C	p.Y46Y	TCACTATCGACAA	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112888882	112888882	+	Missense_Mutation	SNP	A	A	T	rs72805422	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	10	29	0	0.434783	0	A|0.671;T|0.329	0.329	strong	.	YTHDC2	118	.	NM_022828	exon13	c.A1693T	p.T565S	AGTGCTACACTGG	.	PASS	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20640969	20640969	+	Silent	SNP	G	G	A	rs114916291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	68	115	0	0.591304	0	G|0.988;A|0.012	0.012	strong	.	VWA5B1	44	.	NM_001039500	exon4	c.G447A	p.S149S	CTCCTCGGAGCTC	.	PASS	Atlas-SNP
MAPK10	5602	hgsc.bcm.edu	37	4	86950354	86950354	+	Silent	SNP	A	A	G	rs148438622	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	45	103	0	0.45	0	A|1.000;G|0.000	0.000	strong	MAPK10_ENST00000449047,colon,carcinoma,-2,2	MAPK10	106	2	NM_002753	exon13	c.T1248C	p.P416P	ACCTGAAGGAGAA	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15291576	15291576	+	Missense_Mutation	SNP	C	C	G	rs35769976	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	48	96	0	0.516129	0	C|0.886;G|0.114	0.114	strong	.	NOTCH3	340	.	NM_000435	exon19	c.G3058C	p.A1020P	AATAGGCCCCAGT	.	PASS	Atlas-SNP
ACVR1B	91	hgsc.bcm.edu	37	12	52370181	52370181	+	Silent	SNP	G	G	A	rs115556161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	85	154	0	0.508982	0	G|0.994;A|0.006	0.006	strong	.	ACVR1B	167	.	NM_020328	exon3	c.G402A	p.P134P	CGGCCCGGTGTTC	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248085124	248085124	+	Missense_Mutation	SNP	G	G	A	rs4590708	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	587	240	276	0	0.408859	0	G|0.755;A|0.245	0.245	strong	.	OR2T8	67	.	NM_001005522	exon1	c.G805A	p.D269N	AACCACGACAAGG	.	PASS	Atlas-SNP
FAM35A	54537	hgsc.bcm.edu	37	10	88912541	88912541	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	343	12	353	0	0.0349854	0	.	.	none	FAM35A,NS,carcinoma,0,1	FAM35A	48	1	NM_019054	exon3	c.T1430G	p.I477S	CAGTAATTGATCA	.	scavenged	Atlas-SNP
RAB4A	5867	hgsc.bcm.edu	37	1	229431613	229431613	+	Silent	SNP	T	T	C	rs114366150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	41	68	0	0.427083	0	T|0.998;C|0.002	0.002	strong	.	RAB4A	29	.	NM_004578	exon4	c.T246C	p.Y82Y	AAGTTATTACCGA	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66678192	66678192	+	Missense_Mutation	SNP	G	G	C	rs9963788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	97	0	1	0	G|0.928;C|0.072	0.072	strong	.	CCDC102B	92	.	NM_001093729	exon9	c.G1285C	p.A429P	CAACATGCCTACT	.	PASS	Atlas-SNP
FRZB	2487	hgsc.bcm.edu	37	2	183703336	183703336	+	Missense_Mutation	SNP	G	G	A	rs288326	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	79	116	0	0.548611	0	G|0.945;A|0.055	0.055	strong	.	FRZB	42	.	NM_001463	exon4	c.C598T	p.R200W	TAGCCCGAATGAC	.	PASS	Atlas-SNP
ITGA2B	3674	hgsc.bcm.edu	37	17	42457087	42457087	+	Silent	SNP	C	C	T	rs79289329	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	52	107	0	0.448276	0	C|0.994;T|0.006	0.006	strong	.	ITGA2B	88	.	NM_000419	exon18	c.G1848A	p.V616V	ATGCAGCACGACA	.	PASS	Atlas-SNP
OR6Q1	219952	hgsc.bcm.edu	37	11	57799371	57799371	+	Missense_Mutation	SNP	G	G	C	rs1374570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	60	68	0	0.983607	0	G|0.500;C|0.500	0.500	strong	OR6Q1,NS,carcinoma,-1,1	OR6Q1	58	1	NM_001005186	exon1	c.G947C	p.G316A	GGAAGGGACAGTG	.	PASS	Atlas-SNP
SLC1A7	6512	hgsc.bcm.edu	37	1	53558366	53558366	+	Silent	SNP	T	T	C	rs12129653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	65	146	0	0.427632	0	T|0.913;C|0.087	0.087	strong	.	SLC1A7	65	.	NM_006671	exon7	c.A891G	p.S297S	GGTGACTGAGTAG	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	53908062	53908062	+	Missense_Mutation	SNP	T	T	C	rs60404950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	63	143	0	0.488372	0	T|0.871;C|0.129	0.129	strong	.	WDR72	177	.	NM_182758	exon15	c.A2341G	p.K781E	ATGGCTTAGGCTG	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289500	74289500	+	Silent	SNP	G	G	A	rs3803737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	56	127	0	0.448	0	G|0.557;A|0.443	0.443	strong	.	QRICH2	143	.	NM_032134	exon4	c.C810T	p.V270V	ATCCACGACAAAT	.	PASS	Atlas-SNP
AFF4	27125	hgsc.bcm.edu	37	5	132232148	132232148	+	Missense_Mutation	SNP	C	C	G	rs138811630	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	89	173	0	0.454082	0	C|0.999;G|0.001	0.001	strong	.	AFF4	120	.	NM_014423	exon11	c.G2174C	p.R725T	GGTATTCTAGTCA	.	PASS	Atlas-SNP
LMLN	89782	hgsc.bcm.edu	37	3	197701913	197701913	+	Missense_Mutation	SNP	G	G	T	rs7373165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	28	73	0	0.491228	0	G|0.784;T|0.216	0.216	strong	.	LMLN	53	.	NM_001136049	exon3	c.G318T	p.E106D	TTTCAGGTTGCTC	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447679	10447679	+	Missense_Mutation	SNP	C	C	T	rs10007352	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	54	96	0	0.55102	0	C|0.906;T|0.094	0.094	strong	ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	NM_053042	exon3	c.G274A	p.G92S	CTGCACCGAGGCT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036505	33036505	+	Silent	SNP	G	G	C	rs1042434	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	153	273	0	0.993506	0	G|0.663;C|0.337	0.337	strong	.	HLA-DPA1	20	.	NM_033554	exon4	c.C705G	p.V235V	GATGCCGACTAGG	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36493598	36493598	+	Silent	SNP	A	A	G	rs9894059	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	60	67	0	1	0	A|0.762;G|0.238	0.238	strong	.	GPR179	170	.	NM_001004334	exon3	c.T909C	p.V303V	CAGGGGAACACAC	.	PASS	Atlas-SNP
CCDC116	164592	hgsc.bcm.edu	37	22	21991224	21991224	+	Silent	SNP	C	C	T	rs45533832	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	44	87	0	0.488889	0	C|0.974;T|0.026	0.026	strong	.	CCDC116	56	.	NM_152612	exon5	c.C1707T	p.T569T	CTGCACCGGCATG	.	PASS	Atlas-SNP
MSH2	4436	hgsc.bcm.edu	37	2	47637246	47637246	+	Missense_Mutation	SNP	A	A	G	rs17217772	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	103	0	0.5	0	A|0.965;G|0.035	0.035	strong	.	MSH2	198	.	NM_000251	exon3	c.A380G	p.N127S	CTGGCAATCTCTC	.	PASS	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156902678	156902678	+	Missense_Mutation	SNP	G	G	A	rs11264585	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	57	98	0	0.495652	0	G|0.981;A|0.019	0.019	strong	.	LRRC71	33	.	NM_144702	exon15	c.G1597A	p.A533T	GCGTACGCCATAA	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6550004	6550004	+	Missense_Mutation	SNP	A	A	G	rs2344828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	31	65	0	0.449275	0	A|0.275;G|0.725	0.725	strong	DNHD1,colon,carcinoma,0,1	DNHD1	198	1	NM_144666	exon11	c.A2090G	p.Q697R	TACAACAGGTGCT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179554305	179554305	+	Missense_Mutation	SNP	C	C	T	rs2244492	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	139	0	1	0	C|0.624;T|0.376	0.376	strong	.	TTN	18412	.	NM_001267550	exon123	c.G31864A	p.G10622R	CAACTCCCTTCTG	.	PASS	Atlas-SNP
MERTK	10461	hgsc.bcm.edu	37	2	112740561	112740561	+	Silent	SNP	A	A	G	rs115203717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	151	0	0.439024	0	A|0.995;G|0.005	0.005	strong	.	MERTK	112	.	NM_006343	exon8	c.A1287G	p.A429A	GAGTGCAGGGATT	.	PASS	Atlas-SNP
EEF1A2	1917	hgsc.bcm.edu	37	20	62126185	62126185	+	Silent	SNP	A	A	G	rs310617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	50	49	0	0.980392	0	A|0.419;G|0.581	0.581	strong	EEF1A2,NS,carcinoma,0,3	EEF1A2	60	3	NM_001958	exon4	c.T594C	p.G198G	GTTGTCACCGTGC	.	PASS	Atlas-SNP
ZNF708	7562	hgsc.bcm.edu	37	19	21477431	21477431	+	Missense_Mutation	SNP	T	T	C	rs1781873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	52	83	0	0.571429	0	T|0.407;C|0.593	0.593	strong	.	ZNF708	66	.	NM_021269	exon4	c.A337G	p.K113E	CACTTTTACAGCC	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43529027	43529027	+	Silent	SNP	A	A	G	rs1058958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	75	201	0	0.428571	0	A|0.479;G|0.521	0.521	strong	.	PSG11	57	.	NM_002785	exon2	c.T246C	p.Y82Y	TACTACATATGAT	.	PASS	Atlas-SNP
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	9	24	0	0.346154	0	G|0.837;A|0.163	0.163	strong	CXXC5,NS,carcinoma,0,1	CXXC5	27	1	NM_016463	exon2	c.G378A	p.A126A	CATGGCGGTGGAC	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130289687	130289687	+	Silent	SNP	C	C	T	rs59562634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	76	0	0.986667	0	C|0.945;T|0.055	0.055	strong	.	COL6A6	497	.	NM_001102608	exon6	c.C2427T	p.D809D	TTTAGACGTTGTG	.	PASS	Atlas-SNP
ECSIT	51295	hgsc.bcm.edu	37	19	11618846	11618846	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	76	129	0	0.531469	0	.	.	none	.	ECSIT	32	.	NM_001142464	exon5	c.C756G	p.D252E	TGTTGAGTCTTTG	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	50	0	1	0	G|0.292;C|0.708	0.708	strong	.	ATP11A	225	.	NM_032189	exon19	c.G2238C	p.L746L	CAACCTGTCCGGG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57175484	57175484	+	Silent	SNP	A	A	G	rs7250003	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	43	76	0	0.544304	0	A|0.575;G|0.425	0.425	strong	ZNF835,NS,carcinoma,0,2	ZNF835	106	2	NM_001005850	exon2	c.T1083C	p.P361P	GGGGTAAGGCCGC	.	PASS	Atlas-SNP
OR2W1	26692	hgsc.bcm.edu	37	6	29012116	29012116	+	Silent	SNP	G	G	A	rs7341218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	91	263	0	0.421296	0	G|0.748;A|0.252	0.252	strong	.	OR2W1	36	.	NM_030903	exon1	c.C837T	p.T279T	GATGACGGTGTAA	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186459646	186459646	+	Silent	SNP	G	G	A	rs5030085	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	39	74	0	0.534247	0	G|0.965;A|0.035	0.035	strong	.	KNG1	129	.	NM_001102416	exon10	c.G1461A	p.G487G	CCAAGGGGGCCAT	.	PASS	Atlas-SNP
ARHGAP31	57514	hgsc.bcm.edu	37	3	119133183	119133183	+	Missense_Mutation	SNP	G	G	A	rs3732413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	80	68	0	0.987654	0	G|0.160;A|0.840	0.840	strong	.	ARHGAP31	175	.	NM_020754	exon12	c.G2407A	p.G803S	AAGGGCGGCCCGG	.	PASS	Atlas-SNP
NPPA	4878	hgsc.bcm.edu	37	1	11906068	11906068	+	Missense_Mutation	SNP	A	A	G	rs5065	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	71	171	0	0.507143	0	A|0.796;G|0.204	0.204	strong	.	NPPA	14	.	NM_006172	exon3	c.T454C	p.X152R	ATCTTCAGTACTG	.	PASS	Atlas-SNP
TECPR2	9895	hgsc.bcm.edu	37	14	102909991	102909991	+	Silent	SNP	C	C	T	rs17100923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	23	50	0	0.479167	0	C|0.899;T|0.101	0.101	strong	.	TECPR2	114	.	NM_001172631	exon12	c.C2760T	p.S920S	TCTGAGCGTGGAT	.	PASS	Atlas-SNP
IL1R1	3554	hgsc.bcm.edu	37	2	102781466	102781466	+	Silent	SNP	A	A	G	rs144946641	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	44	81	0	0.473118	0	A|0.998;G|0.002	0.002	strong	IL1R1,NS,carcinoma,0,1	IL1R1	52	1	NM_000877	exon3	c.A294G	p.V98V	CGTGGTAAGGTAA	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11592928	11592928	+	Silent	SNP	C	C	T	rs35922062	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	46	75	0	0.522727	0	C|0.988;T|0.012	0.012	strong	.	DNAH9	695	.	NM_001372	exon20	c.C3789T	p.I1263I	GCACATCGAGATC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134659626	134659626	+	Missense_Mutation	SNP	A	A	G	rs10870341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	67	124	0	0.462069	0	A|0.840;G|0.160	0.160	strong	.	TTC40	100	.	NM_001200049	exon44	c.T6373C	p.C2125R	CTTGGCACCGGAG	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57766397	57766397	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	25	35	0	0.531915	0	.	.	none	.	ZNF831	287	.	NM_178457	exon1	c.C323T	p.P108L	GGAAGCCGGCGGC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604721	140604721	+	Silent	SNP	C	C	A	rs2910003	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	83	133	0	0.474286	0	C|0.642;A|0.358	0.358	strong	PCDHB14,NS,carcinoma,+2,1	PCDHB14	132	1	NM_018934	exon1	c.C1644A	p.R548R	GGTGCGCGTGCTG	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116356389	116356389	+	Missense_Mutation	SNP	C	C	T	rs57845277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	94	273	0	0.362934	0	C|0.988;T|0.012	0.012	strong	.	RGS3	251	.	NM_144489	exon1	c.C190T	p.R64W	CAGCCCCGGCTTG	.	PASS	Atlas-SNP
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	22	75	0	0.431373	0	G|0.895;A|0.105	0.105	strong	.	ZNF682	51	.	NM_033196	exon4	c.C626T	p.T209I	TTAAAGGTTTTGC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149474393	149474393	+	Missense_Mutation	SNP	A	A	G	rs709061	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	83	109	0	0.988095	0	A|0.738;G|0.262	0.262	strong	.	.	.	.	NM_198455	exon4	c.A437G	p.Q146R	GGGGACAAAGCTG	.	PASS	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55872620	55872620	+	Silent	SNP	G	G	C	rs61745328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	90	253	2	0.367347	0.00790514	G|0.993;C|0.007	0.007	strong	OR8H2,colon,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.G102C	p.L34L	TCTCCTGATATAC	.	scavenged	Atlas-SNP
CCDC132	55610	hgsc.bcm.edu	37	7	92926102	92926102	+	Missense_Mutation	SNP	A	A	G	rs374290264		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	32	67	0	0.426667	0	.	.	weak	.	CCDC132	136	.	NM_017667	exon15	c.A1216G	p.I406V	TTGTCTATATTCA	.	PASS	Atlas-SNP
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	56	134	1	0.5	0.00746269	C|0.889;T|0.111	0.111	strong	SYNGR2,NS,carcinoma,+2,1	SYNGR2	17	1	NM_004710	exon2	c.C249T	p.A83A	CTCGGCCTTCTTC	.	scavenged	Atlas-SNP
COMMD10	51397	hgsc.bcm.edu	37	5	115428381	115428381	+	Missense_Mutation	SNP	T	T	G	rs1129495	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	53	76	0	0.654321	0	T|0.876;G|0.124	0.124	strong	.	COMMD10	18	.	NM_016144	exon4	c.T383G	p.I128S	AGAGAATTCTGGC	.	PASS	Atlas-SNP
NDNF	79625	hgsc.bcm.edu	37	4	121958691	121958691	+	Silent	SNP	T	T	C	rs3733559	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	39	123	1	0.410526	0.00813008	T|0.796;C|0.204	0.204	strong	NDNF,colon,carcinoma,-2,1	NDNF	72	1	NM_024574	exon4	c.A435G	p.L145L	CTGATATAAACCG	.	scavenged	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12908107	12908107	+	Silent	SNP	G	G	A	rs75413022	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	772	138	951	1	0.178756	0.00105152	G|0.955;A|0.045	0.045	strong	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C36T	p.H12H	CATGGAGTGAGGA	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52115645	52115645	+	Missense_Mutation	SNP	G	G	C	rs3829655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	59	128	0	0.430657	0	G|0.577;C|0.423	0.423	strong	.	SIGLEC5	67	.	NM_003830	exon9	c.C1495G	p.P499A	CTCCGGGGCTGTC	.	PASS	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	37	19	5832209	5832209	+	Missense_Mutation	SNP	G	G	A	rs778805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	73	185	0	0.45625	0	G|0.555;A|0.445	0.445	strong	FUT6,NS,carcinoma,+1,1	FUT6	30	1	NM_000150	exon3	c.C370T	p.P124S	GCCTCGGGGAGCG	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180218831	180218831	+	Silent	SNP	G	G	A	rs2070924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	37	70	0	0.544118	0	G|0.925;A|0.075	0.075	strong	.	MGAT1	48	.	NM_001114617	exon3	c.C1141T	p.L381L	CCCCCAGCTCCTT	.	PASS	Atlas-SNP
CCDC130	81576	hgsc.bcm.edu	37	19	13873793	13873793	+	Missense_Mutation	SNP	C	C	A	rs138278370	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	13	52	0	0.325	0	C|0.994;A|0.006	0.006	strong	.	CCDC130	25	.	NM_030818	exon10	c.C1102A	p.Q368K	TCCTCCCAGGAGG	.	PASS	Atlas-SNP
SLC24A1	9187	hgsc.bcm.edu	37	15	65918277	65918277	+	Missense_Mutation	SNP	C	C	T	rs35398714	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	33	75	0	0.540984	0	C|0.995;T|0.005	0.005	strong	.	SLC24A1	58	.	NM_004727	exon2	c.C1859T	p.A620V	CAGTGGCCAAGGT	.	PASS	Atlas-SNP
GMPPA	29926	hgsc.bcm.edu	37	2	220371035	220371035	+	Silent	SNP	C	C	G	rs1046474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	51	75	0	0.536842	0	C|0.888;G|0.112	0.112	strong	.	GMPPA	50	.	NM_205847	exon12	c.C1053G	p.A351A	CTGGGCCCGCGTG	.	PASS	Atlas-SNP
CCDC127	133957	hgsc.bcm.edu	37	5	205574	205574	+	Silent	SNP	G	G	A	rs73730755	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	107	0	0.491379	0	G|0.900;A|0.100	0.100	strong	CCDC127,NS,carcinoma,-2,2	CCDC127	27	2	NM_145265	exon3	c.C621T	p.A207A	GAGACCGGCTGCC	.	PASS	Atlas-SNP
MC5R	4161	hgsc.bcm.edu	37	18	13826139	13826139	+	Silent	SNP	C	C	T	rs45613135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	97	173	0	0.442922	0	C|0.994;T|0.006	0.006	strong	.	MC5R	83	.	NM_005913	exon1	c.C375T	p.S125S	CATTTCCGTGGTG	.	PASS	Atlas-SNP
MAG	4099	hgsc.bcm.edu	37	19	35790503	35790503	+	Silent	SNP	G	G	A	rs3746248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	105	224	1	0.448718	0.00446429	G|0.616;A|0.384	0.384	strong	.	MAG	172	.	NM_080600	exon5	c.G462A	p.E154E	CACGGAGGTGGAG	.	PASS	Atlas-SNP
RDH8	50700	hgsc.bcm.edu	37	19	10132358	10132358	+	Missense_Mutation	SNP	G	G	A	rs142753796	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	54	108	0	0.568421	0	G|0.999;A|0.001	0.001	strong	.	RDH8	51	.	NM_015725	exon6	c.G929A	p.R310H	GTCCACGCCTCCT	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	74	130	1	0.493333	0.00769231	C|0.770;T|0.230	0.230	strong	ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	NM_022089	exon25	c.G2790A	p.S930S	GCTGAACGAAGTG	.	scavenged	Atlas-SNP
ASPG	374569	hgsc.bcm.edu	37	14	104559919	104559919	+	Missense_Mutation	SNP	T	T	C	rs1770984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	114	116	0	1	0	T|0.635;C|0.365	0.365	strong	.	ASPG	34	.	NM_001080464	exon3	c.T283C	p.C95R	TGGGTTTGCCTTG	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258655	25258655	+	Missense_Mutation	SNP	A	A	G	rs61742723	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	50	82	0	0.520833	0	A|0.891;G|0.109	0.109	strong	.	ZKSCAN2	90	.	NM_001012981	exon5	c.T862C	p.W288R	GAGTCCATGGCTC	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168457966	168457966	+	Silent	SNP	G	G	A	rs3734899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	79	143	0	0.526667	0	G|0.633;A|0.367	0.367	strong	.	FRMD1	52	.	NM_024919	exon11	c.C1461T	p.D487D	CATGTCGTCCAGG	.	PASS	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55823421	55823421	+	Silent	SNP	G	G	C	rs113284733	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	71	0	0.45	0	G|0.998;C|0.002	0.002	strong	.	BRSK1	192	.	NM_032430	exon19	c.G2322C	p.G774G	CAACGGGACCCCT	.	PASS	Atlas-SNP
ACTBL2	345651	hgsc.bcm.edu	37	5	56778213	56778213	+	Missense_Mutation	SNP	C	C	T	rs73757391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	99	169	0	0.529412	0	C|0.973;T|0.027	0.027	strong	.	ACTBL2	65	.	NM_001017992	exon1	c.G322A	p.E108K	GTGCCTCGGTGAG	.	PASS	Atlas-SNP
KLK6	5653	hgsc.bcm.edu	37	19	51465096	51465096	+	Silent	SNP	C	C	G	rs1701950	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	33	80	0	0.434211	0	C|0.883;G|0.117	0.117	strong	.	KLK6	35	.	NM_001012964	exon5	c.G486C	p.L162L	GGACACCAGGTGG	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6269340	6269340	+	Silent	SNP	A	A	G	rs4908865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	10	45	0	0.27027	0	A|0.848;G|0.152	0.152	strong	.	RNF207	45	.	NM_207396	exon6	c.A564G	p.A188A	CCGGGCACACTGC	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123894317	123894317	+	Missense_Mutation	SNP	G	G	T	rs77206991	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	518	288	488	2	0.555985	0.00409836	G|0.950;T|0.050	0.050	strong	OR10G9,NS,carcinoma,0,1	OR10G9	80	1	NM_001001953	exon1	c.G598T	p.V200L	ATCTTTGTGGACA	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43649393	43649393	+	Silent	SNP	T	T	C	rs663336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	72	136	0	0.444444	0	T|0.801;C|0.199	0.199	strong	.	WDR65	76	.	NM_152498	exon4	c.T606C	p.A202A	TCTAGCTCACACC	.	PASS	Atlas-SNP
CXorf36	79742	hgsc.bcm.edu	37	X	45059838	45059838	+	Splice_Site	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	67	155	0	0.527559	0	.	.	none	.	CXorf36	53	.	NM_176819	exon2	c.233+1G>T	.	TTCTGACCTTATT	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167217964	167217964	+	Missense_Mutation	SNP	A	A	G	rs13060964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	77	0	0.514706	0	A|0.662;G|0.338	0.338	strong	.	WDR49	188	.	NM_178824	exon14	c.T1952C	p.L651P	GCCTCCAGAATTT	.	PASS	Atlas-SNP
SPIRE2	84501	hgsc.bcm.edu	37	16	89927102	89927102	+	Missense_Mutation	SNP	G	G	A	rs28478911	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	41	67	0	0.539474	0	G|1.000;|0.000	.	weak	SPIRE2,colon,carcinoma,-1,1	SPIRE2	63	1	NM_032451	exon10	c.G1474A	p.A492T	TGTCCCGCGAGTG	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73759251	73759251	+	Missense_Mutation	SNP	T	T	C	rs1632242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	42	97	0	0.424242	0	T|0.962;C|0.038	0.038	strong	.	C2CD3	288	.	NM_015531	exon28	c.A5494G	p.R1832G	CTCACCTCCCAGG	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784427	140784427	+	Silent	SNP	T	T	C	rs3749769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	238	110	252	0	0.462185	0	T|0.875;C|0.125	0.125	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.T1908C	p.D636D	TAGAGATGCGCTC	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33541216	33541216	+	Missense_Mutation	SNP	G	G	C	rs111814125		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	388	62	303	0	0.159794	0	G|0.500;C|0.500	0.500	weak	ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	NM_001244752	exon7	c.G880C	p.G294R	AAAGAAGGTGCAA	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126294661	126294661	+	Silent	SNP	G	G	A	rs34844660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	54	115	0	0.495413	0	G|0.992;A|0.008	0.008	strong	.	KIRREL3	183	.	NM_032531	exon17	c.C2151T	p.S717S	GCTGTCGCTGAGG	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862653	5862653	+	Missense_Mutation	SNP	T	T	C	rs4357719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	87	136	0	0.5	0	T|0.605;C|0.395	0.395	strong	.	OR52E6	70	.	NM_001005167	exon1	c.A475G	p.I159V	GTGGAATGACCAT	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76570924	76570924	+	Silent	SNP	G	G	A	rs61745225	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	85	206	0	0.414634	0	G|0.948;A|0.052	0.052	strong	.	DNAH17	347	.	NM_173628	exon2	c.C216T	p.L72L	GGACTTGAGGGAC	.	PASS	Atlas-SNP
YY1AP1	55249	hgsc.bcm.edu	37	1	155658085	155658085	+	Silent	SNP	T	T	C	rs2666826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	70	0	1	0	T|0.472;C|0.528	0.528	strong	YY1AP1_ENST00000368339,NS,carcinoma,0,1	YY1AP1	104	1	NM_001198904	exon1	c.A171G	p.E57E	GATCGTTTCCCCT	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49690496	49690496	+	Silent	SNP	C	C	T	rs11709525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	112	0	0.453333	0	C|0.731;G|0.000;T|0.269	0.269	strong	BSN,NS,carcinoma,0,1	BSN	272	1	NM_003458	exon5	c.C3507T	p.S1169S	ACCCTCCGGCAGC	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55524172	55524172	+	Missense_Mutation	SNP	G	G	A	rs7306491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	85	175	0	0.544872	0	G|0.681;A|0.319	0.319	strong	.	OR9K2	63	.	NM_001005243	exon1	c.G620A	p.R207H	ATTCTCGCCCACT	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204939763	204939763	+	Silent	SNP	C	C	T	rs6690894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	60	101	0	0.458015	0	C|0.974;T|0.026	0.026	strong	.	NFASC	396	.	NM_015090	exon11	c.C1056T	p.D352D	GCTGGACGAACCC	.	PASS	Atlas-SNP
ZNF212	7988	hgsc.bcm.edu	37	7	148947564	148947564	+	Silent	SNP	C	C	T	rs138413836	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	59	87	0	0.567308	0	C|0.999;T|0.001	0.001	strong	.	ZNF212	28	.	NM_012256	exon2	c.C339T	p.N113N	GGAGAACGTGGAG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037522	33037522	+	Missense_Mutation	SNP	T	T	C	rs1042178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	124	157	0	0.976378	0	T|0.688;C|0.310	0.310	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.A242G	p.Q81R	AAGGCTTGGCCAA	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52192308	52192308	+	Missense_Mutation	SNP	A	A	C	rs61758384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	17	32	0	0.425	0	A|0.985;C|0.015	0.015	strong	ZNF217,NS,carcinoma,+1,1	ZNF217	227	1	NM_006526	exon3	c.T2995G	p.C999G	GCACACAAGTGTA	.	PASS	Atlas-SNP
RBM12	10137	hgsc.bcm.edu	37	20	34241530	34241530	+	Missense_Mutation	SNP	T	T	C	rs17092928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	78	149	0	0.527027	0	T|0.978;C|0.022	0.022	strong	.	RBM12	93	.	NM_001198840	exon2	c.A1715G	p.N572S	ACAGCATTTTCAT	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94658920	94658920	+	Silent	SNP	C	C	T	rs2230759	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	74	195	0	0.432749	0	C|0.959;T|0.041	0.041	strong	.	PLXNC1	135	.	NM_005761	exon21	c.C3516T	p.P1172P	GGGTCCCGTGGAT	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3840928	3840928	+	Silent	SNP	A	A	G	rs3179783	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	31	91	0	0.392405	0	A|0.782;G|0.218	0.218	strong	.	ATP2A3	148	.	NM_174956	exon15	c.T2103C	p.T701T	ATCGCCAGTCTGT	.	PASS	Atlas-SNP
LRRTM3	347731	hgsc.bcm.edu	37	10	68687179	68687179	+	Silent	SNP	C	C	T	rs35733981	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	51	86	0	0.481132	0	C|0.964;T|0.036	0.036	strong	.	LRRTM3	241	.	NM_178011	exon2	c.C505T	p.L169L	AACTCCCTGAGAA	.	PASS	Atlas-SNP
JMY	133746	hgsc.bcm.edu	37	5	78573790	78573790	+	Missense_Mutation	SNP	A	A	T	rs13182512	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	72	0	0.452381	0	A|0.466;T|0.534	0.534	strong	.	JMY	82	.	NM_152405	exon2	c.A1090T	p.M364L	TATCAGATGGAGG	.	PASS	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156902281	156902281	+	Missense_Mutation	SNP	T	T	G	rs822431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	79	184	0	0.427027	0	T|0.706;G|0.294	0.294	strong	LRRC71,NS,carcinoma,0,1	LRRC71	33	1	NM_144702	exon14	c.T1507G	p.S503A	CAGTTCTCCAAGG	.	PASS	Atlas-SNP
ZNF667	63934	hgsc.bcm.edu	37	19	56952615	56952615	+	Silent	SNP	A	A	G	rs61740673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	40	98	0	0.425532	0	A|0.965;G|0.035	0.035	strong	ZNF667,NS,NS,-2,1	ZNF667	95	1	NM_022103	exon5	c.T1749C	p.Y583Y	ACATTCATAGGGT	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3187831	3187831	+	Missense_Mutation	SNP	C	C	T	rs34837384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	41	100	0	0.506173	0	C|0.992;T|0.008	0.008	strong	.	PITRM1	109	.	NM_001242307	exon21	c.G2417A	p.R806Q	TTACTCCGACCGA	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130488	52130488	+	Silent	SNP	G	G	A	rs17740650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	26	52	0	0.433333	0	G|0.811;A|0.188	0.188	strong	.	SIGLEC5	67	.	NM_003830	exon7	c.C1296T	p.L432L	TGTCCCGAGGTTC	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249530	71249530	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	16	157	1	0.069869	0.00636943	.	.	none	KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	NM_021046	exon1	c.T429C	p.C143C	CTGCTGTTCCCAG	.	scavenged	Atlas-SNP
FAM134B	54463	hgsc.bcm.edu	37	5	16475209	16475209	+	Missense_Mutation	SNP	G	G	C	rs34432513	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	104	196	0	0.504854	0	G|0.984;C|0.016	0.016	strong	.	FAM134B	72	.	NM_001034850	exon9	c.C1135G	p.Q379E	CCAACTGTTCCTT	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs201851784	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	62	295	5	0.269565	0.0169492	A|0.896;G|0.104	0.104	strong	SELPLG_ENST00000550948,NS,carcinoma,0,7	SELPLG	138	7	NM_001206609	exon2	c.T458C	p.V153A	GTGGGCACTGGTT	.	scavenged	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088811	56088811	+	Missense_Mutation	SNP	T	T	C	rs78599516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	85	168	0	0.313653	0	T|0.746;C|0.254	0.254	strong	.	PSPH	23	.	NM_004577	exon4	c.A95G	p.D32G	AGCTCATCGATTC	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	53	102	0	0.473214	0	A|0.603;G|0.397	0.397	strong	.	FBLN2	137	.	NM_001998	exon2	c.A1081G	p.S361G	GCACCGAGCCTGG	.	PASS	Atlas-SNP
CNTN4	152330	hgsc.bcm.edu	37	3	2787338	2787338	+	Silent	SNP	G	G	A	rs116041691	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	48	105	0	0.615385	0	G|0.996;A|0.004	0.004	strong	CNTN4_ENST00000418658,NS,carcinoma,0,1	CNTN4	335	1	NM_175607	exon6	c.G315A	p.S105S	AAACTCGTTTGGA	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	93	0	0.530612	0	G|0.714;C|0.286	0.286	strong	B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	NM_178537	exon3	c.G294C	p.G98G	TGGGGGGGCTGGG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229636561	229636561	+	Missense_Mutation	SNP	C	C	T	rs75411588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	55	0	0.493506	0	C|0.972;T|0.028	0.028	strong	.	NUP133	111	.	NM_018230	exon4	c.G455A	p.S152N	TCGGCACTCCAGT	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135370633	135370633	+	Silent	SNP	C	C	T	rs8181356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	97	166	0	0.532967	0	C|0.889;T|0.111	0.111	strong	SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	NM_001143763	exon7	c.G402A	p.K134K	TCTCTCCTTGCAC	.	PASS	Atlas-SNP
DCP1B	196513	hgsc.bcm.edu	37	12	2102455	2102455	+	Silent	SNP	A	A	C	rs150415068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	85	146	0	0.459459	0	A|0.998;C|0.002	0.002	strong	DCP1B,rectum,carcinoma,0,6	DCP1B	63	6	NM_152640	exon3	c.T294G	p.P98P	AAGGAAAGGGTCC	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	180013235	180013235	+	Missense_Mutation	SNP	T	T	G	rs12124336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	26	56	0	0.565217	0	T|0.934;G|0.066	0.066	strong	.	CEP350	418	.	NM_014810	exon21	c.T4549G	p.S1517A	CTTGACTCAAAGC	.	PASS	Atlas-SNP
PLEKHA7	144100	hgsc.bcm.edu	37	11	16837788	16837788	+	Silent	SNP	G	G	A	rs217750	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	35	67	0	0.546875	0	G|0.854;A|0.146	0.146	strong	.	PLEKHA7	120	.	NM_175058	exon12	c.C1890T	p.R630R	CATGGAGCGTCGG	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61538601	61538601	+	Silent	SNP	C	C	T	rs34820000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	121	226	1	0.461832	0.00442478	C|0.924;T|0.076	0.076	strong	DIDO1_ENST00000370371,NS,carcinoma,-1,2	DIDO1	321	2	NM_080797	exon5	c.G1272A	p.A424A	CATTGTCGCTGCG	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64216797	64216797	+	Missense_Mutation	SNP	G	G	T	rs114459902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	57	156	0	0.387755	0	G|0.993;T|0.007	0.007	strong	.	APOH	45	.	NM_000042	exon5	c.C479A	p.A160D	TTTCCAGCTGATG	.	PASS	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158369210	158369210	+	Missense_Mutation	SNP	A	A	G	rs6660222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	53	96	0	0.477477	0	A|0.976;G|0.024	0.024	strong	.	OR10T2	76	.	NM_001004475	exon1	c.T47C	p.V16A	AAACCCACCAGGA	.	PASS	Atlas-SNP
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	90	181	0	0.542169	0	T|0.794;C|0.206	0.206	strong	.	XCR1	51	.	NM_001024644	exon2	c.A111G	p.L37L	GCAGTATAGGACA	.	PASS	Atlas-SNP
LRRFIP2	9209	hgsc.bcm.edu	37	3	37144480	37144480	+	Missense_Mutation	SNP	G	G	A	rs143314448	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	39	102	0	0.481481	0	G|0.999;A|0.001	0.001	strong	.	LRRFIP2	71	.	NM_006309	exon16	c.C808T	p.R270C	TGGAGCGACTGAA	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30491081	30491081	+	Missense_Mutation	SNP	G	G	A	rs151170709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	34	53	0	0.539683	0	G|0.998;A|0.002	0.002	strong	.	NOD1	79	.	NM_006092	exon6	c.C1952T	p.T651M	ATGAACGTGGGCA	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163128824	163128824	+	Missense_Mutation	SNP	T	T	C	rs3747517	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	212	301	1	1	0.00332226	T|0.368;C|0.632	0.632	strong	IFIH1,face,carcinoma,-1,1	IFIH1	102	1	NM_022168	exon13	c.A2528G	p.H843R	GTCTCATGTTCGA	.	PASS	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	71	104	0	0.541985	0	G|0.973;A|0.027	0.027	strong	.	CCL14	22	.	NM_032962	exon1	c.C74T	p.S25F	CGTGAGGAGGATT	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	24	61	0	0.413793	0	T|0.005;G|0.229	0.229	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon18	c.A2304G	p.A768A	AATAGCAATGTAC	.	PASS	Atlas-SNP
SLC44A2	57153	hgsc.bcm.edu	37	19	10713212	10713212	+	Silent	SNP	G	G	A	rs115559926	byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	13	21	0	0.619048	0	G|0.986;A|0.014	0.014	strong	.	SLC44A2	56	.	NM_001145056	exon1	c.G6A	p.E2E	CATGGAGGACGAG	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124856660	124856660	+	Silent	SNP	T	T	A	rs3741513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	20	49	0	0.526316	0	T|0.535;A|0.465	0.465	strong	.	NCOR2	475	.	NM_006312	exon22	c.A2715T	p.T905T	CTTGGCTGTGGTG	.	PASS	Atlas-SNP
OR2A25	392138	hgsc.bcm.edu	37	7	143771536	143771536	+	Missense_Mutation	SNP	G	G	A	rs6951485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	273	192	0	0.98913	0	G|0.399;A|0.601	0.601	strong	.	OR2A25	66	.	NM_001004488	exon1	c.G224A	p.S75N	CTTGCAGCACGGT	.	PASS	Atlas-SNP
RARS2	57038	hgsc.bcm.edu	37	6	88279282	88279282	+	Silent	SNP	T	T	C	rs7748563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	71	137	0	0.452229	0	T|0.987;C|0.013	0.013	strong	.	RARS2	61	.	NM_020320	exon2	c.A63G	p.P21P	GTTTTCTGGTGGA	.	PASS	Atlas-SNP
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	89	0	0.456311	0	G|0.882;A|0.118	0.118	strong	RDH12,brain,glioma,0,1	RDH12	43	1	NM_152443	exon7	c.G482A	p.R161Q	TGGAGCGGCTAAA	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192301	102192301	+	Silent	SNP	C	C	T	rs34191945	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	252	287	0	0.996047	0	C|0.858;T|0.142	0.142	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.C55T	p.L19L	TTCCTGCTGGTGG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Silent	SNP	C	C	T	rs371465078	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	33	254	0	0.10061	0	.	.	weak	SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.G243A	p.Q81Q	TTCTTTCTGATTG	.	PASS	Atlas-SNP
ALG1L	200810	hgsc.bcm.edu	37	3	125649403	125649403	+	Silent	SNP	C	C	A	rs76888118		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	21	19	0	1	0	.	.	weak	.	ALG1L	12	.	NM_001195223	exon6	c.G405T	p.L135L	TACCTGCAGAGCT	.	PASS	Atlas-SNP
SPATA7	55812	hgsc.bcm.edu	37	14	88852166	88852166	+	Missense_Mutation	SNP	G	G	A	rs4904448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	39	57	1	0.541667	0.0175439	G|0.775;A|0.225	0.225	strong	SPATA7,NS,carcinoma,0,1	SPATA7	58	1	NM_018418	exon1	c.G4A	p.D2N	AGCATGGATGGCA	.	scavenged	Atlas-SNP
ALG3	10195	hgsc.bcm.edu	37	3	183963000	183963000	+	Silent	SNP	A	A	G	rs2233464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	67	128	0	0.492647	0	A|0.962;G|0.038	0.038	strong	.	ALG3	48	.	NM_005787	exon4	c.T591C	p.G197G	GCAGCAACCCCAG	.	PASS	Atlas-SNP
NR1H3	10062	hgsc.bcm.edu	37	11	47282024	47282024	+	Silent	SNP	C	C	T	rs2279238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	120	0	0.444444	0	C|0.733;T|0.267	0.267	strong	.	NR1H3	52	.	NM_001251934	exon4	c.C315T	p.S105S	ATGCAGCGTGTGT	.	PASS	Atlas-SNP
NFATC4	4776	hgsc.bcm.edu	37	14	24839165	24839165	+	Silent	SNP	C	C	T	rs2228233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	57	95	0	0.445312	0	C|0.667;T|0.333	0.333	strong	.	NFATC4	115	.	NM_001198967	exon3	c.C750T	p.D250D	CTCTGACGAGGCA	.	PASS	Atlas-SNP
CTNND2	1501	hgsc.bcm.edu	37	5	10973727	10973727	+	Silent	SNP	G	G	A	rs1566622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	89	155	0	0.5	0	G|0.882;A|0.118	0.118	strong	CTNND2,colon,carcinoma,-2,3	CTNND2	289	3	NM_001332	exon22	c.C3516T	p.F1172F	GTCCTCGAAGAAG	.	PASS	Atlas-SNP
CD163	9332	hgsc.bcm.edu	37	12	7636027	7636027	+	Silent	SNP	A	A	G	rs78817356	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	58	131	0	0.471545	0	A|0.978;G|0.022	0.022	strong	.	CD163	221	.	NM_203416	exon12	c.T3024C	p.C1008C	GGCAGGACAATCC	.	PASS	Atlas-SNP
FOXA3	3171	hgsc.bcm.edu	37	19	46375779	46375779	+	Silent	SNP	C	C	T	rs16980091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	69	81	0	1	0	C|0.807;T|0.193	0.193	strong	.	FOXA3	19	.	NM_004497	exon2	c.C516T	p.N172N	TTTCAACGACTGC	.	PASS	Atlas-SNP
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1506799	1506799	+	Silent	SNP	C	C	T	rs79538691	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	25	36	0	0.5	0	C|0.982;T|0.018	0.018	strong	.	ADAMTSL5	24	.	NM_213604	exon10	c.G981A	p.V327V	AGGCTCCACCCCC	.	PASS	Atlas-SNP
IFITM3	10410	hgsc.bcm.edu	37	11	320649	320649	+	Silent	SNP	G	G	A	rs11553885	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	17	112	0	0.137097	0	G|0.946;A|0.054	0.054	strong	IFITM3,caecum,carcinoma,0,23	IFITM3	132	23	NM_021034	exon1	c.C165T	p.P55P	ATGGTCGGGCACG	.	scavenged	Atlas-SNP
CLEC2D	29121	hgsc.bcm.edu	37	12	9833628	9833628	+	Silent	SNP	C	C	T	rs3764021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	25	51	0	0.446429	0	C|0.519;T|0.481	0.481	strong	CLEC2D_ENST00000290855,colon,carcinoma,0,4	CLEC2D	54	4	NM_001004419	exon2	c.C171T	p.S57S	TTTAAGCGGTAAG	.	PASS	Atlas-SNP
ENAM	10117	hgsc.bcm.edu	37	4	71509086	71509086	+	Missense_Mutation	SNP	T	T	C	rs7671281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	53	133	0	0.430894	0	T|0.819;C|0.181	0.181	strong	.	ENAM	140	.	NM_031889	exon9	c.T1943C	p.I648T	AGGAGATAGTCCC	.	PASS	Atlas-SNP
PPP2R2C	5522	hgsc.bcm.edu	37	4	6325086	6325086	+	Silent	SNP	G	G	A	rs3796403	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	389	388	365	0	0.997429	0	G|0.407;A|0.593	0.593	strong	.	PPP2R2C	63	.	NM_181876	exon9	c.C1287T	p.I429I	GGCGGCGATGGCA	.	PASS	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	37	1	12186058	12186058	+	Missense_Mutation	SNP	A	A	G	rs2230625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	167	269	0	0.504532	0	A|0.922;G|0.078	0.078	strong	TNFRSF8,NS,carcinoma,-2,1	TNFRSF8	70	1	NM_001243	exon11	c.A1204G	p.S402G	GGCTCCAGCGCCT	.	PASS	Atlas-SNP
C1QL2	165257	hgsc.bcm.edu	37	2	119915750	119915750	+	Silent	SNP	G	G	T	rs113019193	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	4	7	0	0.571429	0	G|0.981;T|0.019	0.019	strong	.	C1QL2	25	.	NM_182528	exon1	c.C96A	p.I32I	GTCGCAGATCATG	.	PASS	Atlas-SNP
ISYNA1	51477	hgsc.bcm.edu	37	19	18547209	18547209	+	Silent	SNP	G	G	A	rs61743954	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	12	44	0	0.333333	0	G|0.982;A|0.018	0.018	strong	.	ISYNA1	31	.	NM_016368	exon6	c.C690T	p.N230N	CTCCGTGTTCGCC	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10354747	10354747	+	Missense_Mutation	SNP	C	C	T	rs200121484	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	99	198	0	0.490099	0	.	.	weak	MYH4,caecum,carcinoma,0,1	MYH4	349	1	NM_017533	exon28	c.G3761A	p.R1254H	AGGGTGCGGCACA	.	PASS	Atlas-SNP
RUNDC3A	10900	hgsc.bcm.edu	37	17	42392622	42392622	+	Silent	SNP	T	T	C	rs708386	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	69	0	1	0	T|0.367;C|0.633	0.633	strong	.	RUNDC3A	30	.	NM_001144825	exon7	c.T729C	p.D243D	CACCGATGAGGAC	.	PASS	Atlas-SNP
POU5F1B	5462	hgsc.bcm.edu	37	8	128428721	128428721	+	Silent	SNP	C	C	T	rs192151034	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	86	124	0	0.540881	0	C|0.985;T|0.015	0.015	strong	.	POU5F1B	32	.	NM_001159542	exon1	c.C610T	p.L204L	CCCTTGCTGCAGA	.	PASS	Atlas-SNP
C6orf211	79624	hgsc.bcm.edu	37	6	151789868	151789868	+	Missense_Mutation	SNP	G	G	A	rs35972078	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	44	110	0	0.396396	0	G|0.904;A|0.096	0.096	strong	C6orf211,NS,carcinoma,0,1	C6orf211	30	1	NM_024573	exon5	c.G949A	p.A317T	TGTGGGGCTGACT	.	PASS	Atlas-SNP
BCL10	8915	hgsc.bcm.edu	37	1	85733374	85733374	+	Missense_Mutation	SNP	C	C	T	rs3768235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	37	89	0	0.389474	0	C|0.942;T|0.058	0.058	strong	BCL10,NS,carcinoma,0,2	BCL10	39	2	NM_003921	exon3	c.G638A	p.G213E	CAAGTTCCTTCTT	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124826408	124826408	+	Missense_Mutation	SNP	T	T	C	rs6773138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	207	192	0	1	0	T|0.903;C|0.097	0.097	strong	.	SLC12A8	81	.	NM_024628	exon10	c.A1622G	p.K541R	TCGCTCTTGGAAG	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94461717	94461717	+	Missense_Mutation	SNP	C	C	A	rs6666652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	39	30	0	1	0	C|0.816;A|0.184	0.184	strong	.	ABCA4	275	.	NM_000350	exon49	c.G6764T	p.S2255I	TCATGACTTTCAG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10480377	10480377	+	Missense_Mutation	SNP	G	G	C	rs6601495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	60	0	1	0	G|0.841;C|0.159	0.159	strong	.	RP1L1	453	.	NM_178857	exon2	c.C335G	p.T112S	CTGGGGGTCTTGG	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	118	130	0	1	0	C|0.743;T|0.257	0.257	strong	.	TMEM200A	108	.	NM_001258277	exon3	c.C237T	p.A79A	TATGGCCGTTCTT	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	7	170	3	0.0364583	0.0176471	.	.	none	AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	NM_018046	exon4	c.T666G	p.G222G	CACTGGTTTCTAT	.	scavenged	Atlas-SNP
PRAM1	84106	hgsc.bcm.edu	37	19	8564288	8564288	+	Missense_Mutation	SNP	C	C	T	rs58466313	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	105	100	0	0.990566	0	C|0.891;T|0.109	0.109	strong	.	PRAM1	53	.	NM_032152	exon2	c.G404A	p.G135E	GTGGCCCCCAGCT	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39424253	39424253	+	Missense_Mutation	SNP	C	C	G	rs9548506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	48	104	0	0.505263	0	C|0.913;G|0.087	0.087	strong	.	FREM2	385	.	NM_207361	exon9	c.C6458G	p.T2153S	ATAGGACTGGGGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512181	195512181	+	Silent	SNP	G	G	A	rs202182738	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	63	581	1	0.229927	0.00172117	G|0.965;A|0.034	0.034	strong	.	MUC4	1505	.	NM_018406	exon2	c.C6270T	p.S2090S	ACCTGTGGATATT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680336	100680336	+	Missense_Mutation	SNP	C	C	T	rs74687161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	59	130	0	0.491667	0	C|0.958;T|0.042	0.042	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5639T	p.A1880V	CAGTGGCCAGTTC	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113323785	113323785	+	Missense_Mutation	SNP	G	G	T	rs61732220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	41	75	0	0.525641	0	G|0.981;T|0.019	0.019	strong	.	SIDT1	99	.	NM_017699	exon14	c.G1366T	p.A456S	TTTTACGCGCTGC	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821467	100821467	+	Silent	SNP	G	G	A	rs7496640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	25	28	0	0.675676	0	G|0.576;A|0.424	0.424	strong	ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	NM_139057	exon4	c.C756T	p.A252A	CTGGGCGGCCTCG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1085941	1085941	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	2	53	0	0.030303	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon22	c.G2781A	p.T927T	GAGGACGGAGCTG	.	scavenged	Atlas-SNP
LMBR1L	55716	hgsc.bcm.edu	37	12	49498635	49498635	+	Silent	SNP	G	G	T	rs141166526	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	33	76	0	0.492537	0	G|0.996;T|0.004	0.004	strong	LMBR1L_ENST00000267102,colon,carcinoma,-1,2	LMBR1L	61	2	NM_018113	exon4	c.C225A	p.A75A	ACCCAGGGCAATT	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55340057	55340057	+	Missense_Mutation	SNP	G	G	A	rs144962866	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	85	144	0	0.534591	0	G|0.994;A|0.006	0.006	strong	.	OR4C16	104	.	NM_001004701	exon1	c.G454A	p.V152M	TCCTGTGTGCATT	.	PASS	Atlas-SNP
PKP3	11187	hgsc.bcm.edu	37	11	403764	403764	+	Silent	SNP	C	C	T	rs113114984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	13	31	0	0.371429	0	C|0.969;T|0.031	0.031	strong	.	PKP3	36	.	NM_007183	exon10	c.C2070T	p.D690D	CAAGGACGAGATG	.	PASS	Atlas-SNP
RANBP1	5902	hgsc.bcm.edu	37	22	20112868	20112868	+	Silent	SNP	C	C	T	rs111311060	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	91	166	0	0.505556	0	C|0.997;T|0.003	0.003	strong	.	RANBP1	19	.	NM_002882	exon4	c.C348T	p.S116S	AGGTAGCGACCGT	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65403666	65403666	+	Silent	SNP	C	C	T	rs61732727	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	78	138	0	0.516556	0	C|0.974;T|0.026	0.026	strong	.	PCNXL3	140	.	NM_032223	exon33	c.C5481T	p.A1827A	TGGCGCCGGCTGC	.	PASS	Atlas-SNP
PCED1B	91523	hgsc.bcm.edu	37	12	47629179	47629179	+	Silent	SNP	G	G	T	rs79990001	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	25	36	0	0.555556	0	G|0.974;T|0.026	0.026	strong	FAM113B,rectum,carcinoma,+1,1	.	.	1	NM_138371	exon2	c.G333T	p.S111S	GCAGTCGGGCGAG	.	PASS	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095582	90095582	+	Missense_Mutation	SNP	T	T	C	rs62640380	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	30	267	0	0.123967	0	T|0.833;C|0.167	0.167	strong	C16orf3,rectum,carcinoma,0,1	C16orf3	14	1	NM_001214	exon1	c.A169G	p.S57G	GGCAGCTTACGGG	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31611143	31611143	+	Missense_Mutation	SNP	C	C	T	rs45523133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	79	157	0	0.512987	0	C|0.972;T|0.028	0.028	strong	.	XDH	191	.	NM_000379	exon7	c.G514A	p.G172R	CATCTCCTCCACA	.	PASS	Atlas-SNP
STARD7	56910	hgsc.bcm.edu	37	2	96859034	96859034	+	Silent	SNP	A	A	G	rs997547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	98	247	0	0.4375	0	A|0.904;G|0.096	0.096	strong	STARD7,NS,carcinoma,0,1	STARD7	49	1	NM_020151	exon4	c.T606C	p.I202I	CCTCTCAATCACC	.	PASS	Atlas-SNP
MRPL15	29088	hgsc.bcm.edu	37	8	55047893	55047893	+	Missense_Mutation	SNP	G	G	A	rs200980911	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	106	237	0	0.477477	0	G|0.997;A|0.003	0.003	strong	.	MRPL15	26	.	NM_014175	exon1	c.G50A	p.R17Q	TACTCCGGGGCCT	.	PASS	Atlas-SNP
PWP2	5822	hgsc.bcm.edu	37	21	45538685	45538685	+	Missense_Mutation	SNP	C	C	T	rs150440839	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	95	176	0	0.505319	0	C|0.996;T|0.004	0.004	strong	.	PWP2	64	.	NM_005049	exon9	c.C1022T	p.S341L	ATAGCTCGGGGGA	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20725366	20725366	+	Silent	SNP	T	T	G	rs115722120	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	85	181	0	0.459459	0	T|0.995;G|0.005	0.005	strong	.	ABCB5	357	.	NM_001163941	exon16	c.T1917G	p.T639T	TTCTACTGAAAGA	.	PASS	Atlas-SNP
ENOSF1	55556	hgsc.bcm.edu	37	18	712568	712568	+	Missense_Mutation	SNP	G	G	A	rs3786349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	16	17	0	0.761905	0	G|0.851;A|0.149	0.149	strong	.	ENOSF1	44	.	NM_017512	exon1	c.C20T	p.S7F	AGCCGGGAGATCC	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48151822	48151822	+	Missense_Mutation	SNP	C	C	G	rs11168230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	55	108	0	0.509259	0	C|0.721;G|0.279	0.279	strong	.	RAPGEF3	98	.	NM_001098531	exon2	c.G46C	p.A16P	CCACAGCCAGGCC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14863863	14863863	+	Silent	SNP	A	A	G	rs61740262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	65	107	0	0.53719	0	A|0.975;G|0.025	0.025	strong	.	FREM1	261	.	NM_144966	exon4	c.T273C	p.Y91Y	GTGAACATACTTG	.	PASS	Atlas-SNP
CD80	941	hgsc.bcm.edu	37	3	119256187	119256187	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	3	148	0	0.0215827	0	.	.	none	CD80,NS,malignant_melanoma,-1,1	CD80	35	1	NM_005191	exon4	c.G497A	p.G166E	AAACCTCCAGAGG	.	scavenged	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32190484	32190484	+	Silent	SNP	G	G	A	rs8192569	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	119	1	1	0.00840336	G|0.838;A|0.162	0.162	strong	.	NOTCH4	201	.	NM_004557	exon3	c.C255T	p.P85P	GGGAGCGGGAAGC	.	PASS	Atlas-SNP
FRMD8	83786	hgsc.bcm.edu	37	11	65164357	65164357	+	Silent	SNP	C	C	T	rs12417665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	9	10	0	0.75	0	C|0.850;T|0.150	0.150	strong	.	FRMD8	28	.	NM_031904	exon7	c.C669T	p.A223A	CAGGGCCGGGCCG	.	PASS	Atlas-SNP
EIF3M	10480	hgsc.bcm.edu	37	11	32610617	32610617	+	Missense_Mutation	SNP	G	G	T	rs140562244	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	21	119	0	0.136364	0	G|0.998;T|0.002	0.002	strong	.	EIF3M	37	.	NM_006360	exon4	c.G374T	p.C125F	TGTATTGCAGCCT	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	108	207	0	0.415385	0	A|0.529;G|0.471	0.471	strong	.	MMEL1	64	.	NM_033467	exon16	c.T1553C	p.M518T	CTGTTCATCTCCT	.	PASS	Atlas-SNP
NRK	203447	hgsc.bcm.edu	37	X	105152282	105152282	+	Missense_Mutation	SNP	G	G	A	rs209373	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	444	444	449	0	1	0	0|0.030;A|0.341	0.341	strong	.	NRK	321	.	NM_198465	exon12	c.G1072A	p.V358M	TACACCGTGAGAA	.	PASS	Atlas-SNP
FES	2242	hgsc.bcm.edu	37	15	91436965	91436965	+	Silent	SNP	C	C	T	rs2227989	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	104	1	1	0.00961538	C|0.910;T|0.090	0.090	strong	.	FES	102	.	NM_002005	exon17	c.C2127T	p.A709A	GGAAGCCGATGGG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511734	169511734	+	Missense_Mutation	SNP	T	T	C	rs4525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	322	158	249	0	0.490683	0	T|0.758;C|0.242	0.242	strong	F5,NS,carcinoma,-1,1	F5	301	1	NM_000130	exon13	c.A2594G	p.H865R	CCCTTATGCTTAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509605	195509605	+	Missense_Mutation	SNP	T	T	C	rs78644746	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	29	292	2	0.142157	0.00684932	T|0.625;C|0.375	0.375	strong	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.A8846G	p.D2949G	GAAGTGTCGGTGA	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280788	152280788	+	Missense_Mutation	SNP	T	T	G	rs66954353	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	774	367	417	0	0.47416	0	T|0.500;G|0.500	0.500	strong	.	FLG	900	.	NM_002016	exon3	c.A6574C	p.K2192Q	ATGTTTTTCTGCT	.	PASS	Atlas-SNP
COL21A1	81578	hgsc.bcm.edu	37	6	55925698	55925698	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	23	96	0	0.25	0	.	.	none	.	COL21A1	201	.	NM_030820	exon26	c.T2343G	p.D781E	CTTCCCATCCAAA	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224216	248224216	+	Missense_Mutation	SNP	C	C	T	rs6658227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	409	193	392	0	0.471883	0	C|0.801;T|0.199	0.199	strong	.	OR2L3	97	.	NM_001004687	exon1	c.C233T	p.P78L	TTGTTCCTAAGAT	.	PASS	Atlas-SNP
ANGPTL1	9068	hgsc.bcm.edu	37	1	178834231	178834231	+	Silent	SNP	T	T	C	rs6689778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	48	110	0	0.375	0	T|0.939;C|0.061	0.061	strong	.	ANGPTL1	41	.	NM_004673	exon3	c.A681G	p.Q227Q	ATACTGTTGGCTG	.	PASS	Atlas-SNP
DENND2A	27147	hgsc.bcm.edu	37	7	140225578	140225578	+	Silent	SNP	G	G	A	rs61737086	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	60	92	0	0.540541	0	G|0.968;A|0.032	0.032	strong	.	DENND2A	132	.	NM_015689	exon14	c.C2520T	p.D840D	GACGAGGTCAACC	.	PASS	Atlas-SNP
SNX30	401548	hgsc.bcm.edu	37	9	115580008	115580008	+	Silent	SNP	G	G	C	rs10117709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	228	220	0	0.995633	0	G|0.217;C|0.783	0.783	strong	.	SNX30	32	.	NM_001012994	exon3	c.G372C	p.L124L	TGACCTGCCAGAA	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443887	5443887	+	Missense_Mutation	SNP	T	T	C	rs10838093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	225	298	1	0.995575	0.0033557	C|0.398;N|0.001	0.398	strong	OR51Q1,colon,carcinoma,-1,1	OR51Q1	79	1	NM_001004757	exon1	c.T457C	p.C153R	ATTTGCTGCTGTG	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617693	183617693	+	Missense_Mutation	SNP	G	G	A	rs16861394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	108	227	0	0.486486	0	G|0.928;A|0.072	0.072	strong	.	APOBEC4	45	.	NM_203454	exon2	c.C224T	p.S75F	CTACCAGAAGAAG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149523277	149523277	+	Missense_Mutation	SNP	A	A	G	rs1004200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	52	0	1	0	A|0.586;G|0.414	0.414	strong	.	.	.	.	NM_198455	exon101	c.A14360G	p.H4787R	AGCGACATCGGAC	.	PASS	Atlas-SNP
CPEB2	132864	hgsc.bcm.edu	37	4	15005604	15005604	+	Missense_Mutation	SNP	G	G	A	rs112476821	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	16	10	0	1	0	G|0.440;A|0.560	0.560	strong	.	CPEB2	77	.	NM_001177381	exon1	c.G1307A	p.S436N	CGCTCAGCGCCAT	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63727210	63727210	+	Missense_Mutation	SNP	G	G	A	rs142919190	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	20	24	0	0.588235	0	G|0.997;A|0.003	0.003	strong	ZNF679,NS,carcinoma,0,1	ZNF679	80	1	NM_153363	exon5	c.G1199A	p.S400N	ATAAGAGTATGCA	.	PASS	Atlas-SNP
CDYL	9425	hgsc.bcm.edu	37	6	4892381	4892381	+	Silent	SNP	C	C	T	rs734783	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	47	54	0	0.516484	0	C|0.956;T|0.044	0.044	strong	.	CDYL	74	.	NM_004824	exon2	c.C459T	p.T153T	CAGGACCGCAGTG	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408090	29408090	+	Missense_Mutation	SNP	A	A	G	rs17177632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	74	120	0	0.471338	0	A|0.945;G|0.055	0.055	strong	.	OR10C1	58	.	NM_013941	exon1	c.A298G	p.M100V	CTCCAGATGTTCT	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952017	14952017	+	Missense_Mutation	SNP	T	T	A	rs11880955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	61	0	0.514706	0	T|0.831;A|0.169	0.169	strong	.	OR7A10	33	.	NM_001005190	exon1	c.A673T	p.I225L	CACGTATGGAGGA	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100504575	100504575	+	Missense_Mutation	SNP	G	G	C	rs2306986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	142	250	0	0.464052	0	G|0.897;C|0.103	0.103	strong	.	MTTP	127	.	NM_000253	exon4	c.G294C	p.E98D	AGGAGAGAAGAGC	.	PASS	Atlas-SNP
PCCA	5095	hgsc.bcm.edu	37	13	100992428	100992428	+	Missense_Mutation	SNP	A	A	T	rs112237881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	43	88	0	0.457447	0	A|0.997;T|0.003	0.003	strong	.	PCCA	59	.	NM_001178004	exon18	c.A1558T	p.S520C	ACCAAGAGTGAGA	.	PASS	Atlas-SNP
KIAA1468	57614	hgsc.bcm.edu	37	18	59941254	59941254	+	Silent	SNP	A	A	C	rs17069686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	42	129	0	0.320611	0	A|0.938;C|0.062	0.062	strong	.	KIAA1468	93	.	NM_020854	exon21	c.A2802C	p.V934V	AGATGTAATGACG	.	PASS	Atlas-SNP
FKBP14	55033	hgsc.bcm.edu	37	7	30054492	30054492	+	Silent	SNP	C	C	T	rs142474407	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	42	63	0	0.636364	0	C|0.997;T|0.003	0.003	strong	.	FKBP14	18	.	NM_017946	exon4	c.G495A	p.K165K	CTCCTTCTTTAAA	.	PASS	Atlas-SNP
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	142	147	0	0.993007	0	G|0.508;T|0.492	0.492	strong	.	.	.	.	NM_022774	exon3	c.G515T	p.G172V	GGGAAGGGGAGGG	.	PASS	Atlas-SNP
C4orf51	646603	hgsc.bcm.edu	37	4	146653620	146653620	+	Missense_Mutation	SNP	G	G	A	rs10008599	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	76	149	0	0.531469	0	G|0.908;A|0.092	0.092	strong	.	C4orf51	18	.	NM_001080531	exon6	c.G517A	p.D173N	CGGTGCGATTCTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684593	100684593	+	Missense_Mutation	SNP	G	G	A	rs35988443	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	64	128	0	0.484848	0	G|0.888;A|0.112	0.112	strong	.	MUC17	804	.	NM_001040105	exon3	c.G9896A	p.S3299N	AAACGAGCACCCT	.	PASS	Atlas-SNP
RSL24D1	51187	hgsc.bcm.edu	37	15	55489065	55489065	+	Silent	SNP	G	G	A	rs9300	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	37	76	0	0.440476	0	G|0.721;A|0.279	0.279	strong	RSL24D1,NS,carcinoma,0,1	RSL24D1	11	1	NM_016304	exon1	c.C24T	p.F8F	CGAACAGAAATAA	.	PASS	Atlas-SNP
FZD10	11211	hgsc.bcm.edu	37	12	130647709	130647709	+	Silent	SNP	G	G	C	rs10848026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	58	135	0	0.432836	0	G|0.760;C|0.240	0.240	strong	.	FZD10	95	.	NM_007197	exon1	c.G222C	p.L74L	GCCGCTGGTGGAG	.	PASS	Atlas-SNP
ZNF765	91661	hgsc.bcm.edu	37	19	53911041	53911041	+	Missense_Mutation	SNP	A	A	G	rs116731689	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	129	209	0	0.488636	0	A|0.975;G|0.025	0.025	strong	.	ZNF765	61	.	NM_001040185	exon4	c.A233G	p.E78G	GACATGAAAGTCA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721756	101721756	+	Silent	SNP	A	A	C	rs57799615	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	391	132	216	0	0.337596	0	A|0.887;C|0.113	0.113	strong	.	PABPC1	76	.	NM_002568	exon8	c.T1176G	p.V392V	GTTGGGAACAGCT	.	PASS	Atlas-SNP
UNC45A	55898	hgsc.bcm.edu	37	15	91485730	91485730	+	Missense_Mutation	SNP	C	C	G	rs115978927	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	38	100	0	0.447059	0	C|0.991;G|0.009	0.009	strong	.	UNC45A	57	.	NM_018671	exon7	c.C751G	p.Q251E	GAAAGCCAGGCTG	.	PASS	Atlas-SNP
MAB21L3	126868	hgsc.bcm.edu	37	1	116670774	116670774	+	Silent	SNP	A	A	G	rs10754431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	142	139	0	1	0	A|0.608;G|0.392	0.392	strong	.	MAB21L3	33	.	NM_152367	exon6	c.A669G	p.G223G	GTTTGGATTTAAC	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22473281	22473281	+	Silent	SNP	C	C	G	rs6558166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	54	128	0	0.482143	0	C|0.882;G|0.118	0.118	strong	.	KIAA1967	72	.	NM_021174	exon13	c.C1464G	p.T488T	GGCCACCACACAG	.	PASS	Atlas-SNP
OR8D1	283159	hgsc.bcm.edu	37	11	124179902	124179902	+	Missense_Mutation	SNP	G	G	A	rs57552127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	43	138	0	0.352459	0	G|0.906;A|0.094	0.094	strong	OR8D1,NS,carcinoma,+1,1	OR8D1	53	1	NM_001002917	exon1	c.C761T	p.S254F	GTAATGGACCCAA	.	PASS	Atlas-SNP
SLC6A3	6531	hgsc.bcm.edu	37	5	1409226	1409226	+	Silent	SNP	G	G	C	rs8179035	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	32	44	0	0.507937	0	G|0.995;C|0.005	0.005	strong	SLC6A3,NS,carcinoma,-1,1	SLC6A3	102	1	NM_001044	exon11	c.C1413G	p.V471V	CGTGAAGACGTAG	.	PASS	Atlas-SNP
MAP3K9	4293	hgsc.bcm.edu	37	14	71199452	71199452	+	Silent	SNP	G	G	A	rs3829955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	329	181	286	0	0.550152	0	G|0.774;A|0.226	0.226	strong	.	MAP3K9	109	.	NM_033141	exon12	c.C2676T	p.N892N	CAGGGGGTTGTGG	.	PASS	Atlas-SNP
TBPL2	387332	hgsc.bcm.edu	37	14	55903716	55903716	+	Missense_Mutation	SNP	C	C	A	rs45612333	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	51	96	0	0.525773	0	C|0.933;A|0.067	0.067	strong	.	TBPL2	27	.	NM_199047	exon2	c.G171T	p.R57S	GGGAGACCTGGGT	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	622304	622304	+	Missense_Mutation	SNP	G	G	A	rs41545023	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	23	34	0	0.547619	0	.	.	weak	.	POLRMT	91	.	NM_005035	exon9	c.C1696T	p.P566S	GCCAGGGCTGCTC	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975606	44975606	+	Missense_Mutation	SNP	G	G	T	rs3809429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	66	122	0	0.481752	0	G|0.789;T|0.211	0.211	strong	FSCB,NS,carcinoma,0,1	FSCB	173	1	NM_032135	exon1	c.C585A	p.H195Q	TTCAGGGTGTTCA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228559994	228559994	+	Missense_Mutation	SNP	C	C	T	rs500049	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	101	180	0	0.490291	0	C|0.427;T|0.573	0.573	strong	OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	2	NM_001271223	exon105	c.C24386T	p.A8129V	AACAGGCGACCAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412005	105412005	+	Silent	SNP	A	A	G	rs28564728	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	60	246	0	0.191083	0	A|0.449;G|0.551	0.551	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T9783C	p.D3261D	CGTCACATCCATC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14857744	14857744	+	Missense_Mutation	SNP	A	A	C	rs145369669	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	43	59	0	0.511905	0	A|0.997;C|0.003	0.003	strong	.	FREM1	261	.	NM_144966	exon6	c.T635G	p.L212R	GCTCTCAGTTCTA	.	PASS	Atlas-SNP
KCNJ6	3763	hgsc.bcm.edu	37	21	39087396	39087396	+	Missense_Mutation	SNP	C	C	T	rs202012431	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	3	161	0	0.0182927	0	C|1.000;T|0.000	0.000	strong	KCNJ6,NS,carcinoma,0,1	KCNJ6	58	1	NM_002240	exon3	c.G64A	p.E22K	GGCTTTCGACGTC	.	scavenged	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2825403	2825403	+	Missense_Mutation	SNP	A	A	G	rs2228431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	139	259	0	0.477663	0	0|0.003;G|0.184	0.184	strong	.	ARSD	47	.	NM_001669	exon10	c.T1691C	p.M564T	TTGCTCATGGAAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508188	195508188	+	Missense_Mutation	SNP	G	G	C	rs372617756	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	35	263	9	0.133588	0.0342205	.	.	alt	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,3	MUC4	1505	3	NM_018406	exon2	c.C10263G	p.H3421Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
FAM109B	150368	hgsc.bcm.edu	37	22	42473586	42473586	+	Missense_Mutation	SNP	C	C	T	rs61736039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	60	100	0	0.465116	0	C|0.975;T|0.025	0.025	strong	.	FAM109B	22	.	NM_001002034	exon3	c.C289T	p.R97C	GGAGTGCGCCCAC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50165258	50165258	+	Missense_Mutation	SNP	G	G	A	rs61733228	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	44	105	0	0.556962	0	G|0.988;A|0.012	0.012	strong	.	WDFY4	205	.	NM_020945	exon52	c.G8062A	p.V2688I	AGTGACGTCAGGG	.	PASS	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128192985	128192985	+	Missense_Mutation	SNP	C	C	T	rs11245007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	148	105	0	0.993289	0	C|0.557;T|0.443	0.443	strong	.	C10orf90	121	.	NM_001004298	exon3	c.G784A	p.D262N	TTGAATCTGGACA	.	PASS	Atlas-SNP
BPIFC	254240	hgsc.bcm.edu	37	22	32831830	32831830	+	Missense_Mutation	SNP	G	G	A	rs73884913	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	45	80	0	0.529412	0	G|0.967;A|0.033	0.033	strong	.	.	.	.	NM_174932	exon8	c.C785T	p.P262L	GAGAAGGGGGGGT	.	PASS	Atlas-SNP
USP33	23032	hgsc.bcm.edu	37	1	78184325	78184325	+	Silent	SNP	A	A	G	rs12142671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	179	165	0	0.994444	0	A|0.689;G|0.311	0.311	strong	.	USP33	87	.	NM_015017	exon17	c.T1786C	p.L596L	TTCTCAACCTAAG	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	99	81	0	0.99	0	C|0.700;G|0.300	0.300	strong	CELSR1,NS,carcinoma,0,1	CELSR1	242	1	NM_014246	exon33	c.G8707C	p.E2903Q	GGTACTCTCCACG	.	PASS	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	37	5	180058720	180058720	+	Silent	SNP	G	G	A	rs150736691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	30	45	0	0.588235	0	G|0.999;A|0.001	0.001	strong	.	FLT4	356	.	NM_182925	exon2	c.C117T	p.H39H	GATGACGTGTGAC	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	37	19	50156762	50156762	+	Missense_Mutation	SNP	A	A	T	rs201628577	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	33	0	0.444444	0	.	.	weak	.	SCAF1	78	.	NM_021228	exon7	c.A3116T	p.E1039V	AGGAGGAGCAGCA	.	PASS	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1819125	1819125	+	Missense_Mutation	SNP	T	T	C	rs2396359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	118	130	0	0.991597	0	T|0.668;C|0.332	0.332	strong	REXO1,NS,carcinoma,0,1	REXO1	55	1	NM_020695	exon8	c.A2656G	p.S886G	GGCCACTGGTTTC	.	PASS	Atlas-SNP
PTCD3	55037	hgsc.bcm.edu	37	2	86358214	86358214	+	Missense_Mutation	SNP	G	G	C	rs146203968		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	65	154	0	0.457746	0	G|1.000;C|0.000	0.000	weak	.	PTCD3	51	.	NM_017952	exon16	c.G1251C	p.Q417H	TTTTCAGTCAGCC	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45398438	45398438	+	Missense_Mutation	SNP	T	T	C	rs57659670	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	109	0	1	0	T|0.831;C|0.169	0.169	strong	.	DUOX2	137	.	NM_014080	exon17	c.A2033G	p.H678R	GTGAGATGCCTGT	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56388356	56388356	+	Silent	SNP	C	C	T	rs61745692	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	86	163	0	0.534162	0	C|0.968;T|0.032	0.032	strong	BZRAP1_ENST00000355701,caecum,carcinoma,0,2	BZRAP1	287	2	NM_004758	exon19	c.G3300A	p.A1100A	AAGGGGCGCTCTG	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48628092	48628092	+	Silent	SNP	A	A	G	rs1132414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	77	0	1	0	A|0.652;G|0.348	0.348	strong	.	SPATA20	59	.	NM_022827	exon11	c.A1197G	p.E399E	CGCAGAAGATGCA	.	PASS	Atlas-SNP
GINS1	9837	hgsc.bcm.edu	37	20	25398790	25398790	+	Missense_Mutation	SNP	G	G	A	rs6076347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	95	175	0	0.542857	0	G|0.689;A|0.311	0.311	strong	GINS1,caecum,carcinoma,0,1	GINS1	25	1	NM_021067	exon4	c.G289A	p.V97I	GGTAGCGTCTTGC	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	41	100	0	0.471264	0	G|0.785;C|0.215	0.215	strong	MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	NM_198955	exon8	c.G1083C	p.R361R	AGGCCGGGGAAGC	.	PASS	Atlas-SNP
SRGAP3	9901	hgsc.bcm.edu	37	3	9034605	9034605	+	Missense_Mutation	SNP	C	C	G	rs150617309	bycluster;byfrequency;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	36	70	0	0.521739	0	C|1.000;G|0.000	0.000	alt	.	SRGAP3	146	.	NM_014850	exon20	c.G2543C	p.G848A	ACCCCCCCAAAGC	.	PASS	Atlas-SNP
ZNF781	163115	hgsc.bcm.edu	37	19	38160255	38160255	+	Silent	SNP	A	A	C	rs73932934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	93	0	0.480519	0	A|0.967;C|0.033	0.033	strong	.	ZNF781	66	.	NM_152605	exon4	c.T795G	p.L265L	TGTTAAAAGCTCT	.	PASS	Atlas-SNP
CNTNAP2	26047	hgsc.bcm.edu	37	7	146829390	146829390	+	Silent	SNP	C	C	T	rs78543192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	51	110	0	0.439655	0	C|0.995;T|0.005	0.005	strong	CNTNAP2,colon,carcinoma,0,2	CNTNAP2	392	2	NM_014141	exon8	c.C1137T	p.N379N	TTTCAACGCTACA	.	PASS	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	37	1	87043733	87043733	+	Silent	SNP	C	C	T	rs2231601	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	38	125	0	0.417582	0	C|0.976;T|0.024	0.024	strong	.	CLCA4	131	.	NM_012128	exon12	c.C2100T	p.Y700Y	CGCGTACATACCA	.	PASS	Atlas-SNP
PAQR6	79957	hgsc.bcm.edu	37	1	156213921	156213921	+	Missense_Mutation	SNP	C	C	T	rs7513351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	54	107	0	0.482143	0	C|0.818;T|0.182	0.182	strong	.	PAQR6	23	.	NM_024897	exon7	c.G787A	p.E263K	GGGCCTCACTGTT	.	PASS	Atlas-SNP
SDF2	6388	hgsc.bcm.edu	37	17	26982341	26982341	+	Silent	SNP	A	A	G	rs35579310	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	58	119	0	0.423358	0	A|0.991;G|0.009	0.009	strong	.	SDF2	17	.	NM_006923	exon2	c.T312C	p.H104H	GTGACTATGGAGG	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1803251	1803251	+	Silent	SNP	T	T	C	rs2305181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	15	29	0	0.416667	0	T|0.879;C|0.121	0.121	strong	.	FGFR3	3320	.	NM_001163213	exon5	c.T603C	p.I201I	CCGCATTGGAGGC	.	PASS	Atlas-SNP
UCP2	7351	hgsc.bcm.edu	37	11	73689104	73689104	+	Missense_Mutation	SNP	G	G	A	rs660339	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	75	0	1	0	G|0.573;T|0.004	.	strong	.	UCP2	24	.	NM_003355	exon4	c.C164T	p.A55V	GCGCTGGCTGTAG	.	PASS	Atlas-SNP
HPGD	3248	hgsc.bcm.edu	37	4	175414444	175414444	+	Missense_Mutation	SNP	T	T	G	rs200207595	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	53	135	0	0.438017	0	.	.	weak	.	HPGD	19	.	NM_000860	exon6	c.A520C	p.S174R	CACCACTGTTCAT	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657751	49657751	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	7	114	0	0.0518519	0	.	.	none	HRC,caecum,carcinoma,0,1	HRC	85	1	NM_002152	exon1	c.T744C	p.D248D	ATCATCATCGTCA	.	PASS	Atlas-SNP
ADO	84890	hgsc.bcm.edu	37	10	64564892	64564892	+	Missense_Mutation	SNP	G	G	T	rs2236295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	9	2	0	0.692308	0	G|0.779;T|0.221	0.221	strong	.	ADO	10	.	NM_032804	exon1	c.G73T	p.G25W	GGCAGCGGGGGCG	.	PASS	Atlas-SNP
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24383061	24383061	+	Silent	SNP	C	C	T	rs11796308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	498	249	446	2	0.5	0.00448431	C|0.719;0|0.006	.	strong	.	.	.	.	NM_001136234	exon1	c.C2184T	p.S728S	GGGTTCCGCACTA	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17696526	17696526	+	Silent	SNP	G	G	A	rs61999281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	69	0	0.449438	0	G|0.980;A|0.020	0.020	strong	.	RAI1	121	.	NM_030665	exon3	c.G264A	p.Q88Q	CACACAGCAAGGC	.	PASS	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64681360	64681360	+	Missense_Mutation	SNP	C	C	T	rs12293826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	37	59	0	0.506849	0	C|0.940;T|0.060	0.060	strong	.	ATG2A	133	.	NM_015104	exon4	c.G523A	p.V175I	TCACGACAGTGTC	.	PASS	Atlas-SNP
FHL2	2274	hgsc.bcm.edu	37	2	105977761	105977761	+	Silent	SNP	G	G	A	rs11124029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	46	116	0	0.484211	0	G|0.852;A|0.148	0.148	strong	.	FHL2	18	.	NM_001039492	exon7	c.C819T	p.P273P	ACAGTCGGGGCAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912085	29912085	+	Missense_Mutation	SNP	C	C	T	rs148794540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	377	68	223	0	0.180371	0	C|0.973;T|0.027	0.027	strong	.	HLA-A	89	.	NM_001242758	exon4	c.C806T	p.A269V	AGTGGGCGGCTGT	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239025645	239025645	+	Silent	SNP	C	C	T	rs11897736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	59	117	0	0.546296	0	C|0.808;T|0.192	0.192	strong	.	ESPNL	63	.	NM_194312	exon5	c.C957T	p.C319C	GGACTGCGCCCAG	.	PASS	Atlas-SNP
DLK2	65989	hgsc.bcm.edu	37	6	43418691	43418691	+	Silent	SNP	G	G	A	rs1214748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	164	0	1	0	A|0.330;C|0.006	0.330	strong	.	DLK2	22	.	NM_023932	exon6	c.C738T	p.T246T	CTCACAGGTCTTG	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105821449	105821449	+	Silent	SNP	A	A	G	rs9486069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	43	68	0	0.483146	0	A|0.586;G|0.414	0.414	strong	.	PREP	65	.	NM_002726	exon5	c.T390C	p.Y130Y	GAACGCATAACCT	.	PASS	Atlas-SNP
ERBB3	2065	hgsc.bcm.edu	37	12	56494998	56494998	+	Missense_Mutation	SNP	A	A	T	rs773123	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	31	95	0	0.397436	0	A|0.908;T|0.092	0.092	strong	.	ERBB3	350	.	NM_001982	exon27	c.A3355T	p.S1119C	AGCCGGAGCAGGA	.	PASS	Atlas-SNP
FKBPL	63943	hgsc.bcm.edu	37	6	32097089	32097089	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	51	103	0	0.542553	0	.	.	none	.	FKBPL	25	.	NM_022110	exon2	c.G469A	p.G157R	GCTCCCCCCAAGT	.	PASS	Atlas-SNP
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893170	1893170	+	Silent	SNP	C	C	T	rs9805042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	155	162	0	0.974843	0	C|0.770;T|0.230	0.230	strong	ADIPOR2,NS,carcinoma,0,1	ADIPOR2	30	1	NM_024551	exon7	c.C963T	p.Y321Y	CCTCTACATCACA	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87241847	87241847	+	Silent	SNP	G	G	A	rs7814198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	36	46	0	0.537313	0	G|0.644;A|0.356	0.356	strong	.	SLC7A13	97	.	NM_138817	exon1	c.C660T	p.G220G	TGCCCCGCCTGAA	.	PASS	Atlas-SNP
TXNDC8	255220	hgsc.bcm.edu	37	9	113091523	113091523	+	Missense_Mutation	SNP	T	T	G	rs7041938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	13	38	0	0.619048	0	T|0.904;G|0.096	0.096	strong	.	TXNDC8	30	.	NM_001003936	exon3	c.A178C	p.N60H	AATTGTTCACATC	.	PASS	Atlas-SNP
CDC25B	994	hgsc.bcm.edu	37	20	3782702	3782702	+	Silent	SNP	G	G	A	rs2228465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	72	0	0.506667	0	G|0.956;A|0.044	0.044	strong	.	CDC25B	76	.	NM_021873	exon10	c.G1053A	p.R351R	GCGGAGGCGGAGC	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56477710	56477710	+	Missense_Mutation	SNP	T	T	C	rs306496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	162	0	1	0	T|0.382;C|0.618	0.618	strong	.	NLRP8	225	.	NM_176811	exon5	c.T2345C	p.V782A	GCAGGGTGCTGAG	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138584685	138584685	+	Missense_Mutation	SNP	T	T	G	rs7764091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	30	0	0.530612	0	T|0.728;G|0.272	0.272	strong	.	KIAA1244	236	.	NM_020340	exon12	c.T2065G	p.S689A	CTCCTGTCTCTCT	.	PASS	Atlas-SNP
LIPC	3990	hgsc.bcm.edu	37	15	58833993	58833993	+	Missense_Mutation	SNP	G	G	A	rs6078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	23	47	0	0.418182	0	G|0.926;A|0.074	0.074	strong	.	LIPC	56	.	NM_000236	exon3	c.G283A	p.V95M	GACGGCGTGCTAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511236	195511236	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	19	637	0	0.0808511	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	NM_018406	exon2	c.C7215A	p.D2405E	GGAAGTGTCGGTG	.	PASS	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	37	19	2994921	2994921	+	Silent	SNP	G	G	A	rs34551565	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	65	0	1	0	G|0.736;A|0.264	0.264	strong	.	TLE6	68	.	NM_001143986	exon17	c.G1638A	p.T546T	AGTCACGTGCTGT	.	PASS	Atlas-SNP
ZFP82	284406	hgsc.bcm.edu	37	19	36884651	36884651	+	Silent	SNP	C	C	A	rs114627398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	90	168	0	0.511364	0	C|0.989;A|0.011	0.011	strong	.	ZFP82	71	.	NM_133466	exon5	c.G591T	p.P197P	TTCATACGGTTTT	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55105923	55105923	+	Silent	SNP	C	C	A	rs10416264	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	124	236	1	0.484375	0.00423729	C|0.834;A|0.166	0.166	strong	LILRA1,colon,carcinoma,-1,1	LILRA1	105	1	NM_006863	exon3	c.C52A	p.R18R	GGCCCCCGGACCC	.	PASS	Atlas-SNP
TAB2	23118	hgsc.bcm.edu	37	6	149699333	149699333	+	Silent	SNP	A	A	G	rs13215304	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	70	132	1	0.496454	0.00757576	A|0.977;G|0.023	0.023	strong	TAB2,NS,carcinoma,+2,1	TAB2	55	1	NM_015093	exon5	c.A282G	p.G94G	AGAAGGAAGTAGG	.	scavenged	Atlas-SNP
PGM2	55276	hgsc.bcm.edu	37	4	37836302	37836302	+	Silent	SNP	T	T	C	rs3752683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	275	327	2	1	0.00611621	T|0.651;C|0.349	0.349	strong	.	PGM2	45	.	NM_018290	exon3	c.T312C	p.S104S	GATCAGTTTTGAC	.	PASS	Atlas-SNP
ECT2	1894	hgsc.bcm.edu	37	3	172480580	172480580	+	Missense_Mutation	SNP	A	A	G	rs138074177	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	74	163	0	0.513889	0	A|0.999;G|0.001	0.001	strong	.	ECT2	79	.	NM_001258315	exon10	c.A989G	p.Y330C	AACTTTATGTTGT	.	PASS	Atlas-SNP
DOCK4	9732	hgsc.bcm.edu	37	7	111400275	111400275	+	Missense_Mutation	SNP	T	T	C	rs374962931		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	63	128	0	0.453237	0	.	.	weak	.	DOCK4	365	.	NM_014705	exon39	c.A4097G	p.N1366S	GGCTGGTTGGCGT	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	81	0	0.460526	0	T|0.500;C|0.500	0.500	strong	.	RABEP1	59	.	NM_004703	exon17	c.T2406C	p.N802N	GAAGAATAAAGCT	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906468	129906468	+	Silent	SNP	C	C	T	rs4750936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	158	337	0	0.486154	0	C|0.782;T|0.218	0.218	strong	.	MKI67	363	.	NM_002417	exon13	c.G3636A	p.Q1212Q	AGGAGTCTGTAGC	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	86	0	0.443182	0	G|0.912;C|0.088	0.088	strong	.	MYO18B	322	.	NM_032608	exon43	c.G7184C	p.G2395A	ATGCGGGCTGTCC	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	37	12	53189696	53189696	+	Missense_Mutation	SNP	C	C	G	rs28721426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	57	100	0	0.527778	0	C|0.847;G|0.153	0.153	strong	.	KRT3	65	.	NM_057088	exon1	c.G131C	p.G44A	CGGAAGCCATAGG	.	PASS	Atlas-SNP
HLA-E	3133	hgsc.bcm.edu	37	6	30458933	30458933	+	Silent	SNP	G	G	C	rs11548296	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	122	234	0	0.516949	0	G|0.977;C|0.023	0.023	strong	.	HLA-E	35	.	NM_005516	exon4	c.G630C	p.V210V	ACACGTGACTCAC	.	PASS	Atlas-SNP
CNGA2	1260	hgsc.bcm.edu	37	X	150912502	150912502	+	Silent	SNP	G	G	A	rs113295831	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	140	229	0	0.585774	0	G|0.996;A|0.004	0.004	strong	.	CNGA2	136	.	NM_005140	exon7	c.G1527A	p.Q509Q	GACTCAGTATGCT	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8228948	8228948	+	Silent	SNP	T	T	C	rs55642964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	78	112	0	0.52	0	T|0.759;C|0.241	0.241	strong	.	SH3TC1	105	.	NM_018986	exon12	c.T1527C	p.P509P	CGCCCCTGGGTAC	.	PASS	Atlas-SNP
GPR101	83550	hgsc.bcm.edu	37	X	136112707	136112707	+	Missense_Mutation	SNP	A	A	G	rs5931046	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	480	170	469	1	0.354167	0.0021322	A|0.808;0|0.012	.	strong	.	GPR101	96	.	NM_054021	exon1	c.T1127C	p.L376P	GGTGGGAGGCTCT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218674614	218674614	+	Silent	SNP	C	C	T	rs13417442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	136	241	0	0.591304	0	C|0.934;T|0.066	0.066	strong	.	TNS1	251	.	NM_022648	exon30	c.G4893A	p.T1631T	AGCTGGCGTGGGG	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671755	25671755	+	Silent	SNP	G	G	A	rs116223079	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	5	94	0	0.0431034	0	G|0.911;A|0.089	0.089	strong	PABPC3,bladder,carcinoma,+1,1	PABPC3	129	1	NM_030979	exon1	c.G1419A	p.T473T	GTCAACGCAGCGT	.	scavenged	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218683257	218683257	+	Silent	SNP	A	A	G	rs2571442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	178	150	0	0.988889	0	T|0.000;G|0.418;A|0.582	0.418	strong	.	TNS1	251	.	NM_022648	exon24	c.T3486C	p.A1162A	AGCTCGAGCCTGG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4508905	4508905	+	Missense_Mutation	SNP	C	C	T	rs77763884	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	42	0	0.514706	0	C|0.979;T|0.021	0.021	strong	PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon4	c.G3535A	p.V1179I	AACGAACGAAGTA	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	103	0	0.441176	0	C|0.838;T|0.162	0.162	strong	TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G421A	p.V141I	GACAAACCAAAAA	.	PASS	Atlas-SNP
LRTOMT	220074	hgsc.bcm.edu	37	11	71817250	71817250	+	Missense_Mutation	SNP	G	G	A	rs181092713	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	6	13	0	0.4	0	G|0.998;A|0.002	0.002	strong	.	LRTOMT	20	.	NM_001145309	exon7	c.G352A	p.V118I	GGGCCTGTCAAAG	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11687721	11687721	+	Silent	SNP	G	G	A	rs16945337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	91	200	0	0.473958	0	G|0.956;A|0.044	0.044	strong	DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	NM_001372	exon41	c.G7926A	p.A2642A	CCCGGCGTCCCTG	.	PASS	Atlas-SNP
SERPINF1	5176	hgsc.bcm.edu	37	17	1680002	1680002	+	Silent	SNP	T	T	C	rs6828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	58	145	0	0.42029	0	C|0.782;G|0.000;N|0.000;T|0.218	0.782	strong	.	SERPINF1	31	.	NM_002615	exon7	c.T963C	p.Y321Y	GAGTTATGAAGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515113	195515113	+	Missense_Mutation	SNP	A	A	G	rs71321849	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	335	34	169	0	0.101493	0	A|0.500;G|0.500	0.500	strong	.	MUC4	1505	.	NM_018406	exon2	c.T3338C	p.V1113A	GTGGATACTGAGG	.	PASS	Atlas-SNP
PDE11A	50940	hgsc.bcm.edu	37	2	178682603	178682603	+	Silent	SNP	T	T	C	rs6720891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	65	83	0	1	0	T|0.578;C|0.422	0.422	strong	.	PDE11A	283	.	NM_016953	exon8	c.A1626G	p.A542A	TTGATCTGCATCA	.	PASS	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	37	20	62871232	62871232	+	Silent	SNP	C	C	T	rs3003149	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	14	42	0	0.4	0	C|0.826;T|0.174	0.174	strong	.	MYT1	152	.	NM_004535	exon22	c.C3213T	p.L1071L	AAGTCTCGCCAAT	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671940	238671940	+	Silent	SNP	C	C	T	rs15232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	64	94	0	0.561404	0	C|0.855;T|0.145	0.145	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.C1584T	p.N528N	GGGCAACTGTCAG	.	PASS	Atlas-SNP
PDK2	5164	hgsc.bcm.edu	37	17	48174794	48174794	+	Silent	SNP	C	C	T	rs11546968	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	33	47	0	0.589286	0	C|0.997;T|0.003	0.003	strong	.	PDK2	41	.	NM_002611	exon2	c.C126T	p.S42S	ATCCAGCAATGCC	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	37	X	70339715	70339715	+	Silent	SNP	A	A	G	rs201566660	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	68	121	0	0.447368	0	A|0.999;G|0.001	0.001	strong	.	MED12	984	.	NM_005120	exon3	c.A384G	p.Q128Q	CACGCAACTAGCC	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	37	14	45693152	45693152	+	Missense_Mutation	SNP	A	A	G	rs190280845	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	37	75	0	0.430233	0	A|1.000;G|0.000	0.000	strong	.	MIS18BP1	92	.	NM_018353	exon11	c.T2638C	p.W880R	CATTCCATTCCTT	.	PASS	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	720274	720274	+	Silent	SNP	A	A	G	rs200458521	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	14	52	0	0.4	0	A|0.998;G|0.002	0.002	strong	.	PRKAR1B	32	.	NM_001164760	exon3	c.T267C	p.P89P	CACCACAGGGTTC	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58587737	58587737	+	Silent	SNP	C	C	T	rs11866002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	91	0	1	0	C|0.556;T|0.444	0.444	strong	.	CNOT1	359	.	NM_206999	exon22	c.G2919A	p.Q973Q	CAAATGCTGACAA	.	PASS	Atlas-SNP
ABCA10	10349	hgsc.bcm.edu	37	17	67212046	67212046	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	4	188	0	0.019802	0	.	.	none	ABCA10,NS,carcinoma,0,1	ABCA10	209	1	NM_080282	exon9	c.A768G	p.G256G	AGTGAATCCCAGA	.	scavenged	Atlas-SNP
OR13F1	138805	hgsc.bcm.edu	37	9	107267352	107267352	+	Missense_Mutation	SNP	T	T	C	rs7847413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	44	99	0	0.372881	0	T|0.794;C|0.206	0.206	strong	.	OR13F1	75	.	NM_001004485	exon1	c.T809C	p.I270T	AGGAAATAGACAA	.	PASS	Atlas-SNP
SERPINB12	89777	hgsc.bcm.edu	37	18	61234144	61234144	+	Missense_Mutation	SNP	G	G	A	rs56812375	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	33	73	0	0.458333	0	G|0.972;A|0.028	0.028	strong	SERPINB12,colon,carcinoma,0,1	SERPINB12	55	1	NM_080474	exon7	c.G1118A	p.R373Q	CACTACGATCTTG	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207737312	207737312	+	Silent	SNP	T	T	C	rs77529679		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	9	1018	0	0.642857	0	C|1.000;|0.000	1.000	weak	CR1_ENST00000367049,NS,carcinoma,0,2	CR1	354	2	NM_000651	exon22	c.T3690C	p.Y1230Y	CGGCTATGACCTC	.	scavenged	Atlas-SNP
OR1J1	347168	hgsc.bcm.edu	37	9	125239449	125239449	+	Missense_Mutation	SNP	G	G	A	rs192344372	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	92	125	0	0.671533	0	G|0.999;A|0.001	0.001	strong	OR1J1,colon,carcinoma,0,1	OR1J1	46	1	NM_001004451	exon1	c.C757T	p.R253W	TTGTCCGATAATA	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61944193	61944193	+	Silent	SNP	T	T	C	rs4809530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	75	165	0	0.493421	0	T|0.956;C|0.044	0.044	strong	.	COL20A1	137	.	NM_020882	exon16	c.T1983C	p.D661D	AGGGGATGCAGTC	.	PASS	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32487521	32487521	+	Silent	SNP	T	T	C	rs2274863	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	85	220	0	0.404762	0	T|0.921;C|0.079	0.079	strong	.	DDX58	82	.	NM_014314	exon9	c.A1323G	p.T441T	TTTGACTGTTGCT	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918360	51918360	+	Missense_Mutation	SNP	A	A	G	rs61741672	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	33	98	0	0.37931	0	A|0.792;G|0.208	0.208	strong	.	SIGLEC10	112	.	NM_033130	exon8	c.T1333C	p.S445P	TCGGGGAGTCTGA	.	PASS	Atlas-SNP
GRK4	2868	hgsc.bcm.edu	37	4	3039150	3039150	+	Missense_Mutation	SNP	T	T	C	rs1801058	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	224	220	0	0.995556	0	T|0.327;C|0.673	0.673	strong	.	GRK4	72	.	NM_182982	exon14	c.T1457C	p.V486A	TCTCGGTGGTGAA	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205814485	205814485	+	Missense_Mutation	SNP	G	G	A	rs1104899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	60	117	0	0.504202	0	G|0.759;A|0.241	0.241	strong	.	PM20D1	56	.	NM_152491	exon3	c.C457T	p.R153W	TGCCCCGACCATA	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80761411	80761411	+	Missense_Mutation	SNP	G	G	T	rs11114416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	42	99	1	0.411765	0.010101	G|0.827;T|0.173	0.173	strong	C12orf64,NS,carcinoma,-1,1	OTOGL	235	1	NM_173591	exon53	c.G6375T	p.L2125F	GTATTTGGAAGAA	.	scavenged	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57175121	57175121	+	Silent	SNP	G	G	A	rs115625349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	61	136	0	0.445255	0	G|0.942;A|0.058	0.058	strong	.	ZNF835	106	.	NM_001005850	exon2	c.C1446T	p.A482A	GCTGAAGGCCTTC	.	PASS	Atlas-SNP
FAM13A	10144	hgsc.bcm.edu	37	4	89668859	89668859	+	Missense_Mutation	SNP	C	C	T	rs7657817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	98	200	0	0.460094	0	C|0.745;T|0.255	0.255	strong	.	FAM13A	181	.	NM_014883	exon18	c.G2305A	p.V769I	CTTCAACACTGGG	.	PASS	Atlas-SNP
ZBED5	58486	hgsc.bcm.edu	37	11	10876100	10876100	+	Silent	SNP	C	C	T	rs2232921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	46	77	0	0.582278	0	C|0.891;T|0.109	0.109	strong	.	ZBED5	50	.	NM_021211	exon3	c.G393A	p.Q131Q	TACACACTGAGCA	.	PASS	Atlas-SNP
F8	2157	hgsc.bcm.edu	37	X	154158285	154158285	+	Missense_Mutation	SNP	G	G	C	rs1800291	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	34	88	0	0.357895	0	G|0.649;0|0.032	.	strong	.	F8	646	.	NM_000132	exon14	c.C3780G	p.D1260E	TGCCCCGTCATAT	.	PASS	Atlas-SNP
PGPEP1L	145814	hgsc.bcm.edu	37	15	99512877	99512877	+	Missense_Mutation	SNP	C	C	T	rs78254881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	39	71	0	0.527027	0	C|0.986;T|0.014	0.014	strong	.	PGPEP1L	26	.	NM_001102612	exon4	c.G148A	p.V50I	GCACGACGAGCTG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47754471	47754471	+	Missense_Mutation	SNP	G	G	A	rs58106867	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	11	283	2	0.0340557	0.00706714	G|0.991;A|0.010	0.010	strong	PCNT,caecum,adenoma,0,1	PCNT	283	1	NM_006031	exon3	c.G428A	p.R143H	AACAGCGTGGGAT	.	scavenged	Atlas-SNP
GPHN	10243	hgsc.bcm.edu	37	14	67147887	67147887	+	Missense_Mutation	SNP	G	G	T	rs117256383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	21	38	0	0.552632	0	G|0.993;T|0.007	0.007	strong	GPHN_ENST00000478722,NS,carcinoma,0,2	GPHN	79	2	NM_001024218	exon2	c.G127T	p.V43L	GATCTCGTACAAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1262312	1262312	+	Missense_Mutation	SNP	G	G	A	rs10835639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	52	78	0	0.58427	0	G|0.894;A|0.106	0.106	strong	.	MUC5B	473	.	NM_002458	exon31	c.G4202A	p.R1401H	GTGACCGCATGCG	.	PASS	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36933493	36933493	+	Silent	SNP	G	G	A	rs3917998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	69	131	0	0.485915	0	G|0.991;A|0.009	0.009	strong	.	CSF3R	157	.	NM_156039	exon14	c.C1794T	p.I598I	GAGGTGGATGTGA	.	PASS	Atlas-SNP
LMAN1L	79748	hgsc.bcm.edu	37	15	75116009	75116009	+	Missense_Mutation	SNP	C	C	T	rs114366521	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	59	0	1	0	C|0.981;T|0.019	0.019	strong	.	LMAN1L	43	.	NM_021819	exon12	c.C1309T	p.L437F	GAGGAGCTTCGGG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531931	50531931	+	Silent	SNP	G	G	A	rs75053680	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	45	84	0	0.523256	0	G|0.996;A|0.004	0.004	strong	C10orf71_ENST00000374144,NS,carcinoma,+2,2	C10orf71	179	2	NM_001135196	exon3	c.G1341A	p.L447L	GCTCCTGACCCCC	.	PASS	Atlas-SNP
TAS2R16	50833	hgsc.bcm.edu	37	7	122634843	122634843	+	Silent	SNP	C	C	T	rs1204014	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	46	116	0	0.410714	0	C|0.884;T|0.116	0.116	strong	TAS2R16,right_lower_lobe,carcinoma,-1,2	TAS2R16	57	2	NM_016945	exon1	c.G846A	p.T282T	TTTCAACGTAGGG	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7229619	7229619	+	Silent	SNP	G	G	A	rs12192672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	119	1	1	0.00840336	G|0.736;A|0.264	0.264	strong	.	RREB1	242	.	NM_001003700	exon10	c.G1287A	p.A429A	CCCCGCGACCAAG	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1537953	1537953	+	Missense_Mutation	SNP	C	C	T	rs11553052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	103	156	0	0.578652	0	C|0.858;T|0.142	0.142	strong	.	ASMTL	56	.	NM_004192	exon10	c.G1300A	p.G434S	TCATGCCGTGCAT	.	PASS	Atlas-SNP
CBFA2T3	863	hgsc.bcm.edu	37	16	88968048	88968048	+	Silent	SNP	T	T	C	rs76033980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	32	58	0	0.492308	0	T|0.958;C|0.042	0.042	strong	.	CBFA2T3	47	.	NM_005187	exon2	c.A168G	p.K56K	CTTAGCTTTCCTG	.	PASS	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095484	90095484	+	Silent	SNP	C	C	T	rs3785184	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	42	145	0	0.28	0	C|0.821;T|0.179	0.179	strong	C16orf3,rectum,carcinoma,-2,2	C16orf3	14	2	NM_001214	exon1	c.G267A	p.T89T	GCTGCCCGTCTCC	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52369002	52369002	+	Silent	SNP	G	G	A	rs3212327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	60	138	0	0.447761	0	G|0.880;A|0.120	0.120	strong	.	ITGA2	211	.	NM_002203	exon20	c.G2484A	p.T828T	AGTAACGCTGAAA	.	PASS	Atlas-SNP
ABCC2	1244	hgsc.bcm.edu	37	10	101604107	101604107	+	Missense_Mutation	SNP	C	C	T	rs17216317	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	33	62	0	0.532258	0	C|0.988;T|0.012	0.012	strong	.	ABCC2	160	.	NM_000392	exon28	c.C3872T	p.P1291L	GGCCTCCGCCAGA	.	PASS	Atlas-SNP
TMBIM6	7009	hgsc.bcm.edu	37	12	50152193	50152193	+	Silent	SNP	G	G	A	rs4563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	198	177	1	1	0.00564972	G|0.790;A|0.210	0.210	strong	.	TMBIM6	26	.	NM_001098576	exon6	c.G537A	p.T179T	GGGCACGGCAATG	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184766301	184766301	+	Missense_Mutation	SNP	T	T	C	rs3821750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	50	77	0	0.45045	0	T|0.818;C|0.182	0.182	strong	.	VPS8	109	.	NM_001009921	exon46	c.T4091C	p.I1364T	AGCAAATCCAAGC	.	PASS	Atlas-SNP
CDT1	81620	hgsc.bcm.edu	37	16	88874545	88874545	+	Silent	SNP	G	G	T	rs3218720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	118	131	0	0.975207	0	G|0.953;T|0.047	0.047	strong	.	CDT1	30	.	NM_030928	exon10	c.G1500T	p.L500L	CCTGCTGCTCCTC	.	PASS	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51868289	51868289	+	Silent	SNP	T	T	C	rs34998785	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	31	34	0	0.476923	0	T|0.966;C|0.034	0.034	strong	.	DMXL2	262	.	NM_001174117	exon2	c.A177G	p.Q59Q	GCTGACTTGGATG	.	PASS	Atlas-SNP
TMC3	342125	hgsc.bcm.edu	37	15	81641872	81641872	+	Missense_Mutation	SNP	G	G	T	rs61740148	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	99	218	0	0.469194	0	G|0.990;T|0.010	0.010	strong	.	TMC3	112	.	NM_001080532	exon11	c.C1120A	p.P374T	CTGATGGTGCTAT	.	PASS	Atlas-SNP
TRAPPC8	22878	hgsc.bcm.edu	37	18	29487567	29487567	+	Silent	SNP	C	C	A	rs34176695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	29	64	0	0.491525	0	C|0.935;A|0.065	0.065	strong	.	TRAPPC8	126	.	NM_014939	exon9	c.G1245T	p.P415P	TTCCGGCGGATAC	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103251218	103251218	+	Missense_Mutation	SNP	T	T	C	rs3025962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	73	0	0.453333	0	T|0.978;C|0.022	0.022	strong	.	RELN	593	.	NM_173054	exon22	c.A2932G	p.T978A	CTGATGTAAATTC	.	PASS	Atlas-SNP
TMEM200C	645369	hgsc.bcm.edu	37	18	5891637	5891637	+	Silent	SNP	C	C	A	rs28656885	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	36	61	0	0.48	0	C|0.642;A|0.358	0.358	strong	.	TMEM200C	30	.	NM_001080209	exon1	c.G426T	p.P142P	GGAGGACGGGGAG	.	PASS	Atlas-SNP
HMMR	3161	hgsc.bcm.edu	37	5	162902516	162902516	+	Missense_Mutation	SNP	T	T	C	rs299290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	45	114	0	0.454545	0	C|0.290;N|0.000	0.290	strong	HMMR,NS,carcinoma,0,1	HMMR	64	1	NM_001142556	exon11	c.T1106C	p.V369A	AAATGGTTAAAGA	.	PASS	Atlas-SNP
PBOV1	59351	hgsc.bcm.edu	37	6	138539372	138539372	+	Missense_Mutation	SNP	C	C	T	rs73774688	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	75	178	0	0.46875	0	C|0.991;T|0.009	0.009	strong	PBOV1_ENST00000527246,NS,carcinoma,-1,2	PBOV1	12	2	NM_021635	exon1	c.G161A	p.R54Q	TTTTTTCGAAATA	.	PASS	Atlas-SNP
CAST	831	hgsc.bcm.edu	37	5	96082128	96082128	+	Missense_Mutation	SNP	C	C	T	rs78054235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	112	199	0	0.497778	0	C|0.988;T|0.012	0.012	strong	.	CAST	58	.	NM_001042440	exon15	c.C1160T	p.T387M	CAGCCACGGTAAA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A	rs200513155	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	572	15	547	0	0.0262238	0	G|0.989;A|0.011	0.011	strong	SIRPA_ENST00000400068,NS,carcinoma,0,5	SIRPA	83	5	NM_001040022	exon4	c.G688A	p.V230M	TGCGAGGTGGCCC	.	scavenged	Atlas-SNP
C16orf82	162083	hgsc.bcm.edu	37	16	27078462	27078462	+	Missense_Mutation	SNP	T	T	C	rs114324679	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	48	76	0	0.489796	0	T|0.984;C|0.016	0.016	strong	.	.	.	.	NM_001145545	exon1	c.T146C	p.V49A	CAGGAGTGGCTCA	.	PASS	Atlas-SNP
FNDC7	163479	hgsc.bcm.edu	37	1	109273351	109273351	+	Missense_Mutation	SNP	C	C	A	rs76462144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	77	176	0	0.503268	0	A|0.027;C|0.973;T|0.000	0.027	strong	FNDC7_ENST00000370017,NS,carcinoma,0,2	FNDC7	113	2	NM_001144937	exon9	c.C1680A	p.N560K	AATCAACGTGAGC	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44083519	44083519	+	Silent	SNP	G	G	A	rs641351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	258	333	0	0.996139	0	A|0.793;G|0.207;T|0.000	0.793	strong	.	PTPRF	172	.	NM_002840	exon25	c.G4308A	p.R1436R	CTGGAGGATGGTG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9061559	9061559	+	Silent	SNP	C	C	G	rs1423052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	430	234	421	0	0.544186	0	C|0.616;G|0.384	0.384	strong	.	MUC16	4315	.	NM_024690	exon3	c.G25887C	p.T8629T	TTCAGACGTGGCT	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152324397	152324397	+	Silent	SNP	G	G	A	rs79983774	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	426	211	383	0	0.495305	0	G|0.940;A|0.060	0.060	strong	.	FLG2	431	.	NM_001014342	exon3	c.C5865T	p.H1955H	CTCACTGTGGCCA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385178	16385178	+	Silent	SNP	G	G	A	rs80297394	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	739	176	492	2	0.23816	0.00406504	G|0.931;A|0.069	0.069	strong	FAM131C,NS,carcinoma,0,2	FAM131C	21	2	NM_182623	exon7	c.C597T	p.P199P	GCCGCTGGGAAGG	.	scavenged	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084435	31084435	+	Silent	SNP	G	G	A	rs1062470	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	18	21	0	0.486486	0	G|0.569;A|0.431	0.431	strong	.	CDSN	48	.	NM_001264	exon2	c.C957T	p.Y319Y	CACAGGGTAGATT	.	PASS	Atlas-SNP
NBPF3	84224	hgsc.bcm.edu	37	1	21795287	21795287	+	Silent	SNP	G	G	A	rs10157037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	95	195	0	0.497382	0	G|0.953;A|0.047	0.047	strong	.	NBPF3	55	.	NM_001256416	exon3	c.A240A	p.K80K	GAAATCGCGCCCC	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133473445	133473445	+	Silent	SNP	C	C	T	rs41298987	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	89	139	0	0.542683	0	C|0.988;T|0.012	0.012	strong	TF,rectum,carcinoma,0,1	TF	116	1	NM_001063	exon4	c.C432T	p.S144S	CAGGTCCGCTGGG	.	PASS	Atlas-SNP
GRIA3	2892	hgsc.bcm.edu	37	X	122537277	122537277	+	Silent	SNP	T	T	C	rs502434	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	76	138	0	0.567164	0	T|0.440;0|0.004	.	strong	.	GRIA3	386	.	NM_000828	exon9	c.T1200C	p.N400N	CTGGAATGAGTAT	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241835379	241835379	+	Silent	SNP	G	G	A	rs12105122	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	25	18	0	0.675676	0	G|0.494;A|0.506	0.506	strong	C2orf54,rectum,carcinoma,0,1	C2orf54	14	1	NM_001085437	exon1	c.C36T	p.A12A	CTGCACGGCCATG	.	PASS	Atlas-SNP
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	55	0	1	0	A|0.810;G|0.190	0.190	strong	.	TNFAIP6	98	.	NM_007115	exon4	c.A431G	p.Q144R	CAAAGCAAATTTT	.	PASS	Atlas-SNP
CEACAM8	1088	hgsc.bcm.edu	37	19	43093718	43093718	+	Silent	SNP	C	C	T	rs10413332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	291	123	243	0	0.42268	0	C|0.938;T|0.062	0.062	strong	.	CEACAM8	44	.	NM_001816	exon3	c.G594A	p.R198R	GAGGGTCCTGTTG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249125	71249125	+	Silent	SNP	A	A	G	rs113379698	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	234	55	327	1	0.235043	0.0030581	A|0.500;G|0.500	0.500	weak	KRTAP5-8,rectum,carcinoma,0,2	KRTAP5-8	28	2	NM_021046	exon1	c.A24G	p.G8G	CTCTGGAGGCTGT	.	scavenged	Atlas-SNP
COX10	1352	hgsc.bcm.edu	37	17	14005439	14005439	+	Silent	SNP	G	G	A	rs2159132	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	124	1	1	0.00806452	G|0.468;A|0.532	0.532	strong	.	COX10	36	.	NM_001303	exon4	c.G504A	p.L168L	AGCTCTGGTTGTA	.	PASS	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	37	19	1085690	1085690	+	Silent	SNP	G	G	A	rs149960692	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	63	129	0	0.529412	0	G|0.993;A|0.007	0.007	strong	.	HMHA1	78	.	NM_001258328	exon23	c.G3144A	p.S1048S	GGACTCGGACCTA	.	PASS	Atlas-SNP
ITGAL	3683	hgsc.bcm.edu	37	16	30495496	30495496	+	Silent	SNP	C	C	T	rs7191097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	61	63	0	1	0	C|0.900;T|0.100	0.100	strong	.	ITGAL	149	.	NM_002209	exon9	c.C918T	p.P306P	AAAACCCGCGAGC	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12502161	12502161	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	5	95	1	0.042735	0.0105263	.	.	none	ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	2	NM_001080821	exon4	c.T1051A	p.S351T	TCAGTGAACTAGG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	18	38	0	0.439024	0	C|0.841;A|0.159	0.159	strong	.	OBSCN	2142	.	NM_001271223	exon62	c.C16338A	p.H5446Q	TCACCACGCCCTA	.	PASS	Atlas-SNP
OR5H1	26341	hgsc.bcm.edu	37	3	97852229	97852229	+	Missense_Mutation	SNP	T	T	A	rs9849637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	288	272	0	0.99654	0	T|0.779;A|0.221	0.221	strong	.	OR5H1	71	.	NM_001005338	exon1	c.T688A	p.S230T	AAGAAATCTGATA	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58169996	58169996	+	Missense_Mutation	SNP	T	T	C	rs12279895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	113	207	0	0.489177	0	T|0.672;C|0.328	0.328	strong	OR5B3,NS,carcinoma,0,1	OR5B3	65	1	NM_001005469	exon1	c.A887G	p.K296R	GCACTCTTCACTT	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22847917	22847917	+	Silent	SNP	T	T	C	rs4100176	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	23	310	1	0.884615	0.00322581	T|0.500;C|0.500	0.500	weak	ZNF492_ENST00000456783,NS,carcinoma,+1,1	ZNF492	129	1	NM_020855	exon4	c.T1446C	p.C482C	AGAATGTGGCAAA	.	scavenged	Atlas-SNP
WNT3A	89780	hgsc.bcm.edu	37	1	228238443	228238443	+	Missense_Mutation	SNP	G	G	A	rs61743220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	79	189	0	0.473054	0	G|0.992;A|0.008	0.008	strong	.	WNT3A	40	.	NM_033131	exon3	c.G400A	p.A134T	ACGGCCGCCATCT	.	PASS	Atlas-SNP
LCN15	389812	hgsc.bcm.edu	37	9	139657874	139657874	+	Missense_Mutation	SNP	G	G	C	rs11145871	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	21	37	0	0.567568	0	G|0.994;C|0.006	0.006	strong	.	LCN15	11	.	NM_203347	exon4	c.C353G	p.S118C	GCGAAGGAGCTGT	.	PASS	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166900425	166900425	+	Silent	SNP	C	C	T	rs145035963	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	111	213	0	0.569231	0	C|1.000;T|0.000	0.000	strong	.	SCN1A	641	.	NM_001165964	exon11	c.G1797A	p.E599E	GTTATCCTCAAAG	.	PASS	Atlas-SNP
NEIL2	252969	hgsc.bcm.edu	37	8	11640853	11640853	+	Silent	SNP	C	C	T	rs112549959	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	97	180	0	0.468599	0	C|0.996;T|0.004	0.004	strong	.	NEIL2	14	.	NM_001135746	exon4	c.C633T	p.G211G	TCTAGGCCAGGCT	.	PASS	Atlas-SNP
SKA1	220134	hgsc.bcm.edu	37	18	47908556	47908556	+	Missense_Mutation	SNP	G	G	A	rs6507992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	113	0	1	0	G|0.256;A|0.744	0.744	strong	.	SKA1	21	.	NM_001039535	exon4	c.G271A	p.V91I	GAAAACGTTCCTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677523	100677523	+	Missense_Mutation	SNP	A	A	C	rs10238201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	87	133	3	0.391892	0.0225564	A|0.908;C|0.092	0.092	strong	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.A2826C	p.R942S	GGCTAGAACACTT	.	scavenged	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17942204	17942204	+	Missense_Mutation	SNP	C	C	T	rs13263632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	26	63	0	0.464286	0	C|0.924;T|0.076	0.076	strong	.	ASAH1	71	.	NM_001127505	exon1	c.G107A	p.S36N	GCAAAGCTGCCAA	.	PASS	Atlas-SNP
ERP27	121506	hgsc.bcm.edu	37	12	15070187	15070187	+	Missense_Mutation	SNP	T	T	C	rs79989395	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	120	214	0	0.535714	0	T|0.995;C|0.005	0.005	strong	.	ERP27	37	.	NM_152321	exon5	c.A501G	p.I167M	GTTCATTATCAGG	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289922	98289922	+	Missense_Mutation	SNP	C	C	T	rs200123082	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	18	29	0	0.5625	0	C|0.994;T|0.006	0.006	strong	.	TSPYL5	48	.	NM_033512	exon1	c.G151A	p.A51T	CCTGTGCCGCCTG	.	PASS	Atlas-SNP
APOC2	344	hgsc.bcm.edu	37	19	45452429	45452429	+	Missense_Mutation	SNP	A	A	C	rs5126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	59	122	0	0.479675	0	A|0.991;C|0.009	0.009	strong	.	APOC2	9	.	NM_000483	exon4	c.A229C	p.K77Q	TACAGCAAAAGCA	.	PASS	Atlas-SNP
OR52I1	390037	hgsc.bcm.edu	37	11	4615869	4615869	+	Missense_Mutation	SNP	C	C	G	rs78745657	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	144	244	0	0.516129	0	C|0.983;G|0.017	0.017	strong	.	OR52I1	29	.	NM_001005169	exon1	c.C601G	p.L201V	AGCAGTCTCTACA	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612055	53612055	+	Missense_Mutation	SNP	T	T	C	rs10410030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	30	62	0	0.576923	0	T|0.842;C|0.158	0.158	strong	.	ZNF415	68	.	NM_018355	exon4	c.A1243G	p.N415D	ATTCATTGCATTT	.	PASS	Atlas-SNP
SPATA2	9825	hgsc.bcm.edu	37	20	48522263	48522263	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	371	188	342	0	0.506739	0	.	.	none	.	SPATA2	36	.	NM_006038	exon3	c.G1456A	p.A486T	GGTAAGCGCTGAG	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229770827	229770827	+	Missense_Mutation	SNP	C	C	T	rs115641620	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	62	108	0	0.529915	0	C|0.992;T|0.008	0.008	strong	.	URB2	152	.	NM_014777	exon4	c.C467T	p.S156L	GCTGGTCGGCCTG	.	PASS	Atlas-SNP
ATP5J	522	hgsc.bcm.edu	37	21	27107251	27107251	+	Missense_Mutation	SNP	C	C	G	rs71649640	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	52	100	0	0.525253	0	C|0.990;G|0.010	0.010	strong	.	ATP5J	13	.	NM_001003701	exon1	c.G16C	p.G6R	CCTACCCGCCATC	.	PASS	Atlas-SNP
GAB2	9846	hgsc.bcm.edu	37	11	77936166	77936166	+	Silent	SNP	A	A	G	rs1385600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	43	70	0	0.443299	0	A|0.691;G|0.309	0.309	strong	.	GAB2	63	.	NM_080491	exon5	c.T1290C	p.V430V	AGAGCCAACTCCA	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88963401	88963401	+	Missense_Mutation	SNP	C	C	T	rs141118086	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	34	87	0	0.409639	0	C|0.986;T|0.014	0.014	strong	.	ZNF804B	322	.	NM_181646	exon4	c.C1105T	p.P369S	TTCAGCCCACCAA	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	110	143	0	0.558376	0	G|0.950;C|0.050	0.050	strong	XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	NM_022166	exon3	c.C668G	p.A223G	GCTGCGGCTCTGT	.	PASS	Atlas-SNP
PTPN5	84867	hgsc.bcm.edu	37	11	18751041	18751041	+	Silent	SNP	C	C	T	rs1550870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	28	35	0	0.474576	0	C|0.633;T|0.367	0.367	strong	.	PTPN5	163	.	NM_032781	exon14	c.G1563A	p.V521V	GTCCACCACACCC	.	PASS	Atlas-SNP
HPS5	11234	hgsc.bcm.edu	37	11	18330522	18330522	+	Silent	SNP	A	A	G	rs146455658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	40	97	0	0.454545	0	A|0.999;G|0.001	0.001	strong	.	HPS5	70	.	NM_181507	exon6	c.T582C	p.L194L	TCGAGTAAGTGAA	.	PASS	Atlas-SNP
STAP2	55620	hgsc.bcm.edu	37	19	4333711	4333711	+	Missense_Mutation	SNP	C	C	T	rs7247504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	26	68	0	0.376812	0	C|0.373;T|0.627	0.627	strong	.	STAP2	38	.	NM_001013841	exon3	c.G277A	p.D93N	CCTGATCCCGGAG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	479	244	423	5	0.509395	0.0118203	A|0.980;G|0.020	0.020	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_001081450	exon13	c.T1812C	p.L604L	CCGTCTAAGGGTC	.	scavenged	Atlas-SNP
PNO1	56902	hgsc.bcm.edu	37	2	68385240	68385240	+	Silent	SNP	C	C	G	rs61735657	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	39	56	0	0.5	0	C|0.979;G|0.021	0.021	strong	.	PNO1	17	.	NM_020143	exon1	c.C174G	p.P58P	GAGGCCCGTCTTC	.	PASS	Atlas-SNP
SMARCAL1	50485	hgsc.bcm.edu	37	2	217285104	217285104	+	Missense_Mutation	SNP	C	C	G	rs2066522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	76	164	1	0.475	0.00609756	C|0.957;G|0.043	0.043	strong	SMARCAL1,right_upper_lobe,carcinoma,+1,1	SMARCAL1	93	1	NM_014140	exon5	c.C945G	p.S315R	CACCAGCAGTGAG	.	scavenged	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388817	1388817	+	Missense_Mutation	SNP	C	C	G	rs71299249	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	21	67	0	0.134615	0	CATGT|0.500;GACGC|0.500	.	alt	CRIPAK,rectum,carcinoma,0,7	CRIPAK	185	7	NM_175918	exon1	c.C518G	p.P173R	CGTGCCCATGTGG	.	PASS	Atlas-SNP
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201835	32201835	+	Missense_Mutation	SNP	A	A	C	rs9982675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	104	226	0	0.462222	0	A|0.504;C|0.496	0.496	strong	.	.	.	.	NM_181606	exon2	c.T182G	p.I61S	TTGTTGATGTTGC	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	143359	143359	+	Missense_Mutation	SNP	G	G	A	rs114876243	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	24	61	0	0.489796	0	G|0.985;A|0.015	0.015	strong	.	PLEKHG4B	167	.	NM_052909	exon2	c.G607A	p.V203I	GGGGTCGTCACCC	.	PASS	Atlas-SNP
MROH6	642475	hgsc.bcm.edu	37	8	144654249	144654249	+	Missense_Mutation	SNP	G	G	A	rs10866911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	79	107	0	0.496855	0	G|0.611;A|0.389	0.389	strong	.	.	.	.	NM_001100878	exon2	c.C401T	p.T134I	GACAGGGTGAGCA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132508389	132508389	+	Silent	SNP	A	A	G	rs7133119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	228	229	0	0.991304	0	A|0.700;G|0.300	0.300	strong	EP400,NS,carcinoma,0,1	EP400	370	1	NM_015409	exon24	c.A4758G	p.P1586P	TCAGCCAGAGACG	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5042837	5042837	+	Missense_Mutation	SNP	C	C	T	rs61745111	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	29	53	1	0.47541	0.0188679	C|0.881;T|0.119	0.119	strong	USP6,NS,carcinoma,0,1	USP6	213	1	NM_004505	exon14	c.C1366T	p.R456W	ATGCCCCGGCTCC	.	scavenged	Atlas-SNP
TNFRSF21	27242	hgsc.bcm.edu	37	6	47251772	47251772	+	Missense_Mutation	SNP	C	C	T	rs148459670	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	137	227	0	0.509294	0	C|1.000;T|0.000	0.000	strong	.	TNFRSF21	61	.	NM_014452	exon3	c.G1145A	p.R382Q	TCCTGCCGGGGCC	.	PASS	Atlas-SNP
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	55	112	0	0.458333	0	G|0.710;A|0.290	0.290	strong	ABRA,NS,adenoma,0,1	ABRA	57	1	NM_139166	exon1	c.C84T	p.S28S	GGCCAAGCTGATG	.	PASS	Atlas-SNP
DUOX1	53905	hgsc.bcm.edu	37	15	45444572	45444572	+	Silent	SNP	T	T	C	rs114272662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	116	194	1	0.52968	0.00515464	T|0.968;C|0.032	0.032	strong	.	DUOX1	125	.	NM_017434	exon26	c.T3282C	p.S1094S	CATCTCTTTCATG	.	PASS	Atlas-SNP
GLB1L2	89944	hgsc.bcm.edu	37	11	134226278	134226278	+	Silent	SNP	C	C	T	rs3802928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	77	1	0.467742	0.012987	C|0.888;T|0.112	0.112	strong	GLB1L2,NS,carcinoma,0,1	GLB1L2	79	1	NM_138342	exon6	c.C642T	p.Y214Y	GCCCTACGTCAAG	.	scavenged	Atlas-SNP
GSE1	23199	hgsc.bcm.edu	37	16	85690900	85690900	+	Missense_Mutation	SNP	G	G	A	rs35446008	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	46	101	0	0.5	0	G|0.985;A|0.015	0.015	strong	.	.	.	.	NM_014615	exon8	c.G1330A	p.G444S	GATGCCGGCCTGC	.	PASS	Atlas-SNP
ZNF141	7700	hgsc.bcm.edu	37	4	367290	367290	+	Missense_Mutation	SNP	A	A	G	rs61733102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	31	35	0	0.508197	0	A|0.998;G|0.002	0.002	strong	.	ZNF141	48	.	NM_003441	exon4	c.A1064G	p.N355S	AACTGAATGAACA	.	PASS	Atlas-SNP
CD200R1L	344807	hgsc.bcm.edu	37	3	112545875	112545875	+	Missense_Mutation	SNP	G	G	A	rs61740125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	141	130	0	1	0	G|0.979;A|0.021	0.021	strong	.	CD200R1L	47	.	NM_001008784	exon4	c.C644T	p.T215I	TTGCCAGTCAAAT	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68603345	68603345	+	Missense_Mutation	SNP	C	C	T	rs146663204	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	33	76	0	0.375	0	C|0.997;T|0.003	0.003	strong	.	ITGA11	110	.	NM_001004439	exon26	c.G3161A	p.R1054H	GGAGCACGACGCA	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234529540	234529540	+	Silent	SNP	G	G	A	rs1134756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	64	172	0	0.450704	0	G|0.798;A|0.202	0.202	strong	.	TARBP1	111	.	NM_005646	exon27	c.C4287T	p.D1429D	CTGAACGTCGGTC	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19377859	19377859	+	Missense_Mutation	SNP	T	T	C	rs61969156		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	500	39	556	1	0.078	0.00179856	.	.	weak	OR11H12,NS,carcinoma,0,2	OR11H12	58	2	NM_001013354	exon1	c.T266C	p.V89A	GGTATGTCTCTTC	.	scavenged	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	162	186	0	1	0	G|0.709;A|0.291	0.291	strong	.	OR7A17	37	.	NM_030901	exon1	c.C525T	p.P175P	AAAGTGGGGGATT	.	PASS	Atlas-SNP
PYROXD2	84795	hgsc.bcm.edu	37	10	100144782	100144782	+	Missense_Mutation	SNP	C	C	T	rs2296441	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	37	73	0	0.445783	0	C|0.662;T|0.338	0.338	strong	.	PYROXD2	43	.	NM_032709	exon15	c.G1597A	p.A533T	GGCGGGCGAAGTA	.	PASS	Atlas-SNP
GOLT1A	127845	hgsc.bcm.edu	37	1	204172060	204172060	+	Silent	SNP	G	G	C	rs6689599	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	98	193	0	0.471154	0	G|0.897;C|0.103	0.103	strong	.	GOLT1A	15	.	NM_198447	exon2	c.C81G	p.L27L	GTACAGGAGTGTT	.	PASS	Atlas-SNP
PIH1D1	55011	hgsc.bcm.edu	37	19	49950356	49950356	+	Silent	SNP	C	C	G	rs12443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	45	0	1	0	C|0.246;G|0.754	0.754	strong	PIH1D1,NS,carcinoma,0,1	PIH1D1	23	1	NM_017916	exon7	c.G612C	p.G204G	TTCAGGCCTGAGG	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108690221	108690221	+	Missense_Mutation	SNP	G	G	A	rs2593943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	155	313	1	0.511551	0.00319489	G|0.607;A|0.392	0.392	strong	.	MORC1	211	.	NM_014429	exon25	c.C2506T	p.H836Y	GCTGATGCTCAGG	.	PASS	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	37	1	38197214	38197214	+	Missense_Mutation	SNP	G	G	A	rs141193695	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	38	99	0	0.44186	0	G|0.979;A|0.021	0.021	strong	EPHA10,colon,carcinoma,+1,1	EPHA10	120	1	NM_001099439	exon7	c.C1532T	p.A511V	GTGGGCGCCCCTG	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44489868	44489868	+	Missense_Mutation	SNP	T	T	C	rs1983609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	46	91	0	0.534884	0	T|0.150;C|0.850	0.850	strong	.	PARVB	44	.	NM_001003828	exon3	c.T272C	p.V91A	CCCTGGTGGATGT	.	PASS	Atlas-SNP
MCM9	254394	hgsc.bcm.edu	37	6	119245024	119245024	+	Silent	SNP	C	C	T	rs12197931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	72	147	0	0.503497	0	C|0.923;T|0.077	0.077	strong	MCM9_ENST00000316316,rectum,carcinoma,-1,2	MCM9	73	2	NM_017696	exon2	c.G573A	p.S191S	TGGAGACGAAGAC	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129762112	129762112	+	Silent	SNP	G	G	A	rs2297738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	71	105	0	0.529851	0	G|0.845;A|0.155	0.155	strong	.	LAMA2	481	.	NM_000426	exon43	c.G6237A	p.T2079T	CAAAACGAATGCT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46900062	46900062	+	Missense_Mutation	SNP	G	G	A	rs61738822	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	41	44	0	0.539474	0	G|0.996;A|0.004	0.004	strong	.	COL18A1	129	.	NM_030582	exon10	c.G1930A	p.D644N	AGACACGACAAGC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918903	12918903	+	Silent	SNP	G	G	A	rs17038644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	452	227	358	1	0.502212	0.0027933	G|0.978;A|0.022	0.022	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.G39A	p.A13A	GCTGGCGGGGCAG	.	PASS	Atlas-SNP
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46021546	46021546	+	Missense_Mutation	SNP	C	C	G	rs116074123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	83	59	0	0.72807	0	C|0.974;G|0.026	0.026	strong	.	KRTAP10-7	41	.	NM_198689	exon2	c.C1010G	p.A337G	GCCAGGCCAGCTG	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117576631	117576631	+	Missense_Mutation	SNP	C	C	T	rs34248572	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	53	138	0	0.473214	0	C|0.972;T|0.028	0.028	strong	CD101,NS,carcinoma,-1,1	CD101	95	1	NM_001256109	exon9	c.C2974T	p.R992W	AACACACGGAAAG	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15708540	15708540	+	Missense_Mutation	SNP	A	A	G	rs1010294	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	312	162	272	1	0.519231	0.00367647	T|0.004;G|0.400	0.400	strong	.	FHAD1	78	.	NM_052929	exon30	c.A3973G	p.I1325V	GTGTCCATTGAGA	.	PASS	Atlas-SNP
AP3B2	8120	hgsc.bcm.edu	37	15	83334245	83334245	+	Silent	SNP	C	C	T	rs9806343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	45	72	0	0.542169	0	C|0.956;T|0.044	0.044	strong	.	AP3B2	103	.	NM_004644	exon16	c.G1935A	p.P645P	TTCCTCCGGCCAG	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133212582	133212582	+	Silent	SNP	G	G	A	rs5744990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	32	63	0	0.551724	0	G|0.862;A|0.138	0.138	strong	.	POLE	416	.	NM_006231	exon42	c.C5707T	p.L1903L	TTGTCAGAGAATG	.	PASS	Atlas-SNP
TCF3	6929	hgsc.bcm.edu	37	19	1622116	1622116	+	Silent	SNP	G	G	A	rs2240590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	14	13	0	0.7	0	G|0.722;A|0.278	0.278	strong	.	TCF3	72	.	NM_003200	exon10	c.C759T	p.S253S	CGGGCCGCTACCG	.	PASS	Atlas-SNP
FASLG	356	hgsc.bcm.edu	37	1	172628488	172628488	+	Silent	SNP	G	G	A	rs61756244	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	60	139	0	0.441176	0	G|0.944;A|0.056	0.056	strong	.	FASLG	44	.	NM_000639	exon1	c.G147A	p.P49P	ACCACCGCCACCG	.	PASS	Atlas-SNP
TPRN	286262	hgsc.bcm.edu	37	9	140086940	140086940	+	Silent	SNP	C	C	T	rs115446132	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	41	93	0	0.577465	0	C|0.996;T|0.004	0.004	strong	.	TPRN	28	.	NM_001128228	exon2	c.G1929A	p.V643V	GGGTCTCACGCTG	.	PASS	Atlas-SNP
NRP2	8828	hgsc.bcm.edu	37	2	206610502	206610502	+	Silent	SNP	T	T	G	rs849563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	48	81	0	0.494845	0	T|0.802;G|0.198	0.198	strong	.	NRP2	179	.	NM_201279	exon10	c.T1674G	p.P558P	CACCCCTGACATC	.	PASS	Atlas-SNP
HSH2D	84941	hgsc.bcm.edu	37	19	16263946	16263946	+	Silent	SNP	C	C	T	rs1870354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	33	73	0	0.6	0	C|0.986;T|0.014	0.014	strong	.	HSH2D	16	.	NM_032855	exon6	c.C309T	p.D103D	GCTGGACGCCCTG	.	PASS	Atlas-SNP
PRR16	51334	hgsc.bcm.edu	37	5	120021817	120021817	+	Missense_Mutation	SNP	C	C	A	rs17853861	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	30	60	0	0.434783	0	C|0.881;A|0.119	0.119	strong	PRR16,NS,neuroblastoma,-1,2	PRR16	71	2	NM_016644	exon3	c.C259A	p.P87T	GCACACCCGTCTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412227	228412227	+	Silent	SNP	T	T	C	rs1771480	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	230	285	1	0.978723	0.00350877	T|0.612;C|0.388	0.388	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.T2997C	p.S999S	AGCCAGTGCCACA	.	PASS	Atlas-SNP
SLC22A1	6580	hgsc.bcm.edu	37	6	160557643	160557643	+	Missense_Mutation	SNP	C	C	T	rs2282143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	58	129	1	0.491525	0.00775194	C|0.949;T|0.051	0.051	strong	SLC22A1,NS,carcinoma,-1,1	SLC22A1	69	1	NM_153187	exon6	c.C1022T	p.P341L	GCACGCCGCGCCT	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105407031	105407031	+	Silent	SNP	A	A	G	rs11623422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	66	60	0	1	0	A|0.459;G|0.541	0.541	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.T14757C	p.S4919S	GCCCTGAGACACA	.	PASS	Atlas-SNP
VPS13D	55187	hgsc.bcm.edu	37	1	12339619	12339619	+	Missense_Mutation	SNP	A	A	T	rs4845898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	85	175	0	0.494186	0	A|0.831;T|0.169	0.169	strong	.	VPS13D	316	.	NM_015378	exon20	c.A4514T	p.E1505V	AGAGAGAATCTGA	.	PASS	Atlas-SNP
GNAO1	2775	hgsc.bcm.edu	37	16	56368689	56368689	+	Silent	SNP	C	C	T	rs1065375	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	59	79	0	0.495798	0	C|0.556;T|0.444	0.444	strong	.	GNAO1	95	.	NM_138736	exon5	c.C513T	p.T171T	GCCCACCGAGCAG	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95078413	95078413	+	Missense_Mutation	SNP	T	T	C	rs41305617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	91	223	0	0.376033	0	T|0.986;C|0.014	0.014	strong	.	NOL8	118	.	NM_017948	exon7	c.A494G	p.K165R	TCATATTTGATGA	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90136732	90136732	+	Missense_Mutation	SNP	C	C	G	rs61748627	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	30	63	0	0.517241	0	C|0.988;G|0.012	0.012	strong	.	GPR98	605	.	NM_032119	exon78	c.C16949G	p.T5650S	TCCATACCATCAG	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5356913	5356913	+	Silent	SNP	C	C	T	rs16954697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	42	96	0	0.403846	0	C|0.819;N|0.001	.	strong	.	DHX33	41	.	NM_020162	exon8	c.G1383A	p.S461S	TGGCTTCGACATG	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444900	61444900	+	Missense_Mutation	SNP	A	A	C	rs61735508	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	37	64	0	0.578125	0	A|0.975;C|0.025	0.025	strong	.	OGFR	63	.	NM_007346	exon7	c.A1933C	p.S645R	GGCCCCAGCCCGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179395560	179395560	+	Missense_Mutation	SNP	G	G	A	rs16866380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	171	351	1	0.489971	0.002849	G|0.921;A|0.079	0.079	strong	.	TTN	18412	.	NM_001267550	exon358	c.C105782T	p.P35261L	GCTTTCGGGTGAG	.	PASS	Atlas-SNP
ASB18	401036	hgsc.bcm.edu	37	2	237103623	237103623	+	Silent	SNP	A	A	G	rs10166966	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	143	134	0	1	0	A|0.899;G|0.101	0.101	strong	.	ASB18	34	.	NM_212556	exon6	c.T1293C	p.A431A	GCGAAGAGCACAG	.	PASS	Atlas-SNP
PGBD1	84547	hgsc.bcm.edu	37	6	28269663	28269663	+	Missense_Mutation	SNP	A	A	G	rs1997660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	157	155	1	1	0.00645161	A|0.464;G|0.536	0.536	strong	.	PGBD1	106	.	NM_001184743	exon7	c.A2032G	p.I678V	TTCCGAATAGAAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179577870	179577870	+	Silent	SNP	T	T	C	rs61232800	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	134	285	0	0.465278	0	T|0.981;C|0.019	0.019	strong	.	TTN	18412	.	NM_001267550	exon93	c.A26991G	p.T8997T	TATACATGTGTAG	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117691490	117691490	+	Silent	SNP	G	G	A	rs9658446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	51	121	0	0.342282	0	G|0.985;A|0.015	0.015	strong	NOS1,NS,carcinoma,0,1	NOS1	240	1	NM_001204218	exon18	c.C2703T	p.P901P	GAGGTCGGGCCCA	.	PASS	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36931364	36931364	+	Missense_Mutation	SNP	C	C	G	rs16889318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	57	122	0	0.463415	0	C|0.929;G|0.071	0.071	strong	.	PI16	50	.	NM_001199159	exon6	c.C1246G	p.L416V	CGTGCCCTGGCTC	.	PASS	Atlas-SNP
PENK	5179	hgsc.bcm.edu	37	8	57358432	57358432	+	Silent	SNP	G	G	A	rs3808633	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	93	163	0	0.502703	0	G|0.909;A|0.091	0.091	strong	.	PENK	59	.	NM_001135690	exon3	c.C81T	p.S27S	ATCCTGGCTGCAT	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	37	8	140999002	140999002	+	Silent	SNP	G	G	A	rs28710457	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	49	0	0.483871	0	G|0.986;A|0.014	0.014	strong	.	TRAPPC9	114	.	NM_031466	exon19	c.C3036T	p.T1012T	ATGCTCGGTGGAG	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140562756	140562756	+	Missense_Mutation	SNP	C	C	G	rs28398442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	39	65	0	0.534247	0	C|0.991;G|0.009	0.009	strong	.	PCDHB16	159	.	NM_020957	exon1	c.C622G	p.L208V	CCTCAACTAAGAT	.	PASS	Atlas-SNP
NEDD4	4734	hgsc.bcm.edu	37	15	56208535	56208535	+	Silent	SNP	G	G	A	rs12440230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	101	208	0	0.448889	0	G|0.846;A|0.154	0.154	strong	.	NEDD4	167	.	NM_198400	exon1	c.C495T	p.N165N	ACTACCGTTGCTG	.	PASS	Atlas-SNP
SIAE	54414	hgsc.bcm.edu	37	11	124506967	124506967	+	Silent	SNP	C	C	T	rs7941327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	97	180	0	0.554286	0	C|0.852;T|0.148	0.148	strong	.	SIAE	37	.	NM_170601	exon10	c.G1452A	p.T484T	AGGCCACGTGGTC	.	PASS	Atlas-SNP
KBTBD13	390594	hgsc.bcm.edu	37	15	65369395	65369395	+	Missense_Mutation	SNP	C	C	T	rs2919358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	8	0	0	1	.	C|0.451;T|0.549	0.549	strong	.	KBTBD13	9	.	NM_001101362	exon1	c.C242T	p.A81V	TGCAGGCCGTGGA	.	PASS	Atlas-SNP
ECM1	1893	hgsc.bcm.edu	37	1	150482639	150482639	+	Silent	SNP	C	C	T	rs74352693	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	101	0	0.463636	0	C|0.982;T|0.018	0.018	strong	.	ECM1	96	.	NM_001202858	exon5	c.C447T	p.H149H	CCAGCACCCCAAT	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39422624	39422624	+	Missense_Mutation	SNP	C	C	T	rs9548505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	72	115	0	0.5625	0	C|0.894;G|0.000;T|0.106	0.106	strong	.	FREM2	385	.	NM_207361	exon8	c.C6196T	p.R2066C	ATCAGCCGTAATT	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90085654	90085654	+	Missense_Mutation	SNP	T	T	C	rs62000408	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	42	100	0	0.392523	0	T|0.959;C|0.041	0.041	strong	.	GPR98	605	.	NM_032119	exon69	c.T14029C	p.F4677L	GGCACCTTTGGAG	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108479432	108479432	+	Missense_Mutation	SNP	G	G	A	rs700866	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	881	644	985	2	0.730987	0.00203046	G|0.250;A|0.750	0.750	weak	RGPD4,NS,other,0,1	RGPD4	112	1	NM_182588	exon17	c.G2413A	p.A805T	CGATGGGCAGAAG	.	scavenged	Atlas-SNP
PODXL2	50512	hgsc.bcm.edu	37	3	127387388	127387388	+	Silent	SNP	C	C	T	rs34716022	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	133	230	0	0.525692	0	C|0.938;T|0.062	0.062	strong	.	PODXL2	53	.	NM_015720	exon5	c.C1311T	p.S437S	TCTGAGCAAGCCC	.	PASS	Atlas-SNP
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	155	166	1	1	0.0060241	G|0.708;A|0.292	0.292	strong	.	LRRC42	29	.	NM_052940	exon7	c.G978A	p.E326E	ACGGGAGACCTCG	.	PASS	Atlas-SNP
HELQ	113510	hgsc.bcm.edu	37	4	84374692	84374692	+	Missense_Mutation	SNP	A	A	G	rs17006837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	64	124	0	0.520325	0	A|0.864;G|0.136	0.136	strong	.	HELQ	95	.	NM_133636	exon2	c.T704C	p.L235P	TGGGGCAGTTCCT	.	PASS	Atlas-SNP
TM7SF2	7108	hgsc.bcm.edu	37	11	64882441	64882441	+	Silent	SNP	G	G	A	rs33981236	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	93	130	0	0.534483	0	G|0.981;A|0.019	0.019	strong	TM7SF2,NS,carcinoma,+1,1	TM7SF2	30	1	NM_003273	exon7	c.G780A	p.A260A	GCTGGCGTTTGGG	.	PASS	Atlas-SNP
DEFB135	613209	hgsc.bcm.edu	37	8	11842019	11842019	+	Missense_Mutation	SNP	G	G	A	rs73663074	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	57	105	0	0.553398	0	G|0.959;A|0.041	0.041	strong	.	DEFB135	7	.	NM_001033017	exon2	c.G154A	p.E52K	AAAAACGAACAAT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9065510	9065510	+	Silent	SNP	G	G	A	rs1867692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	27	63	0	0.574468	0	G|0.825;A|0.175	0.175	strong	.	MUC16	4315	.	NM_024690	exon3	c.C21936T	p.F7312F	AGTAGGGAACTTA	.	PASS	Atlas-SNP
MAG	4099	hgsc.bcm.edu	37	19	35793589	35793589	+	Silent	SNP	C	C	T	rs1126770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	32	55	0	0.516129	0	C|0.728;T|0.272	0.272	strong	.	MAG	172	.	NM_080600	exon7	c.C1209T	p.T403T	GGCCACCGCCTTC	.	PASS	Atlas-SNP
TRPV6	55503	hgsc.bcm.edu	37	7	142573613	142573613	+	Silent	SNP	C	C	T	rs79832568	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	83	167	0	0.488235	0	C|0.976;T|0.024	0.024	strong	.	TRPV6	108	.	NM_018646	exon7	c.G807A	p.T269T	TCCATACGTCCAC	.	PASS	Atlas-SNP
TCF25	22980	hgsc.bcm.edu	37	16	89940232	89940232	+	Missense_Mutation	SNP	A	A	C	rs13338056	bycluster;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	27	80	0	0.341772	0	A|0.803;C|0.197	0.197	strong	.	TCF25	61	.	NM_014972	exon1	c.A157C	p.K53Q	GCAGGGAAGGAGG	.	PASS	Atlas-SNP
IFI44	10561	hgsc.bcm.edu	37	1	79115905	79115905	+	Missense_Mutation	SNP	T	T	C	rs2070123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	57	122	0	0.419118	0	T|0.891;C|0.109	0.109	strong	IFI44,NS,carcinoma,-1,1	IFI44	55	1	NM_006417	exon2	c.T25C	p.W9R	TTGACATGGTTGC	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672290	238672290	+	Missense_Mutation	SNP	C	C	T	rs3739040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	76	127	0	0.481013	0	C|0.882;T|0.118	0.118	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.C1934T	p.P645L	ATTGTCCGGAGAA	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112648127	112648127	+	Missense_Mutation	SNP	T	T	G	rs4596117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	316	316	322	0	1	0	T|0.404;G|0.596	0.596	strong	CD200R1_ENST00000440122,colon,carcinoma,+2,2	CD200R1	91	2	NM_138806	exon4	c.A430C	p.T144P	CCACGGTACGAAT	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123452859	123452859	+	Silent	SNP	C	C	T	rs115018449	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	65	114	0	0.436242	0	C|0.998;T|0.002	0.002	strong	MYLK,caecum,carcinoma,0,1	MYLK	224	1	NM_053025	exon10	c.G984A	p.S328S	TCTGGGCGAGTCC	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122419993	122419993	+	Silent	SNP	C	C	T	rs16833421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	56	0	0.493333	0	C|0.965;T|0.035	0.035	strong	.	PARP14	242	.	NM_017554	exon6	c.C2592T	p.A864A	CAATGCCACCATC	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31761885	31761885	+	Silent	SNP	G	G	T	rs61734343	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	58	121	0	0.42029	0	A|0.003;G|0.992;T|0.005	0.005	strong	.	.	.	.	NM_080574	exon4	c.G303T	p.G101G	ACACAGGTTGAAA	.	PASS	Atlas-SNP
MCHR1	2847	hgsc.bcm.edu	37	22	41077548	41077548	+	Silent	SNP	C	C	T	rs137903389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	42	56	0	0.512195	0	C|0.997;T|0.003	0.003	strong	MCHR1,NS,carcinoma,0,1	MCHR1	45	1	NM_005297	exon2	c.C885T	p.A295A	CACAGCCGCATAC	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19655670	19655670	+	Silent	SNP	C	C	T	rs11669558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	7	7	0	0.583333	0	C|0.874;T|0.126	0.126	strong	.	CILP2	84	.	NM_153221	exon8	c.C2316T	p.S772S	CTTCTCCGCCAAC	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39424254	39424254	+	Silent	SNP	T	T	C	rs9548507	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	48	105	0	0.510638	0	T|0.912;C|0.088	0.088	strong	.	FREM2	385	.	NM_207361	exon9	c.T6459C	p.T2153T	TAGGACTGGGGAT	.	PASS	Atlas-SNP
SGCD	6444	hgsc.bcm.edu	37	5	155771579	155771579	+	Silent	SNP	T	T	C	rs1801193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	136	303	1	0.415902	0.00330033	T|0.516;C|0.484	0.484	strong	.	SGCD	52	.	NM_000337	exon3	c.T84C	p.Y28Y	GATTTATGGCTGG	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3177944	3177944	+	Silent	SNP	C	C	T	rs61731934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	40	51	0	0.526316	0	C|0.983;T|0.017	0.017	strong	PFKP_ENST00000381075,NS,carcinoma,+2,2	PFKP	182	2	NM_002627	exon21	c.C2139T	p.T713T	TACCACCGATGAT	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107343	55107343	+	Missense_Mutation	SNP	T	T	C	rs10425981	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	161	269	0	0.925287	0	T|0.832;C|0.168	0.168	strong	.	LILRA1	105	.	NM_006863	exon6	c.T901C	p.Y301H	GGTGCATACAACC	.	PASS	Atlas-SNP
SPATA31C1	441452	hgsc.bcm.edu	37	9	90537856	90537856	+	Missense_Mutation	SNP	A	A	G	rs79747501	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	509	501	840	0	0.984283	0	A|0.767;G|0.233	0.233	strong	.	.	.	.	NM_001145124	exon4	c.A3034G	p.I1012V	CCTTCAATAAGCC	.	PASS	Atlas-SNP
TATDN2	9797	hgsc.bcm.edu	37	3	10312534	10312534	+	Silent	SNP	G	G	A	rs56261813	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	54	79	0	0.5	0	G|0.960;A|0.040	0.040	strong	.	TATDN2	59	.	NM_014760	exon4	c.G1668A	p.L556L	GGATCTGGTCTGG	.	PASS	Atlas-SNP
VNN1	8876	hgsc.bcm.edu	37	6	133035098	133035098	+	Missense_Mutation	SNP	G	G	A	rs2294757	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	97	78	0	0.989796	0	G|0.474;A|0.525	0.525	strong	.	VNN1	69	.	NM_004666	exon1	c.C77T	p.T26I	GCTGCAGTGAAAG	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	37	17	66928468	66928468	+	Missense_Mutation	SNP	G	G	C	rs62638729	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	46	80	0	0.464646	0	G|0.945;C|0.055	0.055	strong	.	ABCA8	213	.	NM_007168	exon6	c.C758G	p.A253G	ATCAAGGCCTTCA	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88396123	88396123	+	Silent	SNP	C	C	G	rs2970912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	154	237	0	0.987179	0	C|0.650;G|0.350	0.350	strong	.	SMYD1	95	.	NM_198274	exon6	c.C708G	p.L236L	TGAGCTCCGGGCC	.	PASS	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90771787	90771787	+	Missense_Mutation	SNP	G	G	A	rs16944065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	58	0	0.428571	0	G|0.979;A|0.021	0.021	strong	.	SEMA4B	51	.	NM_020210	exon15	c.G2426A	p.S809N	CACTCAGCATCCA	.	PASS	Atlas-SNP
CD80	941	hgsc.bcm.edu	37	3	119263607	119263607	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	5	273	0	0.0162338	0	.	.	none	CD80,rectum,carcinoma,+2,1	CD80	35	1	NM_005191	exon3	c.A208G	p.K70E	TTTTCTTCTCCTT	.	scavenged	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41497274	41497274	+	Missense_Mutation	SNP	C	C	T	rs8192709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	83	0	0.528571	0	C|0.950;T|0.050	0.050	strong	CYP2B6,NS,carcinoma,0,1	CYP2B6	79	1	NM_000767	exon1	c.C64T	p.R22C	GTTCAGCGCCACC	.	PASS	Atlas-SNP
C19orf54	284325	hgsc.bcm.edu	37	19	41248532	41248532	+	Silent	SNP	G	G	A	rs36071297	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	78	127	0	0.537931	0	G|0.905;A|0.095	0.095	strong	.	C19orf54	13	.	NM_198476	exon6	c.C862T	p.L288L	TGGACAGCAGGTA	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152193049	152193049	+	Silent	SNP	C	C	T	rs114845154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	114	0	0.439024	0	C|0.985;T|0.015	0.015	strong	HRNR,NS,carcinoma,-2,1	HRNR	403	1	NM_001009931	exon3	c.G1056A	p.E352E	GCCAGACTCATGT	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	715	290	807	3	0.405594	0.00371747	T|0.787;A|0.213	0.213	strong	OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.T178A	p.C60S	CTACTTTGTGTGG	.	scavenged	Atlas-SNP
LRFN3	79414	hgsc.bcm.edu	37	19	36435564	36435564	+	Silent	SNP	G	G	A	rs2293756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	3	0	1	0	G|0.934;A|0.066	0.066	strong	.	LRFN3	43	.	NM_024509	exon3	c.G1530A	p.T510T	GGCCACGCGGCCT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1075850	1075850	+	Silent	SNP	G	G	A	rs11825969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	49	81	0	0.494949	0	G|0.844;A|0.156	0.156	strong	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon2	c.G276A	p.E92E	GGTGGAGTCCATC	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33406328	33406328	+	Missense_Mutation	SNP	G	G	A	rs113919201	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	128	218	1	0.52459	0.00458716	G|0.991;A|0.009	0.009	strong	CEP89,NS,carcinoma,+1,1	CEP89	82	1	NM_032816	exon14	c.C1480T	p.R494C	TGGCACGTAAAAT	.	PASS	Atlas-SNP
GPC3	2719	hgsc.bcm.edu	37	X	132730541	132730541	+	Silent	SNP	A	A	G	rs2314298	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	461	297	421	0	0.644252	0	A|0.905;G|0.095	0.095	strong	.	GPC3	88	.	NM_001164617	exon8	c.T1569C	p.D523D	TTCATCATCACCG	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107978342	107978342	+	Silent	SNP	T	T	A	rs80131334	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	66	97	0	0.594595	0	T|0.950;A|0.050	0.050	strong	.	IRS4	253	.	NM_003604	exon1	c.A1233T	p.R411R	TCTTCCTCGCCTG	.	PASS	Atlas-SNP
R3HDML	140902	hgsc.bcm.edu	37	20	42965863	42965863	+	Silent	SNP	C	C	T	rs3746570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	65	0	0.514706	0	C|0.845;T|0.155	0.155	strong	.	R3HDML	33	.	NM_178491	exon1	c.C66T	p.N22N	AGTGAACGCCTTG	.	PASS	Atlas-SNP
ITIH2	3698	hgsc.bcm.edu	37	10	7759595	7759595	+	Silent	SNP	C	C	T	rs7072478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	53	0	1	0	C|0.819;T|0.181	0.181	strong	ITIH2,NS,carcinoma,0,1	ITIH2	144	1	NM_002216	exon6	c.C474T	p.S158S	GAGCAGCGCTCTT	.	PASS	Atlas-SNP
OR2A14	135941	hgsc.bcm.edu	37	7	143826697	143826697	+	Missense_Mutation	SNP	C	C	G	rs2961161	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	335	352	1	0.997024	0.00284091	C|0.374;G|0.626	0.626	strong	.	OR2A14	66	.	NM_001001659	exon1	c.C492G	p.S164R	CCTGAGCCTGCCC	.	PASS	Atlas-SNP
CIZ1	25792	hgsc.bcm.edu	37	9	130941451	130941451	+	Silent	SNP	C	C	T	rs45536439	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	70	118	0	0.59322	0	C|0.961;T|0.039	0.039	strong	.	CIZ1	75	.	NM_001257975	exon8	c.G1125A	p.A375A	TGTTTGCGCCTGC	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133881996	133881996	+	Missense_Mutation	SNP	G	G	A	rs116340633	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	48	100	0	0.64	0	G|0.992;A|0.008	0.008	strong	.	TG	416	.	NM_003235	exon3	c.G199A	p.G67S	AACGACGGCCGCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678740	100678740	+	Missense_Mutation	SNP	T	T	C	rs4269454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	70	110	0	0.486111	0	T|0.821;C|0.179	0.179	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4043C	p.L1348P	CCACACTGGTGGC	.	PASS	Atlas-SNP
CDC42BPB	9578	hgsc.bcm.edu	37	14	103406169	103406169	+	Silent	SNP	C	C	T	rs60475222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	96	163	0	0.444444	0	C|0.992;T|0.008	0.008	strong	.	CDC42BPB	123	.	NM_006035	exon33	c.G4707A	p.R1569R	CTACCGCCTCTGC	.	PASS	Atlas-SNP
CTF1	1489	hgsc.bcm.edu	37	16	30910830	30910830	+	Silent	SNP	C	C	T	rs8059269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	83	194	0	0.441489	0	C|0.965;T|0.035	0.035	strong	.	CTF1	3	.	NM_001330	exon2	c.C120T	p.Y40Y	CAAATACGCTGAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	10873	10873	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	6	5	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.T114C	p.P38P	CATCCCTCTACTA	.	PASS	Atlas-SNP
ZNF596	169270	hgsc.bcm.edu	37	8	195254	195254	+	Missense_Mutation	SNP	C	C	A	rs2074718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	84	151	0	0.56	0	C|0.837;A|0.163	0.163	strong	.	ZNF596	34	.	NM_173539	exon6	c.C407A	p.T136K	TGAGAACGAAACA	.	PASS	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	37	1	87045696	87045696	+	Missense_Mutation	SNP	G	G	C	rs2231604	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	59	110	0	0.395973	0	G|0.950;C|0.050	0.050	strong	.	CLCA4	131	.	NM_012128	exon14	c.G2428C	p.V810L	CTTCAAGTAAATA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505813	195505813	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	22	237	1	0.0873016	0.00421941	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	NM_018406	exon2	c.A12638G	p.D4213G	GAAGTGTCGGTGA	.	scavenged	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56413532	56413532	+	Silent	SNP	G	G	A	rs7258847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	30	69	0	0.410959	0	G|0.824;A|0.176	0.176	strong	.	NLRP13	220	.	NM_176810	exon9	c.C2658T	p.H886H	TGACAAGTGCTTG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26422980	26422980	+	Missense_Mutation	SNP	A	A	G	rs2236005	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	41	44	0	1	0	A|0.618;G|0.382	0.382	strong	MYO18B,NS,carcinoma,-1,1	MYO18B	322	1	NM_032608	exon43	c.A7040G	p.Q2347R	AAACCCAATTCAG	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43414875	43414875	+	Missense_Mutation	SNP	A	A	C	rs59587483	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	133	278	0	0.452381	0	A|0.960;C|0.040	0.040	strong	.	PSG6	89	.	NM_001031850	exon3	c.T563G	p.M188R	TGAGTCATAGGGA	.	PASS	Atlas-SNP
RPP40	10799	hgsc.bcm.edu	37	6	4999011	4999011	+	Silent	SNP	A	A	G	rs12214401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	60	121	0	0.48	0	A|0.944;G|0.056	0.056	strong	.	RPP40	36	.	NM_006638	exon5	c.T498C	p.S166S	AGACCAAGATATT	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19221784	19221784	+	Missense_Mutation	SNP	A	A	G	rs35319139	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	89	0	0.477612	0	A|0.973;G|0.027	0.027	strong	.	SH2D4A	49	.	NM_022071	exon7	c.A908G	p.K303R	CTCAAAAACCTCT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801493	27801493	+	Missense_Mutation	SNP	T	T	C	rs1919127	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	75	163	0	0.5	0	T|0.680;C|0.320	0.320	strong	.	C2orf16	357	.	NM_032266	exon1	c.T2054C	p.V685A	AGGCTGTGAAATC	.	PASS	Atlas-SNP
SLC47A2	146802	hgsc.bcm.edu	37	17	19607432	19607432	+	Silent	SNP	C	C	T	rs34169093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	20	45	0	0.512821	0	C|0.935;T|0.065	0.065	strong	.	SLC47A2	61	.	NM_152908	exon11	c.G1077A	p.A359A	AGTATCCGCAGCC	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110804809	110804809	+	Silent	SNP	G	G	A	rs650724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	34	72	0	0.492754	0	G|0.870;A|0.130	0.130	strong	.	COL4A1	372	.	NM_001845	exon51	c.C4800T	p.S1600S	GCCGGGGGACGCC	.	PASS	Atlas-SNP
ENAM	10117	hgsc.bcm.edu	37	4	71508869	71508869	+	Missense_Mutation	SNP	T	T	C	rs2609428	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	62	125	0	0.452555	0	T|0.952;C|0.048	0.048	strong	.	ENAM	140	.	NM_031889	exon9	c.T1726C	p.F576L	CCACCTTTTAAGG	.	PASS	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	722548	722548	+	Silent	SNP	A	A	G	rs1128550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	33	84	1	0.428571	0.0119048	A|0.452;G|0.548	0.548	strong	RHOT2,NS,carcinoma,0,1	RHOT2	35	1	NM_138769	exon16	c.A1386G	p.G462G	CAATGGACAGGAG	.	scavenged	Atlas-SNP
OAS2	4939	hgsc.bcm.edu	37	12	113425154	113425154	+	Missense_Mutation	SNP	C	C	G	rs1293767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	64	0	1	0	C|0.212;G|0.788	0.788	strong	.	OAS2	86	.	NM_001032731	exon2	c.C489G	p.S163R	AAGAAGCGGGTGC	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Missense_Mutation	SNP	T	T	G	rs1199457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	175	344	0	0.528701	0	T|0.841;0|0.015	.	strong	.	KIF4A	118	.	NM_012310	exon11	c.T1265G	p.L422W	TCATTTTGGTAAG	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36485753	36485753	+	Silent	SNP	G	G	C	rs35803744	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	159	176	1	0.99375	0.00568182	G|0.772;C|0.228	0.228	strong	.	GPR179	170	.	NM_001004334	exon11	c.C3699G	p.L1233L	GCTGCCGAGGGAC	.	PASS	Atlas-SNP
SRRT	51593	hgsc.bcm.edu	37	7	100486110	100486110	+	Silent	SNP	C	C	T	rs11171	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	125	220	0	0.512295	0	C|0.905;T|0.095	0.095	strong	.	SRRT	108	.	NM_015908	exon20	c.C2571T	p.D857D	TGGAGACCCAAGG	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176636882	176636882	+	Silent	SNP	C	C	T	rs1363405	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	96	152	0	0.979592	0	C|0.607;T|0.393	0.393	strong	.	NSD1	416	.	NM_022455	exon5	c.C1482T	p.C494C	GCCTTGCGCTAAA	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140811114	140811114	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	6	87	1	0.0612245	0.0114943	.	.	none	MAML3_ENST00000509479,colon,carcinoma,0,4	MAML3	192	4	NM_018717	exon2	c.G1476A	p.Q492Q	CTGCTGCTGCTGC	.	scavenged	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744826	23744826	+	Missense_Mutation	SNP	T	T	A	rs76331664	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	15	159	0	0.111111	0	.	.	weak	.	HOMEZ	80	.	NM_020834	exon2	c.A1611T	p.E537D	ATCATCTTCCTCC	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123887164	123887164	+	Missense_Mutation	SNP	A	A	C	rs4936881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	154	191	0	0.980892	0	A|0.539;C|0.461	0.461	strong	OR10G4,NS,carcinoma,-2,2	OR10G4	77	2	NM_001004462	exon1	c.A883C	p.K295Q	GAGGTGAAGAAAG	.	PASS	Atlas-SNP
PROSER2	254427	hgsc.bcm.edu	37	10	11912381	11912381	+	Silent	SNP	G	G	A	rs191542752	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	10	20	0	0.526316	0	G|0.993;A|0.007	0.007	strong	.	.	.	.	NM_153256	exon4	c.G1284A	p.L428L	GAAGCTGGGGCTG	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	334	333	400	0	0.997006	0	G|0.751;A|0.249	0.249	strong	.	SLC12A6	205	.	NM_133647	exon4	c.C475T	p.L159L	GAGTCAGATTAGT	.	PASS	Atlas-SNP
SAG	6295	hgsc.bcm.edu	37	2	234235820	234235820	+	Silent	SNP	C	C	T	rs2304773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	59	127	0	0.517544	0	C|0.893;T|0.107	0.107	strong	.	SAG	77	.	NM_000541	exon7	c.C489T	p.A163A	CGATGCCGAAGAG	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385134	33385134	+	Missense_Mutation	SNP	C	C	T	rs61073250	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	87	113	0	0.58	0	C|0.964;T|0.036	0.036	strong	.	AQP7	58	.	NM_001170	exon8	c.G898A	p.V300I	GCAATACGGTTAT	.	PASS	Atlas-SNP
BCAR3	8412	hgsc.bcm.edu	37	1	94049576	94049576	+	Silent	SNP	A	A	G	rs78645541	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	81	144	0	0.554795	0	A|0.992;G|0.008	0.008	strong	.	BCAR3	62	.	NM_001261409	exon6	c.T1032C	p.I344I	CATACCAATCGGC	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108384207	108384207	+	Missense_Mutation	SNP	C	C	T	rs2846412	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	131	149	1	1	0.00671141	C|0.440;T|0.560	0.560	strong	.	EXPH5	193	.	NM_015065	exon6	c.G2027A	p.S676N	TTGCTGCTGGTCA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171162583	171162583	+	Missense_Mutation	SNP	T	T	C	rs2020860	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	24	66	0	0.436364	0	T|0.895;C|0.105	0.105	strong	FMO2,colon,carcinoma,+1,1	FMO2	66	1	NM_001460	exon3	c.T242C	p.F81S	CAAACTTCCTGCA	.	PASS	Atlas-SNP
XPR1	9213	hgsc.bcm.edu	37	1	180804033	180804033	+	Silent	SNP	C	C	T	rs61742073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	30	71	0	0.447761	0	C|0.949;T|0.051	0.051	strong	.	XPR1	76	.	NM_004736	exon10	c.C1158T	p.F386F	CCCCTTCCATAAG	.	PASS	Atlas-SNP
GPR75-ASB3	100302652	hgsc.bcm.edu	37	2	53955850	53955850	+	Silent	SNP	C	C	T	rs17521008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	23	61	0	0.410714	0	C|0.834;T|0.166	0.166	strong	ASB3,NS,carcinoma,0,1	.	.	1	NM_001164165	exon5	c.G717A	p.S239S	CTTACCCGATGAA	.	PASS	Atlas-SNP
RBP1	5947	hgsc.bcm.edu	37	3	139257727	139257727	+	Missense_Mutation	SNP	T	T	C	rs34674353	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	141	260	0	0.514599	0	T|0.992;C|0.008	0.008	strong	.	RBP1	39	.	NM_002899	exon2	c.A334G	p.M112V	TGATCATATGGTC	.	PASS	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209215571	209215571	+	Silent	SNP	T	T	C	rs13020468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	166	0	1	0	T|0.967;C|0.033	0.033	strong	.	PIKFYVE	223	.	NM_015040	exon37	c.T5511C	p.I1837I	AGTGATTCTGGAC	.	PASS	Atlas-SNP
ADCY3	109	hgsc.bcm.edu	37	2	25064193	25064193	+	Silent	SNP	G	G	A	rs2241759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	42	62	0	0.525	0	G|0.520;A|0.480	0.480	strong	.	ADCY3	114	.	NM_004036	exon5	c.C1131T	p.P377P	GTAGTCGGGCAAG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242036769	242036769	+	Silent	SNP	G	G	A	rs10171090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	52	129	0	0.440678	0	G|0.978;A|0.022	0.022	strong	.	MTERFD2	33	.	NM_182501	exon3	c.C594T	p.V198V	AAGCCTGACAGTG	.	PASS	Atlas-SNP
SNAI1	6615	hgsc.bcm.edu	37	20	48600631	48600631	+	Missense_Mutation	SNP	T	T	C	rs4647958	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	76	0	1	0	T|0.722;C|0.278	0.278	strong	.	SNAI1	28	.	NM_005985	exon2	c.T353C	p.V118A	CTTCAGTCTCTTC	.	PASS	Atlas-SNP
GBA	2629	hgsc.bcm.edu	37	1	155210498	155210498	+	Missense_Mutation	SNP	T	T	C	rs150466109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	31	53	0	0.516667	0	T|0.979;C|0.021	0.021	strong	.	GBA	46	.	NM_001005742	exon3	c.A38G	p.K13R	AAAGGCTTGGGAC	.	PASS	Atlas-SNP
TNNC2	7125	hgsc.bcm.edu	37	20	44452697	44452697	+	Silent	SNP	C	C	A	rs4629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	62	84	0	0.53913	0	C|0.569;A|0.431	0.431	strong	.	TNNC2	12	.	NM_003279	exon5	c.G384T	p.T128T	CTCGTCCGTCACG	.	PASS	Atlas-SNP
NCF1	653361	hgsc.bcm.edu	37	7	74193672	74193672	+	Missense_Mutation	SNP	C	C	T	rs146125534	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	367	61	304	0	0.166213	0	C|0.999;T|0.001	0.001	strong	NCF1,NS,carcinoma,0,1	NCF1	26	1	NM_000265	exon4	c.C299T	p.T100M	GCGGCACGCTCAT	.	scavenged	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	37	19	54802105	54802105	+	Silent	SNP	C	C	T	rs1975046	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	89	173	0	0.511494	0	C|0.794;T|0.206	0.206	strong	.	LILRA3	65	.	NM_006865	exon6	c.G1083A	p.G361G	AGCTGCCCCCTCC	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54755922	54755922	+	Missense_Mutation	SNP	C	C	T	rs34889610	bycluster;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	106	263	0	0.50237	0	TG|1.000;|0.000	.	alt	.	LILRB5	176	.	NM_001081442	exon12	c.G1624A	p.A542T	CCCGAGCATCCAT	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130760850	130760850	+	Missense_Mutation	SNP	A	A	G	rs4144738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	176	147	1	1	0.00680272	A|0.363;G|0.637	0.637	strong	GSDMC,NS,carcinoma,0,1	GSDMC	71	1	NM_031415	exon14	c.T1424C	p.M475T	AGCTCCATCCTAA	.	PASS	Atlas-SNP
SPNS2	124976	hgsc.bcm.edu	37	17	4436354	4436354	+	Silent	SNP	C	C	T	rs61746307	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	68	119	0	0.489209	0	C|0.989;T|0.011	0.011	strong	.	SPNS2	24	.	NM_001124758	exon7	c.C1018T	p.L340L	CTCTACCTGCACC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	716273	716273	+	Missense_Mutation	SNP	T	T	C	rs11866949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	48	83	0	0.5	0	T|0.694;C|0.306	0.306	strong	.	WDR90	107	.	NM_145294	exon37	c.T4663C	p.C1555R	CACCCCTGCACAG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38380501	38380501	+	Silent	SNP	G	G	A	rs143655348	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	95	207	1	0.487179	0.00483092	G|0.994;A|0.006	0.006	strong	.	WDR87	191	.	NM_031951	exon6	c.C3693T	p.G1231G	CCTGCGGCCAGAT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133953676	133953676	+	Missense_Mutation	SNP	A	A	G	rs61744679	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	144	241	0	0.503497	0	A|0.964;G|0.036	0.036	strong	.	TG	416	.	NM_003235	exon26	c.A5122G	p.I1708V	AACCCCATTGTGT	.	PASS	Atlas-SNP
MXD3	83463	hgsc.bcm.edu	37	5	176734855	176734855	+	Silent	SNP	G	G	C	rs4568379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	25	25	0	0.961538	0	G|0.800;C|0.200	0.200	strong	.	MXD3	13	.	NM_001142935	exon5	c.C432G	p.A144A	CCGCTCGGCCGCC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341575	55341575	+	Missense_Mutation	SNP	G	G	C	rs1130513	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	45	40	0	0.39823	0	G|0.828;C|0.172	0.172	strong	.	KIR3DL1	174	.	NM_013289	exon9	c.G1180C	p.E394Q	GACCCTGAGGAGG	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	105	201	0	0.470852	0	G|0.747;C|0.253	0.253	strong	PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	NM_018939	exon1	c.G1014C	p.V338V	GGACGTGAATGAC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379823	31379823	+	Missense_Mutation	SNP	C	C	G	rs1051799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	124	0	1	0	C|0.703;G|0.297	0.297	strong	.	MICA	21	.	NM_001177519	exon4	c.C713G	p.T238S	TACTGACCTGGCG	.	PASS	Atlas-SNP
RPL8	6132	hgsc.bcm.edu	37	8	146015749	146015749	+	Silent	SNP	C	C	T	rs1060859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	72	139	0	0.521739	0	C|0.908;T|0.092	0.092	strong	.	RPL8	29	.	NM_033301	exon5	c.G606A	p.V202V	CATGGCCACACCC	.	PASS	Atlas-SNP
TMEM44	93109	hgsc.bcm.edu	37	3	194325103	194325103	+	Missense_Mutation	SNP	G	G	A	rs745169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	65	104	0	0.496183	0	G|0.930;A|0.070	0.070	strong	.	TMEM44	42	.	NM_001166306	exon9	c.C1085T	p.P362L	CGACGGGGGGTCC	.	PASS	Atlas-SNP
CCBL2	56267	hgsc.bcm.edu	37	1	89453966	89453966	+	Missense_Mutation	SNP	G	G	A	rs74100109	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	328	159	266	0	0.484756	0	G|0.988;A|0.012	0.012	strong	.	CCBL2	138	.	NM_001008661	exon2	c.C68T	p.S23F	TTGGAAGAAGAAA	.	PASS	Atlas-SNP
FUT1	2523	hgsc.bcm.edu	37	19	49253717	49253717	+	Silent	SNP	G	G	T	rs838138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	77	0	1	0	G|0.955;T|0.045	0.045	strong	.	FUT1	44	.	NM_000148	exon4	c.C822A	p.T274T	CTGGGAGGTGTCG	.	PASS	Atlas-SNP
C1orf27	54953	hgsc.bcm.edu	37	1	186355168	186355168	+	Missense_Mutation	SNP	A	A	G	rs115570554	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	24	41	0	0.428571	0	A|0.997;G|0.003	0.003	strong	.	C1orf27	41	.	NM_001164245	exon4	c.A283G	p.I95V	TTTATTATTACTA	.	PASS	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44192574	44192574	+	Missense_Mutation	SNP	C	C	T	rs147305658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	38	100	0	0.612903	0	C|0.999;T|0.001	0.001	strong	.	PDE9A	69	.	NM_002606	exon19	c.C1712T	p.T571M	GCTTGACGTCTGG	.	PASS	Atlas-SNP
OR6C76	390326	hgsc.bcm.edu	37	12	55820358	55820358	+	Silent	SNP	G	G	A	rs12322458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	72	165	0	0.473684	0	G|0.978;A|0.022	0.022	strong	.	OR6C76	98	.	NM_001005183	exon1	c.G321A	p.T107T	CTCAACGGAGTTT	.	PASS	Atlas-SNP
ADAM12	8038	hgsc.bcm.edu	37	10	127753478	127753478	+	Silent	SNP	G	G	A	rs1278279	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	37	103	0	0.5	0	G|0.726;A|0.274	0.274	strong	.	ADAM12	388	.	NM_021641	exon14	c.C1515T	p.N505N	GTACACGTTGGCT	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30831144	30831144	+	Silent	SNP	C	C	T	rs16875355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	84	0	0.456311	0	C|0.861;T|0.139	0.139	strong	.	FAM188B	62	.	NM_032222	exon5	c.C1027T	p.L343L	GAGAGGCTGGAAA	.	PASS	Atlas-SNP
IRGQ	126298	hgsc.bcm.edu	37	19	44098963	44098963	+	Silent	SNP	C	C	G	rs304725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	17	66	0	0.326923	0	C|0.497;G|0.503	0.503	strong	.	IRGQ	40	.	NM_001007561	exon2	c.G528C	p.R176R	TCACCTCCGCAGC	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48597114	48597114	+	Silent	SNP	C	C	T	rs28498091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	45	67	0	0.5625	0	C|0.802;T|0.198	0.198	strong	.	MYCBPAP	135	.	NM_032133	exon7	c.C1011T	p.H337H	CACTCACATCAGG	.	PASS	Atlas-SNP
MRPS11	64963	hgsc.bcm.edu	37	15	89015930	89015930	+	Silent	SNP	T	T	C	rs9920196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	100	222	0	0.497512	0	T|0.922;C|0.078	0.078	strong	.	MRPS11	14	.	NM_022839	exon3	c.T255C	p.I85I	CCCAATTGCACAC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6549995	6549995	+	Missense_Mutation	SNP	A	A	G	rs7480644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	31	70	0	0.469697	0	A|0.284;G|0.716	0.716	strong	DNHD1,colon,carcinoma,0,1	DNHD1	198	1	NM_144666	exon11	c.A2081G	p.N694S	CACTGAATATACA	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919240	51919240	+	Silent	SNP	C	C	T	rs79484306	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	50	165	0	0.224215	0	C|0.910;T|0.090	0.090	strong	SIGLEC12_ENST00000439889,NS,carcinoma,-2,2	SIGLEC10	112	2	NM_001171157	exon5	c.G936A	p.G312G	CTTCACCCCGGGC	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41522407	41522407	+	Missense_Mutation	SNP	G	G	C	rs112350393	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	28	68	0	0.444444	0	G|0.969;C|0.031	0.031	strong	.	ANK1	497	.	NM_020478	exon1	c.C135G	p.D45E	CTCCTTGTCCAGC	.	PASS	Atlas-SNP
DDC	1644	hgsc.bcm.edu	37	7	50607694	50607694	+	Silent	SNP	G	G	A	rs11575302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	70	150	0	0.39548	0	G|0.948;A|0.052	0.052	strong	.	DDC	100	.	NM_001082971	exon3	c.C234T	p.A78A	GAAGTAGGCGAAG	.	PASS	Atlas-SNP
THAP11	57215	hgsc.bcm.edu	37	16	67876805	67876805	+	Silent	SNP	A	A	G	rs28434205	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	7	19	0	0.368421	0	A|0.991;G|0.009	0.009	strong	THAP11,bladder,carcinoma,0,3	THAP11	27	3	NM_020457	exon1	c.A348G	p.Q116Q	GCAGCAACAGCAG	.	PASS	Atlas-SNP
CDRT4	284040	hgsc.bcm.edu	37	17	15341183	15341183	+	Missense_Mutation	SNP	A	A	C	rs2954759	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	189	184	0	0.994737	0	A|0.767;C|0.233	0.233	strong	.	CDRT4	11	.	NM_001204477	exon4	c.T366G	p.H122Q	ATCCGCATGTAAG	.	PASS	Atlas-SNP
SF3A1	10291	hgsc.bcm.edu	37	22	30733111	30733111	+	Silent	SNP	C	C	A	rs2229807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	77	192	0	0.574627	0	C|0.795;A|0.205	0.205	strong	.	SF3A1	61	.	NM_005877	exon13	c.G2010T	p.V670V	GGGATGCACAGGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149509691	149509691	+	Missense_Mutation	SNP	G	G	A	rs73727635	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	43	108	0	0.457447	0	G|0.960;A|0.040	0.040	strong	.	.	.	.	NM_198455	exon70	c.G9965A	p.C3322Y	GCCCCTGTGGCCC	.	PASS	Atlas-SNP
SH3RF2	153769	hgsc.bcm.edu	37	5	145428665	145428665	+	Silent	SNP	C	C	A	rs35937996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	33	74	0	0.44	0	C|0.982;A|0.018	0.018	strong	.	SH3RF2	58	.	NM_152550	exon7	c.C1179A	p.A393A	CTCAGCCCATGGA	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156084	39156084	+	Missense_Mutation	SNP	T	T	C	rs9897046	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	61	173	0	0.342697	0	C|0.266;N|0.000	0.266	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.A22G	p.S8G	TGCAGCTGCGAGA	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371409	240371409	+	Silent	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	7	142	0	0.0469799	0	.	.	none	FMN2,NS,neuroblastoma,0,1	FMN2	451	1	NM_020066	exon5	c.G3297T	p.P1099P	CCCTCCGCCCCCT	.	scavenged	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	37	19	2994903	2994903	+	Silent	SNP	T	T	C	rs34831575	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	66	0	1	0	T|0.715;C|0.285	0.285	strong	.	TLE6	68	.	NM_001143986	exon17	c.T1620C	p.P540P	GGTGCCTGAGATG	.	PASS	Atlas-SNP
EIF1AD	84285	hgsc.bcm.edu	37	11	65767578	65767578	+	Missense_Mutation	SNP	G	G	A	rs35497370	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	47	110	0	0.516484	0	G|0.997;A|0.003	0.003	strong	EIF1AD,colon,carcinoma,+1,1	EIF1AD	10	1	NM_001242483	exon3	c.C142T	p.R48C	GGAAGCGCTGCCC	.	PASS	Atlas-SNP
FERMT3	83706	hgsc.bcm.edu	37	11	63988045	63988045	+	Silent	SNP	G	G	A	rs3802932	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	46	67	1	0.575	0.0149254	G|0.808;A|0.192	0.192	strong	URP2,NS,carcinoma,0,2	FERMT3	51	2	NM_178443	exon12	c.G1461A	p.P487P	GGGCCCGGGCAAC	.	scavenged	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12400783	12400783	+	Missense_Mutation	SNP	C	C	T	rs35171886	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	81	0	0.459459	0	C|0.884;T|0.116	0.116	strong	.	VWDE	123	.	NM_001135924	exon15	c.G3149A	p.C1050Y	ATAGTACATGAGT	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1431105	1431105	+	Missense_Mutation	SNP	A	A	G	rs199599542	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	14	128	0	0.0818713	0	A|0.994;G|0.006	0.006	strong	.	ATAD3B	68	.	NM_031921	exon16	c.A1855G	p.M619V	TCCTGGATGGGGA	.	PASS	Atlas-SNP
KCNV2	169522	hgsc.bcm.edu	37	9	2717922	2717922	+	Silent	SNP	C	C	G	rs10967705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	177	159	1	1	0.00628931	C|0.389;G|0.611	0.611	strong	.	KCNV2	72	.	NM_133497	exon1	c.C183G	p.G61G	AGACGGCGAGGAG	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186459775	186459775	+	Silent	SNP	C	C	T	rs5030086	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	63	159	0	0.488372	0	C|0.965;T|0.035	0.035	strong	.	KNG1	129	.	NM_001102416	exon10	c.C1590T	p.D530D	TGAAGACAGTACT	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57327420	57327420	+	Missense_Mutation	SNP	C	C	A	rs35947541	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	132	268	0	0.490706	0	C|0.993;A|0.007	0.007	strong	.	PEG3	414	.	NM_001146184	exon9	c.G2390T	p.S797I	GGTTTACTGGGCC	.	PASS	Atlas-SNP
ATP8A1	10396	hgsc.bcm.edu	37	4	42629038	42629038	+	Silent	SNP	C	C	T	rs16854624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	57	147	0	0.387755	0	C|0.910;T|0.090	0.090	strong	.	ATP8A1	206	.	NM_001105529	exon2	c.G138A	p.L46L	TTTTGTCAGCTGG	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70332672	70332672	+	Missense_Mutation	SNP	T	T	A	rs12773594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	23	53	0	0.38983	0	T|0.854;A|0.146	0.146	strong	.	TET1	255	.	NM_030625	exon2	c.T577A	p.S193T	TTTTGGTCCCAAA	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20443751	20443751	+	Missense_Mutation	SNP	T	T	G	rs139828094	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	102	187	0	0.528497	0	T|0.994;G|0.006	0.006	strong	.	OR4K15	82	.	NM_001005486	exon1	c.T74G	p.M25R	AATCGATGAATGA	.	PASS	Atlas-SNP
C17orf78	284099	hgsc.bcm.edu	37	17	35743010	35743010	+	Missense_Mutation	SNP	C	C	G	rs1714987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	57	145	0	0.467213	0	C|0.700;G|0.300	0.300	strong	C17orf78,NS,carcinoma,0,1	C17orf78	23	1	NM_173625	exon4	c.C455G	p.T152S	CCACCACTGCCCC	.	PASS	Atlas-SNP
MMP14	4323	hgsc.bcm.edu	37	14	23312923	23312923	+	Silent	SNP	T	T	C	rs2236307	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	82	120	1	0.97619	0.00833333	A|0.000;C|0.247;G|0.000;T|0.753	0.247	strong	.	MMP14	40	.	NM_004995	exon6	c.T855C	p.G285G	AGGGGGTGAGTCA	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109395230	109395230	+	Silent	SNP	A	A	G	rs142279898	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	49	83	0	0.494949	0	A|0.998;G|0.002	0.002	strong	.	AKNAD1	83	.	NM_152763	exon2	c.T57C	p.Y19Y	CCCATCATAAGGC	.	PASS	Atlas-SNP
GLIS3	169792	hgsc.bcm.edu	37	9	4118262	4118262	+	Missense_Mutation	SNP	C	C	A	rs75462592	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	18	10	0	0.75	0	C|0.993;A|0.007	0.007	strong	.	GLIS3	152	.	NM_001042413	exon4	c.G1216T	p.G406C	CCAGGCCTGGCTG	.	PASS	Atlas-SNP
LRRC6	23639	hgsc.bcm.edu	37	8	133637659	133637659	+	Missense_Mutation	SNP	G	G	A	rs2293979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	210	201	0	1	0	G|0.487;A|0.513	0.513	strong	.	LRRC6	58	.	NM_012472	exon6	c.C695T	p.T232I	TCCTCTGTGTCTG	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	57935442	57935442	+	Missense_Mutation	SNP	G	G	A	rs112002818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	47	96	0	0.505376	0	G|0.958;A|0.042	0.042	strong	.	CNGB1	105	.	NM_001297	exon28	c.C2882T	p.A961V	AAGAGTGCGACTT	.	PASS	Atlas-SNP
MAP2K2	5605	hgsc.bcm.edu	37	19	4110552	4110552	+	Silent	SNP	C	C	G	rs10424722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	38	45	0	0.678571	0	C|0.956;G|0.044	0.044	strong	.	MAP2K2	72	.	NM_030662	exon3	c.G405C	p.G135G	GAAGGCCCCGTAG	.	PASS	Atlas-SNP
MAL2	114569	hgsc.bcm.edu	37	8	120233968	120233968	+	Missense_Mutation	SNP	G	G	A	rs2303398	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	88	138	0	0.651852	0	G|0.895;A|0.105	0.105	strong	.	.	.	.	NM_052886	exon3	c.G274A	p.A92T	ATGGTGGCTCAAA	.	PASS	Atlas-SNP
ITGB5	3693	hgsc.bcm.edu	37	3	124515308	124515308	+	Silent	SNP	A	A	G	rs1803825	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	50	0	0.5	0	A|0.723;G|0.277	0.277	strong	.	ITGB5	66	.	NM_002213	exon10	c.T1620C	p.F540F	CTTGCCAAACTCG	.	PASS	Atlas-SNP
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	37	66	0	0.506849	0	T|0.778;C|0.222	0.222	strong	.	BBS2	67	.	NM_031885	exon3	c.A367G	p.I123V	GCACAATTGCATT	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106158216	106158216	+	Silent	SNP	G	G	A	rs3796927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	69	146	0	0.433962	0	G|0.895;A|0.105	0.105	strong	.	TET2	1762	.	NM_001127208	exon3	c.G3117A	p.S1039S	CAAGTCGTTATTT	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61906216	61906216	+	Missense_Mutation	SNP	G	G	A	rs61751226	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	26	44	0	0.52	0	G|0.995;A|0.005	0.005	strong	.	INCENP	122	.	NM_001040694	exon6	c.G1147A	p.E383K	GAGGCTGAGCCTG	.	PASS	Atlas-SNP
IRGC	56269	hgsc.bcm.edu	37	19	44223125	44223125	+	Silent	SNP	C	C	T	rs346049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	42	0	1	0	C|0.805;T|0.195	0.195	strong	.	IRGC	67	.	NM_019612	exon2	c.C415T	p.L139L	TTCCTGCTGGTCT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27804114	27804114	+	Missense_Mutation	SNP	C	C	T	rs13392197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	44	90	0	0.54321	0	C|0.983;T|0.017	0.017	strong	.	C2orf16	357	.	NM_032266	exon1	c.C4675T	p.H1559Y	ACCCGTCATAACC	.	PASS	Atlas-SNP
TPPP	11076	hgsc.bcm.edu	37	5	665280	665280	+	Silent	SNP	T	T	C	rs1697963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	53	72	0	0.473214	0	T|0.288;C|0.712	0.712	strong	TPPP,caecum,carcinoma,0,1	TPPP	24	1	NM_007030	exon4	c.A597G	p.S199S	ATAGCCTGACTCG	.	PASS	Atlas-SNP
C15orf54	400360	hgsc.bcm.edu	37	15	39544809	39544809	+	Missense_Mutation	SNP	G	G	C	rs115130297	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	88	145	0	0.533333	0	G|0.997;C|0.003	0.003	strong	.	C15orf54	18	.	NM_207445	exon2	c.G473C	p.R158T	GAGAGAGGGGACA	.	PASS	Atlas-SNP
PLSCR5	389158	hgsc.bcm.edu	37	3	146311832	146311832	+	Missense_Mutation	SNP	G	G	T	rs12107687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	72	141	0	0.507042	0	G|0.987;T|0.013	0.013	strong	.	PLSCR5	35	.	NM_001085420	exon4	c.C328A	p.R110S	AAGTACGATTGAA	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	20	47	0	0.714286	0	G|0.808;A|0.192	0.192	strong	.	DYNC2H1	246	.	NM_001080463	exon73	c.G10794A	p.T3598T	GGATACGTTTACA	.	PASS	Atlas-SNP
CD300LD	100131439	hgsc.bcm.edu	37	17	72584764	72584764	+	Missense_Mutation	SNP	C	C	T	rs783239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	111	218	0	0.488987	0	C|0.680;T|0.320	0.320	strong	CD300LD,NS,carcinoma,0,1	CD300LD	16	1	NM_001115152	exon2	c.G265A	p.V89M	TGAACACGTGGTT	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168377012	168377012	+	Silent	SNP	G	G	T	rs78475769	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	401	25	330	0	0.0623441	0	T|1.000;|0.000	1.000	weak	.	.	.	.	NM_001129895	exon1	c.C321A	p.S107S	GTGTGGGGAGGAG	.	PASS	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	37	5	137754695	137754695	+	Silent	SNP	T	T	C	rs7726234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	97	228	1	0.442922	0.00438596	T|0.382;C|0.618	0.618	strong	KDM3B,NS,carcinoma,0,1	KDM3B	177	1	NM_016604	exon14	c.T3489C	p.G1163G	CTCTGGTGGAGGA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76422599	76422599	+	Missense_Mutation	SNP	C	C	T	rs35973257	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	49	111	0	0.395161	0	C|0.976;T|0.024	0.024	strong	.	DNAH17	347	.	NM_173628	exon79	c.G12854A	p.R4285Q	TAGGCCCGGGCCA	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883036	152883036	+	Missense_Mutation	SNP	C	C	T	rs4459054	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	88	169	0	0.423077	0	C|0.986;T|0.014	0.014	strong	IVL,NS,carcinoma,-2,1	IVL	100	1	NM_005547	exon2	c.C763T	p.L255F	CTGGAGCTCTCTG	.	PASS	Atlas-SNP
RBM20	282996	hgsc.bcm.edu	37	10	112540884	112540884	+	Missense_Mutation	SNP	C	C	A	rs7908490	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	54	129	0	0.418605	0	C|0.970;A|0.030	0.030	strong	.	RBM20	50	.	NM_001134363	exon2	c.C517A	p.P173T	TTTTCACCCCCCA	.	PASS	Atlas-SNP
ROS1	6098	hgsc.bcm.edu	37	6	117681560	117681560	+	Silent	SNP	G	G	T	rs140639104	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	24	75	0	0.328767	0	G|0.998;T|0.002	0.002	strong	.	ROS1	728	.	NM_002944	exon22	c.C3390A	p.A1130A	TGTAAAGGCCCTA	.	PASS	Atlas-SNP
LRIT2	340745	hgsc.bcm.edu	37	10	85981756	85981756	+	Missense_Mutation	SNP	G	G	T	rs74145770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	119	159	0	0.572115	0	G|0.957;T|0.043	0.043	strong	.	LRIT2	81	.	NM_001017924	exon3	c.C1573A	p.P525T	CAGCTGGATGTTC	.	PASS	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32463353	32463353	+	Missense_Mutation	SNP	A	A	G	rs202095832	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	61	91	0	0.539823	0	.	.	weak	.	NLRC4	165	.	NM_001199138	exon6	c.T2369C	p.L790P	TTCTTCAGGTTTT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9068990	9068990	+	Missense_Mutation	SNP	G	G	T	rs35092547	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	499	277	428	1	0.55511	0.00233645	G|0.981;T|0.019	0.019	strong	.	MUC16	4315	.	NM_024690	exon3	c.C18456A	p.H6152Q	GGTCTTGTGTGTA	.	PASS	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61672265	61672265	+	Silent	SNP	T	T	C	rs174474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	120	268	0	0.402685	0	T|0.759;C|0.241	0.241	strong	RAB3IL1,NS,carcinoma,-2,1	RAB3IL1	39	1	NM_013401	exon6	c.A747G	p.R249R	GTCCTCTCGGTAC	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	86	126	0	0.661538	0	T|0.967;A|0.033	0.033	strong	.	EXPH5	193	.	NM_015065	exon6	c.A2674T	p.N892Y	AAGAATTCTTTGA	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	185958737	185958737	+	Missense_Mutation	SNP	A	A	G	rs7539719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	82	182	0	0.488095	0	A|0.821;G|0.179	0.179	strong	.	HMCN1	797	.	NM_031935	exon21	c.A3166G	p.T1056A	ACCAATACAGCCG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512093	169512093	+	Silent	SNP	A	A	G	rs6017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	68	149	0	0.482269	0	A|0.760;G|0.240	0.240	strong	.	F5	301	.	NM_000130	exon13	c.T2235C	p.N745N	TTCCTGATTCAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511397	195511397	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	9	377	1	0.0633803	0.00265252	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	NM_018406	exon2	c.C7054T	p.P2352S	GAAGAGGGGTGGC	.	scavenged	Atlas-SNP
ABCA6	23460	hgsc.bcm.edu	37	17	67109493	67109493	+	Silent	SNP	A	A	G	rs2058128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	30	53	0	0.46875	0	A|0.876;G|0.124	0.124	strong	.	ABCA6	210	.	NM_080284	exon15	c.T1911C	p.L637L	ATCTAAAAGCAAA	.	PASS	Atlas-SNP
ODF1	4956	hgsc.bcm.edu	37	8	103573086	103573086	+	Missense_Mutation	SNP	T	T	C	rs11995900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	31	93	0	0.392405	0	T|0.911;C|0.089	0.089	strong	.	ODF1	55	.	NM_024410	exon2	c.T727C	p.F243L	AGCCGATTTTCCT	.	PASS	Atlas-SNP
PON2	5445	hgsc.bcm.edu	37	7	95039394	95039394	+	Missense_Mutation	SNP	C	C	G	rs17876152	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	58	83	0	0.537037	0	C|0.983;G|0.017	0.017	strong	.	PON2	32	.	NM_000305	exon6	c.G514C	p.V172L	GTCCAACAGCTGT	.	PASS	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	59	102	0	0.457364	0	A|0.865;C|0.135	0.135	strong	.	BRDT	133	.	NM_001242806	exon6	c.A726C	p.K242N	AGAAAAATCAGTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179393111	179393111	+	Missense_Mutation	SNP	A	A	G	rs16866378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	57	110	0	0.508929	0	A|0.906;G|0.094	0.094	strong	.	TTN	18412	.	NM_001267550	exon361	c.T107267C	p.V35756A	GAGTATACATTTC	.	PASS	Atlas-SNP
TAF1	6872	hgsc.bcm.edu	37	X	70595132	70595132	+	Silent	SNP	T	T	C	rs5981106	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	67	141	0	0.424051	0	T|0.891;C|0.109	0.109	strong	.	TAF1	439	.	NM_004606	exon4	c.T528C	p.T176T	TATTACTGGTGGT	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390162	208390162	+	Missense_Mutation	SNP	T	T	C	rs4844658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	45	96	0	0.463918	0	T|0.865;C|0.135	0.135	strong	.	PLXNA2	178	.	NM_025179	exon2	c.A1106G	p.E369G	AGGCGCTCCTTGA	.	PASS	Atlas-SNP
KIAA0319L	79932	hgsc.bcm.edu	37	1	35900615	35900615	+	Silent	SNP	A	A	G	rs3814302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	119	229	1	0.495833	0.00436681	A|0.669;G|0.331	0.331	strong	.	KIAA0319L	156	.	NM_024874	exon21	c.T3030C	p.D1010D	GGCATCATCGCTG	.	PASS	Atlas-SNP
GALR1	2587	hgsc.bcm.edu	37	18	74962810	74962810	+	Silent	SNP	G	G	T	rs5375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	93	132	0	0.560241	0	G|0.936;T|0.064	0.064	strong	GALR1,NS,carcinoma,0,1	GALR1	53	1	NM_001480	exon1	c.G306T	p.V102V	CTGGGTGCTGGGC	.	PASS	Atlas-SNP
ISLR2	57611	hgsc.bcm.edu	37	15	74425505	74425505	+	Missense_Mutation	SNP	C	C	T	rs3889598	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	62	0	0.493333	0	C|0.973;T|0.027	0.027	strong	ISLR2,rectum,carcinoma,0,2	ISLR2	78	2	NM_001130138	exon4	c.C410T	p.S137F	TGGGCTCTCTGCC	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141752213	141752213	+	Silent	SNP	C	C	A	rs2961085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	41	66	0	0.482353	0	C|0.723;A|0.277	0.277	strong	MGAM_ENST00000549489,NS,carcinoma,0,4	MGAM	767	4	NM_004668	exon25	c.C2925A	p.A975A	TTCTGCCGAAAAC	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	55	294	4	0.237069	0.0136054	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	NM_001206609	exon2	c.G459A	p.V153V	CGTGGGCACTGGT	.	scavenged	Atlas-SNP
THSD7B	80731	hgsc.bcm.edu	37	2	138030234	138030234	+	Splice_Site	SNP	C	C	T	rs12622896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	31	94	0	0.413333	0	C|0.961;T|0.039	0.039	strong	.	THSD7B	506	.	NM_001080427	exon10	c.2303+2C>T	.	TATCGGCAAGTAG	.	PASS	Atlas-SNP
MFRP	83552	hgsc.bcm.edu	37	11	119216867	119216867	+	Missense_Mutation	SNP	G	G	C	rs139436396	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	23	48	0	0.5	0	G|0.990;C|0.010	0.010	strong	.	MFRP	63	.	NM_031433	exon3	c.C160G	p.R54G	GACGCCGACCTGC	.	PASS	Atlas-SNP
OR1L3	26735	hgsc.bcm.edu	37	9	125437725	125437725	+	Missense_Mutation	SNP	T	T	C	rs16912096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	136	152	1	1	0.00657895	T|0.931;C|0.069	0.069	strong	OR1L3,NS,carcinoma,+1,1	OR1L3	51	1	NM_001005234	exon1	c.T317C	p.V106A	TCCTGGTTTTTGG	.	PASS	Atlas-SNP
MCM5	4174	hgsc.bcm.edu	37	22	35815880	35815880	+	Silent	SNP	G	G	A	rs133427	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	79	127	0	0.481707	0	G|0.878;A|0.122	0.122	strong	.	MCM5	54	.	NM_006739	exon14	c.G1707A	p.K569K	CAGGAAGTGTGGC	.	PASS	Atlas-SNP
RASA2	5922	hgsc.bcm.edu	37	3	141248572	141248572	+	Missense_Mutation	SNP	A	A	C	rs144759014	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	17	35	0	0.404762	0	A|1.000;C|0.000	0.000	strong	RASA2_ENST00000286364,temporal_lobe,glioma,+2,2	RASA2	169	2	NM_006506	exon4	c.A378C	p.E126D	AAAAGAAGACTTG	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	37	MT	6071	6071	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	13	0	1	0	.	.	none	.	.	.	.	ENST00000361624	exon1	c.T168C	p.V56V	CAACGTTATCGTC	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	37	12	53189427	53189427	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	36	156	0	0.211765	0	.	.	none	.	KRT3	65	.	NM_057088	exon1	c.G400C	p.A134P	CACCAGCCCCTCC	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56386118	56386118	+	Silent	SNP	A	A	G	rs2680689	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	48	82	0	0.545455	0	A|0.709;G|0.291	0.291	strong	BZRAP1_ENST00000355701,NS,carcinoma,0,4	BZRAP1	287	4	NM_004758	exon22	c.T4515C	p.D1505D	CTGCTCATCCTCC	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	37	9	138651648	138651648	+	Silent	SNP	A	A	G	rs61739517	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	39	135	0	0.336207	0	A|0.967;G|0.033	0.033	strong	.	KCNT1	139	.	NM_020822	exon11	c.A978G	p.P326P	CTGGCCATCGCAG	.	PASS	Atlas-SNP
UBR1	197131	hgsc.bcm.edu	37	15	43237572	43237572	+	Silent	SNP	T	T	C	rs16957277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	96	171	0	0.554913	0	T|0.928;C|0.072	0.072	strong	.	UBR1	124	.	NM_174916	exon47	c.A5205G	p.Q1735Q	AGTCTCTTGGCTC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74288410	74288410	+	Missense_Mutation	SNP	C	C	T	rs80109605	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	22	139	0	0.144737	0	.	.	weak	.	QRICH2	143	.	NM_032134	exon4	c.G1900A	p.G634S	CCAAACCACGCTG	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167262835	167262835	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	5	329	0	0.0167785	0	.	.	none	SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	NM_002976	exon25	c.G4304A	p.G1435D	TCCCAACCAGCAA	.	scavenged	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	89	0	1	0	G|0.512;A|0.488	0.488	strong	.	DDX20	50	.	NM_007204	exon11	c.G1926A	p.V642V	CCCTGTGTTGGCA	.	PASS	Atlas-SNP
HSDL1	83693	hgsc.bcm.edu	37	16	84158248	84158248	+	Missense_Mutation	SNP	G	G	C	rs4378600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	54	113	0	0.435484	0	G|0.737;C|0.263	0.263	strong	.	HSDL1	23	.	NM_031463	exon6	c.C980G	p.S327C	GTGCAGGATAAGG	.	PASS	Atlas-SNP
GAS8	2622	hgsc.bcm.edu	37	16	90097748	90097748	+	Silent	SNP	C	C	T	rs2302513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	21	25	0	0.567568	0	T|0.179;G|0.000;C|0.821	0.179	strong	GAS8,NS,carcinoma,+1,1	GAS8	29	1	NM_001481	exon3	c.C132T	p.R44R	GGACCGCGAGCGG	.	PASS	Atlas-SNP
TMEM259	91304	hgsc.bcm.edu	37	19	1014398	1014398	+	Silent	SNP	A	A	G	rs7146	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	87	177	0	0.505814	0	A|0.317;G|0.683	0.683	strong	.	.	.	.	NM_033420	exon2	c.T300C	p.H100H	ACGCACATGCTCC	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109637234	109637234	+	Silent	SNP	G	G	T	rs73398054	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	46	109	0	0.479167	0	A|0.006;G|0.992;T|0.002	0.002	strong	.	ACACB	330	.	NM_001093	exon17	c.G2655T	p.T885T	TAAGACGTGTGTG	.	PASS	Atlas-SNP
BAZ2A	11176	hgsc.bcm.edu	37	12	56994170	56994170	+	Silent	SNP	C	C	T	rs1527140	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	94	0	0.450549	0	C|0.900;T|0.100	0.100	strong	.	BAZ2A	263	.	NM_013449	exon24	c.G4713A	p.E1571E	CAGTCCCTCCCTG	.	PASS	Atlas-SNP
FAM71E2	284418	hgsc.bcm.edu	37	19	55870478	55870478	+	Silent	SNP	C	C	T	rs79366553	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	33	83	0	0.5	0	C|0.934;T|0.066	0.066	strong	.	FAM71E2	41	.	NM_001145402	exon9	c.G1758A	p.P586P	CGGCTCCGGTTTC	.	PASS	Atlas-SNP
UTP23	84294	hgsc.bcm.edu	37	8	117783975	117783975	+	Missense_Mutation	SNP	C	C	T	rs16888728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	50	84	0	0.561798	0	C|0.812;N|0.001;T|0.186	0.186	strong	UTP23,NS,carcinoma,0,1	UTP23	38	1	NM_032334	exon3	c.C644T	p.P215L	AGGCACCGGACAC	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38841101	38841101	+	Silent	SNP	G	G	A	rs9380795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	43	100	0	0.483146	0	G|0.558;A|0.442	0.442	strong	.	DNAH8	1239	.	NM_001206927	exon52	c.G7569A	p.K2523K	TATGAAGCTAAAT	.	PASS	Atlas-SNP
TMEM251	26175	hgsc.bcm.edu	37	14	93652734	93652734	+	Silent	SNP	C	C	T	rs61744704	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	263	133	246	0	0.505703	0	C|0.997;T|0.003	0.003	strong	.	.	.	.	NM_001098621	exon2	c.C228T	p.A76A	GCTGGCCTTGGAA	.	PASS	Atlas-SNP
F2RL2	2151	hgsc.bcm.edu	37	5	75913784	75913784	+	Missense_Mutation	SNP	T	T	C	rs2069683	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	45	80	0	0.46875	0	T|0.957;C|0.043	0.043	strong	.	F2RL2	57	.	NM_004101	exon2	c.A748G	p.N250D	AAGTGTTGTGAAC	.	PASS	Atlas-SNP
ERP27	121506	hgsc.bcm.edu	37	12	15070169	15070169	+	Silent	SNP	T	T	A	rs35203261	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	102	229	0	0.445415	0	T|0.980;A|0.020	0.020	strong	.	ERP27	37	.	NM_152321	exon5	c.A519T	p.P173P	ATACTCTGGGGAG	.	PASS	Atlas-SNP
C15orf39	56905	hgsc.bcm.edu	37	15	75499995	75499995	+	Missense_Mutation	SNP	T	T	G	rs28509789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	64	86	0	0.5	0	T|0.662;G|0.338	0.338	strong	C15orf39,bladder,carcinoma,-1,1	C15orf39	64	1	NM_015492	exon2	c.T1606G	p.S536A	CCTGACTCAGCCC	.	PASS	Atlas-SNP
CEACAM8	1088	hgsc.bcm.edu	37	19	43093793	43093793	+	Silent	SNP	G	G	A	rs10418988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	104	206	0	0.450216	0	G|0.977;A|0.023	0.023	strong	.	CEACAM8	44	.	NM_001816	exon3	c.C519T	p.N173N	GGTTGTGTTCTGA	.	PASS	Atlas-SNP
AP4E1	23431	hgsc.bcm.edu	37	15	51294832	51294832	+	Silent	SNP	G	G	A	rs3825798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	115	222	1	0.50885	0.0045045	G|0.794;A|0.206	0.206	strong	AP4E1,NS,carcinoma,0,1	AP4E1	78	1	NM_007347	exon21	c.G3387A	p.Q1129Q	GTATCAGTGTCAA	.	PASS	Atlas-SNP
FKTN	2218	hgsc.bcm.edu	37	9	108366499	108366499	+	Missense_Mutation	SNP	G	G	A	rs34006675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	40	88	0	0.465116	0	G|0.968;A|0.032	0.032	strong	.	FKTN	47	.	NM_006731	exon5	c.G373A	p.G125S	TAGGAAGGCTGGT	.	PASS	Atlas-SNP
KIAA1239	57495	hgsc.bcm.edu	37	4	37435524	37435524	+	Silent	SNP	C	C	T	rs17604216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	112	154	0	0.528302	0	C|0.902;T|0.098	0.098	strong	.	KIAA1239	79	.	NM_001144990	exon5	c.C588T	p.N196N	TGAAAACGAGAAG	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45644589	45644589	+	Missense_Mutation	SNP	G	G	T	rs1367580	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	22	51	0	0.611111	0	G|0.796;T|0.204	0.204	strong	.	FANCM	225	.	NM_020937	exon14	c.G2632T	p.V878L	GATTCTGTAGATA	.	PASS	Atlas-SNP
EML2	24139	hgsc.bcm.edu	37	19	46142624	46142624	+	Missense_Mutation	SNP	A	A	C	rs201822741	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	45	0	0.517857	0	A|0.994;C|0.006	0.006	strong	.	EML2	64	.	NM_012155	exon1	c.T11G	p.F4C	GCTCCAAAGCTAC	.	PASS	Atlas-SNP
MRPS10	55173	hgsc.bcm.edu	37	6	42185564	42185564	+	Silent	SNP	A	A	C	rs9471809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	77	0	1	0	A|0.679;C|0.321	0.321	strong	.	MRPS10	9	.	NM_018141	exon1	c.T24G	p.G8G	CACAGCACCGAAC	.	PASS	Atlas-SNP
LNP1	348801	hgsc.bcm.edu	37	3	100174722	100174722	+	Silent	SNP	G	G	A	rs1132022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	431	222	366	1	0.515081	0.00273224	G|0.515;A|0.485	0.485	strong	.	LNP1	26	.	NM_001085451	exon4	c.G489A	p.E163E	AGAAGAGCATGGA	.	PASS	Atlas-SNP
ZNF778	197320	hgsc.bcm.edu	37	16	89294595	89294595	+	Silent	SNP	C	C	T	rs74466939	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	33	79	0	0.370787	0	C|0.863;T|0.137	0.137	strong	.	ZNF778	67	.	NM_001201407	exon7	c.C1899T	p.I633I	CCTTATCGTGCAC	.	PASS	Atlas-SNP
RESP18	389075	hgsc.bcm.edu	37	2	220197321	220197321	+	Missense_Mutation	SNP	C	C	T	rs2385405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	89	145	0	0.511494	0	C|0.555;T|0.445	0.445	strong	.	RESP18	13	.	NM_001007089	exon2	c.G157A	p.E53K	GCCCCTCGGAGCT	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72518009	72518009	+	Missense_Mutation	SNP	A	A	G	rs4747096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	61	99	0	0.54955	0	A|0.804;G|0.196;N|0.001	0.196	strong	.	ADAMTS14	148	.	NM_139155	exon21	c.A3155G	p.E1052G	AATCTGAACCCCT	.	PASS	Atlas-SNP
CLSPN	63967	hgsc.bcm.edu	37	1	36225948	36225948	+	Missense_Mutation	SNP	T	T	C	rs7537203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	119	153	0	1	0	T|0.628;C|0.372	0.372	strong	.	CLSPN	248	.	NM_001190481	exon8	c.A1574G	p.N525S	CCTCTGTTGGTTT	.	PASS	Atlas-SNP
B3GNT4	79369	hgsc.bcm.edu	37	12	122689181	122689181	+	Missense_Mutation	SNP	C	C	G	rs7136356	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	27	51	0	0.529412	0	C|0.628;G|0.372	0.372	strong	.	B3GNT4	35	.	NM_030765	exon2	c.C16G	p.P6A	CCCCAGCCTTCCG	.	PASS	Atlas-SNP
DSE	29940	hgsc.bcm.edu	37	6	116720466	116720466	+	Missense_Mutation	SNP	G	G	T	rs76186865	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	34	100	0	0.435897	0	G|0.970;T|0.030	0.030	strong	.	DSE	98	.	NM_001080976	exon2	c.G53T	p.C18F	TGCTTTGCTTTGT	.	PASS	Atlas-SNP
CNGA4	1262	hgsc.bcm.edu	37	11	6262945	6262945	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	2	141	0	0.0113636	0	.	.	none	CNGA4,arm,malignant_melanoma,-1,1	CNGA4	96	1	NM_001037329	exon5	c.T1202C	p.I401T	ATGGTATCACACA	.	scavenged	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234301	45234301	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	2	76	1	0.0434783	0.0131579	.	.	none	CDC27_ENST00000531206,NS,carcinoma,+1,10	CDC27	337	10	NM_001114091	exon7	c.G820T	p.A274S	TAAGAGCTGCTGG	.	scavenged	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45431636	45431636	+	Silent	SNP	C	C	T	rs141982460	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	29	51	0	0.483333	0	C|0.998;T|0.002	0.002	strong	.	FAM179B	115	.	NM_015091	exon1	c.C12T	p.A4A	GGCTGCCCCCTCC	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473933	18473933	+	Missense_Mutation	SNP	T	T	G	rs201637656	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	121	287	0	0.472656	0	.	.	weak	PIK3C2G_ENST00000433979,NS,carcinoma,+1,2	PIK3C2G	315	2	NM_004570	exon7	c.T1175G	p.L392R	ATCAACTTCTAGA	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519270	43519270	+	Missense_Mutation	SNP	A	A	G	rs111493043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	112	192	0	0.474576	0	A|0.982;G|0.018	0.018	strong	PSG11,NS,carcinoma,0,1	PSG11	57	1	NM_002785	exon4	c.T962C	p.I321T	TTACCAATGACTC	.	PASS	Atlas-SNP
KIAA1456	57604	hgsc.bcm.edu	37	8	12879016	12879016	+	Silent	SNP	T	T	A	rs75377133	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	47	91	0	0.419643	0	T|0.989;A|0.011	0.011	strong	.	KIAA1456	20	.	NM_020844	exon5	c.T828A	p.V276V	AGAAGTTTGGGCC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511791	4511791	+	Silent	SNP	A	A	C	rs62115193	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	505	84	443	0	0.166337	0	A|0.500;C|0.500	0.500	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T2139G	p.T713T	GGTACCAGTTAGG	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139292751	139292751	+	Missense_Mutation	SNP	C	C	T	rs7031489	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	30	88	0	0.32967	0	C|0.991;T|0.009	0.009	strong	.	SNAPC4	82	.	NM_003086	exon1	c.G130A	p.D44N	GCTTACCTGCTTC	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10775855	10775855	+	Silent	SNP	G	G	A	rs71389065	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	80	173	0	0.47619	0	ATG|0.500;GTC|0.500	.	alt	TEKT5,pharynx,carcinoma,-2,1	TEKT5	66	1	NM_144674	exon4	c.C858T	p.D286D	CGTGCCGTCAATT	.	PASS	Atlas-SNP
OR7D2	162998	hgsc.bcm.edu	37	19	9296664	9296664	+	Silent	SNP	T	T	C	rs56246934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	47	120	0	0.451923	0	T|0.761;C|0.239	0.239	strong	.	OR7D2	55	.	NM_175883	exon1	c.T207C	p.V69V	CTGGGTTGACATC	.	PASS	Atlas-SNP
NKX2-5	1482	hgsc.bcm.edu	37	5	172662024	172662024	+	Silent	SNP	T	T	C	rs2277923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	73	192	0	0.445122	0	T|0.555;C|0.445	0.445	strong	.	NKX2-5	42	.	NM_004387	exon1	c.A63G	p.E21E	CTGCTGTTCCAGG	.	PASS	Atlas-SNP
GSDMA	284110	hgsc.bcm.edu	37	17	38122117	38122117	+	Silent	SNP	G	G	A	rs16965465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	16	56	0	0.380952	0	G|0.930;A|0.070	0.070	strong	GSDMA,NS,carcinoma,+1,1	GSDMA	26	1	NM_178171	exon2	c.G177A	p.T59T	CTACACGCTGCTG	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101822220	101822220	+	Silent	SNP	C	C	T	rs4480177	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	139	213	1	0.637615	0.00469484	C|0.706;T|0.294	0.294	strong	.	COL15A1	211	.	NM_001855	exon36	c.C3387T	p.P1129P	GCTTCCCGGATCC	.	PASS	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21385843	21385843	+	Silent	SNP	G	G	A	rs2072549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	20	41	0	0.487805	0	G|0.789;A|0.211	0.211	strong	.	SLC7A4	50	.	NM_004173	exon2	c.C259T	p.L87L	AGCATAGGGCTGC	.	PASS	Atlas-SNP
XPR1	9213	hgsc.bcm.edu	37	1	180849394	180849394	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	66	111	0	0.507692	0	.	.	none	.	XPR1	76	.	NM_004736	exon14	c.A1991G	p.N664S	AGTACAACCAGAG	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235972867	235972867	+	Silent	SNP	T	T	C	rs1063128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	38	83	0	0.475	0	T|0.619;C|0.381	0.381	strong	.	LYST	370	.	NM_000081	exon5	c.A1251G	p.Q417Q	TGCACTTTGAAGA	.	PASS	Atlas-SNP
OR1L1	26737	hgsc.bcm.edu	37	9	125424507	125424507	+	Silent	SNP	A	A	C	rs70156	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	125	148	0	0.637755	0	A|0.606;C|0.394	0.394	strong	.	OR1L1	54	.	NM_001005236	exon1	c.A513C	p.S171S	TGCCTCAAATGTC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45033485	45033485	+	Silent	SNP	A	A	G	rs62116895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	116	0	1	0	A|0.815;G|0.185	0.185	strong	.	CEACAM20	31	.	NM_001102600	exon1	c.T48C	p.L16L	ACCTGAAAGCAGG	.	PASS	Atlas-SNP
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	82	158	0	0.515723	0	G|0.611;A|0.389	0.389	strong	.	EIF4ENIF1	80	.	NM_019843	exon17	c.C2226T	p.S742S	TACAGAGCTGGAT	.	PASS	Atlas-SNP
EHD4	30844	hgsc.bcm.edu	37	15	42192885	42192885	+	Silent	SNP	G	G	A	rs113393602	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	16	35	0	0.592593	0	A|0.047;C|0.000;G|0.953	0.047	strong	.	EHD4	46	.	NM_139265	exon6	c.C1584T	p.L528L	GGGCACGAGGTGG	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390155	208390155	+	Silent	SNP	C	C	T	rs4844657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	40	92	0	0.444444	0	C|0.856;T|0.144	0.144	strong	.	PLXNA2	178	.	NM_025179	exon2	c.G1113A	p.L371L	GGACTGCAGGCGC	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158587368	158587368	+	Missense_Mutation	SNP	T	T	C	rs111980420	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	112	231	0	0.589474	0	T|0.994;C|0.006	0.006	strong	.	SPTA1	720	.	NM_003126	exon47	c.A6559G	p.K2187E	TTTCTTTGAGCAA	.	PASS	Atlas-SNP
GCLC	2729	hgsc.bcm.edu	37	6	53365102	53365102	+	Silent	SNP	C	C	T	rs17881359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	82	179	0	0.465909	0	C|0.994;T|0.006	0.006	strong	.	GCLC	58	.	NM_001498	exon14	c.G1524A	p.T508T	GAGCTCCGTGCTG	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228882588	228882588	+	Silent	SNP	T	T	C	rs73994847	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	53	85	0	0.524752	0	T|0.953;C|0.047	0.047	strong	.	SPHKAP	750	.	NM_030623	exon7	c.A2982G	p.K994K	CTTGTGTTTCCTC	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78387356	78387356	+	Silent	SNP	C	C	T	rs59660398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	67	0	0.443182	0	C|0.963;T|0.037	0.037	strong	.	.	.	.	NM_001098816	exon30	c.G5337A	p.A1779A	CTGCAGCGCCACC	.	PASS	Atlas-SNP
PTPN1	5770	hgsc.bcm.edu	37	20	49191191	49191191	+	Silent	SNP	A	A	G	rs35414863	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	89	0	0.515152	0	A|0.976;G|0.024	0.024	strong	.	PTPN1	36	.	NM_002827	exon5	c.A492G	p.T164T	CCTTACAGTGAGT	.	PASS	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Silent	SNP	C	C	T	rs11274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	15	43	0	0.46875	0	C|0.685;N|0.000	.	strong	.	C20orf111	28	.	NM_016470	exon4	c.G192A	p.G64G	TGTAGACCTAAAG	.	PASS	Atlas-SNP
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	61	0	1	0	T|0.579;C|0.421	0.421	strong	.	RNASEH1	27	.	NM_002936	exon4	c.A498G	p.P166P	ATGGCCTGGCCCC	.	PASS	Atlas-SNP
ODAM	54959	hgsc.bcm.edu	37	4	71062426	71062426	+	Silent	SNP	C	C	T	rs17704351	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	105	182	0	0.481651	0	C|0.741;T|0.259	0.259	strong	.	ODAM	38	.	NM_017855	exon2	c.C69T	p.L23L	GCGTCTCATGTCT	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3650987	3650987	+	Missense_Mutation	SNP	T	T	C	rs113490934	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	44	217	0	0.30137	0	T|0.945;C|0.055	0.055	strong	.	SLX4	173	.	NM_032444	exon5	c.A1156G	p.M386V	TGAACATGGGTGG	.	PASS	Atlas-SNP
NLGN4X	57502	hgsc.bcm.edu	37	X	5821468	5821468	+	Silent	SNP	C	C	G	rs61741754	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	125	173	0	0.545852	0	C|0.870;G|0.130	0.130	strong	.	NLGN4X	191	.	NM_181332	exon5	c.G1251C	p.R417R	AGTCTCCCGCAAA	.	PASS	Atlas-SNP
CDC42BPG	55561	hgsc.bcm.edu	37	11	64594212	64594212	+	Missense_Mutation	SNP	T	T	G	rs61744174	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	13	43	0	0.325	0	T|0.987;G|0.013	0.013	strong	.	CDC42BPG	101	.	NM_017525	exon35	c.A4444C	p.S1482R	AGAAGCTGTGGGG	.	PASS	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101304193	101304193	+	Missense_Mutation	SNP	C	C	T	rs369347155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	3	111	0	0.0238095	0	.	.	weak	GABBR2,NS,carcinoma,0,1	GABBR2	126	1	NM_005458	exon3	c.G592A	p.V198M	TGCCCACGCGCTT	.	scavenged	Atlas-SNP
TRIM17	51127	hgsc.bcm.edu	37	1	228601506	228601506	+	Missense_Mutation	SNP	C	C	T	rs116188608	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	44	93	0	0.40367	0	C|0.986;T|0.014	0.014	strong	.	TRIM17	66	.	NM_001024940	exon3	c.G517A	p.E173K	GCCACTCGGCTAA	.	PASS	Atlas-SNP
ASCL1	429	hgsc.bcm.edu	37	12	103352649	103352649	+	Silent	SNP	C	C	G	rs731682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	73	107	0	0.424419	0	C|0.917;G|0.083	0.083	strong	.	ASCL1	16	.	NM_004316	exon1	c.C627G	p.V209V	GCCGGTCTCATCC	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186379735	186379735	+	Missense_Mutation	SNP	T	T	C	rs6827370	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	24	53	0	0.615385	0	T|0.816;C|0.184	0.184	strong	.	CCDC110	78	.	NM_152775	exon6	c.A2006G	p.Q669R	GTAGATTGGTAGG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38382328	38382328	+	Silent	SNP	C	C	T	rs953370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	47	112	0	0.394958	0	C|0.366;T|0.634	0.634	strong	.	WDR87	191	.	NM_031951	exon5	c.G3141A	p.P1047P	AAAAGCCGGCTTT	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786737	75786737	+	Missense_Mutation	SNP	A	A	T	rs78297221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	20	18	0	0.465116	0	A|0.517;T|0.483	0.483	strong	ZNF717,colon,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.T2037A	p.N679K	TTCCACATTCATT	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101716112	101716112	+	Missense_Mutation	SNP	G	G	C	rs35924554	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	44	123	0	0.458333	0	G|0.947;C|0.053	0.053	strong	.	DNMBP	173	.	NM_015221	exon4	c.C1119G	p.N373K	ATAAGAGTTTCTG	.	PASS	Atlas-SNP
TRPM8	79054	hgsc.bcm.edu	37	2	234863788	234863788	+	Missense_Mutation	SNP	G	G	A	rs7593557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	83	121	0	0.572414	0	G|0.732;A|0.268	0.268	strong	TRPM8,NS,carcinoma,0,1	TRPM8	146	1	NM_024080	exon11	c.G1256A	p.S419N	GCACCAGTGAGCA	.	PASS	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	37	4	2826912	2826912	+	Silent	SNP	C	C	G	rs16843413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	62	150	0	0.418919	0	C|0.875;G|0.125	0.125	strong	.	SH3BP2	43	.	NM_001145856	exon5	c.C588G	p.P196P	CCTGCCCTTGGAC	.	PASS	Atlas-SNP
RIPK3	11035	hgsc.bcm.edu	37	14	24805463	24805463	+	Missense_Mutation	SNP	G	G	T	rs3212254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	45	80	0	0.463918	0	G|0.896;T|0.104	0.104	strong	.	RIPK3	43	.	NM_006871	exon10	c.C1475A	p.P492Q	ACTGGTGGGGGGT	.	PASS	Atlas-SNP
BRD7	29117	hgsc.bcm.edu	37	16	50368671	50368671	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	58	136	0	0.298969	0	.	.	none	.	BRD7	61	.	NM_013263	exon7	c.G838C	p.G280R	CATCTCCAGAGTC	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57578696	57578696	+	Silent	SNP	C	C	T	rs140921686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	79	110	0	0.548611	0	C|0.999;T|0.001	0.001	strong	.	LRP1	428	.	NM_002332	exon39	c.C6261T	p.R2087R	GAACCGCGAGGTG	.	PASS	Atlas-SNP
GLB1L2	89944	hgsc.bcm.edu	37	11	134244123	134244123	+	Silent	SNP	C	C	G	rs3741097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	84	172	0	0.485549	0	C|0.793;G|0.207	0.207	strong	.	GLB1L2	79	.	NM_138342	exon17	c.C1680G	p.T560T	CTCCACCCCTTGT	.	PASS	Atlas-SNP
DEPDC5	9681	hgsc.bcm.edu	37	22	32194581	32194581	+	Silent	SNP	A	A	G	rs16989495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	28	52	0	0.528302	0	A|0.965;G|0.035	0.035	strong	.	DEPDC5	266	.	NM_001242897	exon14	c.A885G	p.Q295Q	TCCTCAAGGAGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515434	195515434	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	580	21	215	1	0.0362069	0.00465116	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	NM_018406	exon2	c.C3017T	p.A1006V	GGGGTGGCGTGAC	.	scavenged	Atlas-SNP
ARHGEF1	9138	hgsc.bcm.edu	37	19	42392310	42392310	+	Silent	SNP	C	C	T	rs2288509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	77	60	1	1	0.0166667	C|0.782;T|0.218	0.218	strong	ARHGEF1,colon,carcinoma,0,2	ARHGEF1	95	2	NM_199002	exon3	c.C117T	p.I39I	CATCATCGGGGCT	.	scavenged	Atlas-SNP
PLA2R1	22925	hgsc.bcm.edu	37	2	160901403	160901403	+	Silent	SNP	C	C	T	rs35005192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	58	132	0	0.423358	0	C|0.994;T|0.006	0.006	strong	.	PLA2R1	153	.	NM_001195641	exon2	c.G375A	p.P125P	CTGCAGCGGGCCT	.	PASS	Atlas-SNP
UTP18	51096	hgsc.bcm.edu	37	17	49350802	49350802	+	Silent	SNP	A	A	C	rs2318789	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	27	43	0	0.509434	0	A|0.569;C|0.431	0.431	strong	.	UTP18	28	.	NM_016001	exon5	c.A702C	p.G234G	AAGAGGAATCTTG	.	PASS	Atlas-SNP
DCST1	149095	hgsc.bcm.edu	37	1	155006999	155006999	+	Silent	SNP	C	C	T	rs6680600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	76	0	1	0	C|0.550;T|0.450	0.450	strong	.	DCST1	69	.	NM_152494	exon3	c.C150T	p.L50L	TGCTCTCCTGCTG	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15554561	15554561	+	Missense_Mutation	SNP	C	C	A	rs2074890	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	80	165	0	0.418848	0	C|0.869;A|0.131	0.131	strong	TRIM16,NS,carcinoma,0,1	TRIM16	45	1	NM_006470	exon4	c.G363T	p.E121D	CACTGGCTCGGTC	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	59	134	0	0.437037	0	G|0.878;A|0.122	0.122	strong	.	TRIM31	40	.	NM_007028	exon2	c.C309T	p.H103H	GAAATAGTGGAAC	.	PASS	Atlas-SNP
DNM1L	10059	hgsc.bcm.edu	37	12	32860302	32860302	+	Silent	SNP	G	G	A	rs2272238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	167	172	0	1	0	G|0.839;A|0.161	0.161	strong	.	DNM1L	52	.	NM_012062	exon3	c.G252A	p.G84G	TCCAGGGGTGGAA	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171256771	171256771	+	Missense_Mutation	SNP	C	C	T	rs148136770	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	56	166	0	0.434109	0	C|0.999;T|0.001	0.001	strong	.	MYO3B	320	.	NM_001083615	exon17	c.C1865T	p.S622F	TTTCCTCTCAACA	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44377991	44377991	+	Silent	SNP	G	G	A	rs78841585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	33	183	0	0.275	0	G|0.939;A|0.061	0.061	strong	.	ZNF404	46	.	NM_001033719	exon2	c.C366T	p.N122N	TCTTGTGTTATTT	.	PASS	Atlas-SNP
C1orf64	149563	hgsc.bcm.edu	37	1	16330816	16330816	+	Silent	SNP	C	C	T	rs1763617	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	116	204	0	0.497854	0	C|0.835;T|0.165	0.165	strong	.	C1orf64	16	.	NM_178840	exon1	c.C18T	p.D6D	AGAAGACCCCAGG	.	PASS	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	744510	744510	+	Silent	SNP	G	G	A	rs3746806	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	37	71	0	0.425287	0	A|0.009;C|0.000;G|0.991	0.009	strong	C20orf54,colon,carcinoma,-2,1	.	.	1	NM_033409	exon3	c.C705T	p.L235L	CGCCACGAGGCAG	.	PASS	Atlas-SNP
AMOT	154796	hgsc.bcm.edu	37	X	112022687	112022687	+	Missense_Mutation	SNP	T	T	C	rs147791527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	82	94	0	0.706897	0	T|0.990;C|0.010	0.010	strong	.	AMOT	204	.	NM_001113490	exon10	c.A2695G	p.T899A	CAGCAGTGGCAGT	.	PASS	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41900463	41900463	+	Missense_Mutation	SNP	G	G	A	rs35577124	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	62	131	1	0.410596	0.00763359	G|0.921;A|0.079	0.079	strong	PDZRN4_ENST00000402685,NS,malignant_melanoma,+1,2	PDZRN4	346	2	NM_001164595	exon4	c.G1049A	p.R350H	AGCTTCGTCCACC	.	scavenged	Atlas-SNP
CCDC37	348807	hgsc.bcm.edu	37	3	126142189	126142189	+	Silent	SNP	C	C	A	rs78360289	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	79	128	0	0.533784	0	C|0.992;T|0.008	.	alt	.	CCDC37	69	.	NM_182628	exon12	c.C1104A	p.P368P	CCCCCCCACGCAG	.	PASS	Atlas-SNP
CALHM1	255022	hgsc.bcm.edu	37	10	105215071	105215071	+	Missense_Mutation	SNP	C	C	T	rs114015468	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	75	90	0	0.609756	0	C|0.988;T|0.012	0.012	strong	.	CALHM1	33	.	NM_001001412	exon2	c.G989A	p.G330D	GGCCCACCCCCAG	.	PASS	Atlas-SNP
CALML3	810	hgsc.bcm.edu	37	10	5567366	5567366	+	Silent	SNP	G	G	A	rs1142825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	34	54	0	0.485714	0	G|0.641;A|0.359	0.359	strong	.	CALML3	12	.	NM_005185	exon1	c.G318A	p.L106L	CGAGCTGCGACAC	.	PASS	Atlas-SNP
MC1R	4157	hgsc.bcm.edu	37	16	89985984	89985984	+	Silent	SNP	G	G	A	rs3212364	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	62	0	0.421687	0	G|0.991;A|0.009	0.009	strong	.	MC1R	20	.	NM_002386	exon1	c.G318A	p.L106L	TGCACTGGTGGCC	.	PASS	Atlas-SNP
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360282	71360282	+	Missense_Mutation	SNP	G	G	A	rs13010513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	79	145	0	0.473054	0	G|0.825;A|0.175	0.175	strong	.	MPHOSPH10	81	.	NM_005791	exon2	c.G344A	p.R115H	AGGAACGTGAAGA	.	PASS	Atlas-SNP
C1orf158	93190	hgsc.bcm.edu	37	1	12819401	12819401	+	Silent	SNP	G	G	A	rs115263357	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	53	111	0	0.495327	0	G|0.993;A|0.007	0.007	strong	.	C1orf158	28	.	NM_152290	exon3	c.G384A	p.K128K	AGAGAAGTCTGAC	.	PASS	Atlas-SNP
DCTN1	1639	hgsc.bcm.edu	37	2	74596321	74596321	+	Silent	SNP	T	T	C	rs13429423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	151	252	0	0.495082	0	T|0.956;C|0.044	0.044	strong	.	DCTN1	110	.	NM_004082	exon15	c.A1605G	p.T535T	CTGGTTTGTCAGT	.	PASS	Atlas-SNP
MMAA	166785	hgsc.bcm.edu	37	4	146576418	146576418	+	Missense_Mutation	SNP	G	G	C	rs2270655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	57	124	0	0.452381	0	G|0.944;C|0.056	0.056	strong	.	MMAA	46	.	NM_172250	exon7	c.G1089C	p.Q363H	GCAACAGAAAGTT	.	PASS	Atlas-SNP
ZNF566	84924	hgsc.bcm.edu	37	19	36940675	36940675	+	Missense_Mutation	SNP	T	T	C	rs35217571	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	89	183	0	0.559748	0	T|0.986;C|0.014	0.014	strong	.	ZNF566	40	.	NM_001145343	exon5	c.A464G	p.H155R	GGATGGTGACTCA	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	37	14	71514668	71514668	+	Missense_Mutation	SNP	G	G	C	rs78161372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	102	206	0	0.451327	0	G|0.995;C|0.005	0.005	strong	.	PCNX	198	.	NM_014982	exon22	c.G4305C	p.L1435F	GCTGTTGGATCTC	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248636934	248636934	+	Missense_Mutation	SNP	G	G	T	rs9435929		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	441	278	635	2	0.630385	0.00314961	G|1.000;|0.000	.	weak	.	OR2T3	79	.	NM_001005495	exon1	c.G283T	p.D95Y	GGAGATGATACCA	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25010746	25010746	+	Silent	SNP	T	T	C	rs4049881	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	127	230	0	0.472119	0	T|0.970;C|0.030	0.030	strong	.	GGT1	68	.	NM_013430	exon6	c.T168C	p.D56D	CAGGGATGCACTG	.	PASS	Atlas-SNP
NCL	4691	hgsc.bcm.edu	37	2	232326417	232326417	+	Silent	SNP	C	C	T	rs1131171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	444	196	419	0	0.441441	0	C|0.662;T|0.338	0.338	strong	.	NCL	80	.	NM_005381	exon3	c.G447A	p.E149E	ATCATCCTCCTCT	.	PASS	Atlas-SNP
AGRN	375790	hgsc.bcm.edu	37	1	978804	978804	+	Missense_Mutation	SNP	C	C	T	rs144164397	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	38	65	0	0.5	0	C|0.999;T|0.001	0.001	strong	.	AGRN	110	.	NM_198576	exon8	c.C1570T	p.R524W	CTCGGGCGGGAGA	.	PASS	Atlas-SNP
SEC14L3	266629	hgsc.bcm.edu	37	22	30860831	30860831	+	Missense_Mutation	SNP	G	G	A	rs115090125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	75	135	0	0.506757	0	G|0.997;A|0.003	0.003	strong	.	SEC14L3	46	.	NM_174975	exon8	c.C640T	p.R214C	TCCTGCGAGTGTC	.	PASS	Atlas-SNP
PYGM	5837	hgsc.bcm.edu	37	11	64520569	64520569	+	Silent	SNP	G	G	A	rs11231865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	121	200	1	0.547511	0.005	G|0.963;A|0.037	0.037	strong	.	PYGM	77	.	NM_005609	exon12	c.C1494T	p.P498P	CAGCCCGGGGTTA	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104432462	104432462	+	Silent	SNP	A	A	G	rs200841145	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	48	96	0	0.607595	0	A|1.000;G|0.000	0.000	strong	.	GRIN3A	186	.	NM_133445	exon3	c.T2232C	p.F744F	CATTAGAAACCTT	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12315186	12315186	+	Missense_Mutation	SNP	G	G	A	rs10741578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	53	107	0	0.486239	0	G|0.506;A|0.494	0.494	strong	.	MICALCL	59	.	NM_032867	exon3	c.G208A	p.V70I	CGAGCCGTAGCCC	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10444603	10444603	+	Missense_Mutation	SNP	C	C	G	rs2230399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	233	252	0	1	0	C|0.889;G|0.111	0.111	strong	ICAM3,NS,adenoma,0,1	ICAM3	29	1	NM_002162	exon7	c.G1574C	p.S525T	TAGGTGCTCTCCT	.	PASS	Atlas-SNP
CXorf65	158830	hgsc.bcm.edu	37	X	70325881	70325881	+	Silent	SNP	G	G	A	rs138762266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	77	200	0	0.442529	0	G|0.996;A|0.004	0.004	strong	.	CXorf65	23	.	NM_001025265	exon3	c.C219T	p.Y73Y	AACGTAGTAGGTG	.	PASS	Atlas-SNP
CYB5B	80777	hgsc.bcm.edu	37	16	69458746	69458746	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	4	67	0	0.0449438	0	.	.	none	.	CYB5B	12	.	NM_030579	exon1	c.C160T	p.R54C	GTCACCCGCTTCC	.	PASS	Atlas-SNP
EXOC6B	23233	hgsc.bcm.edu	37	2	72707874	72707874	+	Silent	SNP	A	A	G	rs653220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	84	75	0	0.988235	0	A|0.639;G|0.361	0.361	strong	.	EXOC6B	93	.	NM_015189	exon17	c.T1671C	p.V557V	AATCTGAACAAGC	.	PASS	Atlas-SNP
SHROOM2	357	hgsc.bcm.edu	37	X	9863929	9863929	+	Missense_Mutation	SNP	G	G	A	rs146519576	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	63	106	0	0.456522	0	G|0.998;A|0.002	0.002	strong	.	SHROOM2	139	.	NM_001649	exon4	c.G1981A	p.G661S	GGCACCGGCCGCT	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141754629	141754629	+	Missense_Mutation	SNP	G	G	C	rs145885349	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	94	169	0	0.492147	0	G|0.997;C|0.003	0.003	strong	MGAM_ENST00000549489,caecum,carcinoma,-2,3	MGAM	767	3	NM_004668	exon27	c.G3235C	p.E1079Q	ACCCCTGAGGGTC	.	PASS	Atlas-SNP
MOGS	7841	hgsc.bcm.edu	37	2	74690378	74690378	+	Missense_Mutation	SNP	C	C	T	rs1063588	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	248	296	0	1	0	C|0.531;T|0.469	0.469	strong	.	MOGS	58	.	NM_006302	exon3	c.G715A	p.D239N	GGAAGTCACCAAG	.	PASS	Atlas-SNP
TMEM66	51669	hgsc.bcm.edu	37	8	29927182	29927182	+	Missense_Mutation	SNP	G	G	A	rs34416759	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	64	126	0	0.402516	0	G|0.990;A|0.010	0.010	strong	.	TMEM66	23	.	NM_016127	exon3	c.C676T	p.P226S	AGCCTGGGGGAGG	.	PASS	Atlas-SNP
CD5L	922	hgsc.bcm.edu	37	1	157805650	157805650	+	Missense_Mutation	SNP	A	A	T	rs11537583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	91	166	0	0.548193	0	A|0.920;T|0.080	0.080	strong	.	CD5L	112	.	NM_005894	exon3	c.T351A	p.D117E	ATCTTCATCATGT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037626	33037626	+	Silent	SNP	C	C	G	rs1042174	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	126	0	0.990654	0	C|0.687;G|0.313	0.313	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.G138C	p.T46T	TCTATGCGTCTGT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085589	17085589	+	Missense_Mutation	SNP	A	A	C	rs3863807	bycluster;byfrequency;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	18	153	0	0.0918367	0	A|0.994;C|0.006	0.006	strong	.	.	.	.	NM_001271733	exon9	c.T1132G	p.W378G	CGGACCAGCGCTG	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135744416	135744416	+	Missense_Mutation	SNP	C	C	G	rs1112542	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	56	156	0	0.448	0	C|0.915;G|0.085	0.085	strong	.	.	.	.	NM_025052	exon7	c.G2026C	p.E676Q	CAGTCTCTCGCAC	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	140	211	1	0.546875	0.00473934	G|0.854;A|0.146	0.146	strong	CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	NM_001287	exon7	c.C660T	p.H220H	CACCACGTGGGGG	.	PASS	Atlas-SNP
ZCCHC6	79670	hgsc.bcm.edu	37	9	88959938	88959938	+	Silent	SNP	C	C	T	rs791323	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	62	188	0	0.331551	0	C|0.379;N|0.000	.	strong	ZCCHC6,colon,carcinoma,0,1	ZCCHC6	105	1	NM_024617	exon5	c.G951A	p.L317L	AATTTCCAGCCTC	.	PASS	Atlas-SNP
ACTG2	72	hgsc.bcm.edu	37	2	74140616	74140616	+	Silent	SNP	C	C	T	rs34286914	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	66	144	0	0.481752	0	C|0.976;T|0.024	0.024	strong	.	ACTG2	37	.	NM_001615	exon6	c.C456T	p.I152I	AGGCATCGTCCTG	.	PASS	Atlas-SNP
AGFG2	3268	hgsc.bcm.edu	37	7	100151719	100151719	+	Missense_Mutation	SNP	G	G	A	rs61742738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	43	83	0	0.5	0	G|0.959;A|0.041	0.041	strong	.	AGFG2	44	.	NM_006076	exon5	c.G589A	p.V197I	AAGCCCGTCAGTC	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536140	1536140	+	Missense_Mutation	SNP	C	C	T	rs79505704	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	40	65	0	0.533333	0	C|0.987;T|0.013	0.013	strong	.	PTX4	46	.	NM_001013658	exon3	c.G1222A	p.G408R	CGAATCCGCCCCC	.	PASS	Atlas-SNP
IFNAR1	3454	hgsc.bcm.edu	37	21	34721782	34721782	+	Missense_Mutation	SNP	C	C	T	rs17875834	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	49	117	0	0.462264	0	C|0.930;T|0.070	0.070	strong	IFNAR1,caecum,carcinoma,0,1	IFNAR1	44	1	NM_000629	exon8	c.C1076T	p.T359M	GAAACACGCCTGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149488909	149488909	+	Silent	SNP	C	C	T	rs893600	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	77	188	0	0.484277	0	C|0.979;T|0.021	0.021	strong	.	.	.	.	NM_198455	exon35	c.C5250T	p.D1750D	AGTGGACGGTGAA	.	PASS	Atlas-SNP
POLG2	11232	hgsc.bcm.edu	37	17	62492582	62492582	+	Missense_Mutation	SNP	C	C	T	rs1427463	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	78	165	0	0.5	0	C|0.726;T|0.274	0.274	strong	.	POLG2	29	.	NM_007215	exon1	c.G505A	p.A169T	GAAATGCTACTAG	.	PASS	Atlas-SNP
ZNF449	203523	hgsc.bcm.edu	37	X	134483151	134483151	+	Silent	SNP	C	C	T	rs2286479	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	62	155	0	0.568807	0	0|0.003;T|0.143	0.143	strong	.	ZNF449	68	.	NM_152695	exon3	c.C471T	p.A157A	GGAGGCCCCAGTA	.	PASS	Atlas-SNP
WWC3	55841	hgsc.bcm.edu	37	X	10085227	10085227	+	Silent	SNP	T	T	C	rs7058143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	51	106	0	0.414634	0	0|0.004;C|0.221	0.221	strong	.	WWC3	142	.	NM_015691	exon11	c.T1128C	p.R376R	CAGCCGTGGGTCT	.	PASS	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	37	17	28381141	28381141	+	Silent	SNP	C	C	G	rs4074170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	98	242	0	0.47343	0	C|0.514;G|0.486	0.486	strong	.	EFCAB5	122	.	NM_198529	exon10	c.C2169G	p.T723T	TCCAACCTTAAGC	.	PASS	Atlas-SNP
CTNNBL1	56259	hgsc.bcm.edu	37	20	36396429	36396429	+	Missense_Mutation	SNP	C	C	G	rs186475150	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	107	180	0	0.537688	0	C|0.995;G|0.005	0.005	strong	.	CTNNBL1	78	.	NM_030877	exon7	c.C733G	p.L245V	CAGTGGCTGTTGA	.	PASS	Atlas-SNP
OR5F1	338674	hgsc.bcm.edu	37	11	55761528	55761528	+	Missense_Mutation	SNP	T	T	C	rs35607186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	69	134	1	0.489362	0.00746269	T|0.905;C|0.095	0.095	strong	OR5F1,NS,carcinoma,+1,1	OR5F1	116	1	NM_003697	exon1	c.A574G	p.T192A	GGATTGTGTCAGA	.	scavenged	Atlas-SNP
GJB4	127534	hgsc.bcm.edu	37	1	35227306	35227306	+	Missense_Mutation	SNP	C	C	A	rs78499418	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	41	73	0	0.546667	0	C|0.966;A|0.034	0.034	strong	.	GJB4	51	.	NM_153212	exon2	c.C451A	p.R151S	TTCCACCGCCTCT	.	PASS	Atlas-SNP
ALKBH4	54784	hgsc.bcm.edu	37	7	102098035	102098035	+	Missense_Mutation	SNP	G	G	A	rs150409598	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	28	58	0	0.583333	0	G|0.996;A|0.004	0.004	strong	.	ALKBH4	21	.	NM_017621	exon3	c.C715T	p.R239C	GGGAGCGGGCGGG	.	PASS	Atlas-SNP
TDP1	55775	hgsc.bcm.edu	37	14	90429749	90429749	+	Silent	SNP	A	A	G	rs3825663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	73	59	0	1	0	A|0.735;G|0.265	0.265	strong	.	TDP1	47	.	NM_018319	exon3	c.A291G	p.Q97Q	GCTGCAACCAGAA	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818162	55818162	+	Missense_Mutation	SNP	C	C	T	rs74050979	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	90	195	0	0.434783	0	C|0.979;T|0.021	0.021	strong	.	FBXO34	61	.	NM_017943	exon2	c.C1054T	p.P352S	TGTGGCCCTTCAA	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43017426	43017426	+	Silent	SNP	T	T	G	rs16957091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	170	217	2	1	0.00921659	T|0.565;G|0.435	0.435	strong	.	CDAN1	70	.	NM_138477	exon27	c.A3474C	p.L1158L	CTCCCGTAGCAAG	.	PASS	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	37	11	71945332	71945332	+	Silent	SNP	A	A	G	rs61736312	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	61	127	0	0.409396	0	A|0.867;G|0.133	0.133	strong	.	INPPL1	120	.	NM_001567	exon20	c.A2220G	p.S740S	GCTCTCAAAGACT	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160517481	160517481	+	Silent	SNP	C	C	T	rs1803989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	75	117	0	0.438596	0	C|0.839;T|0.161	0.161	strong	.	IGF2R	251	.	NM_000876	exon45	c.C6666T	p.L2222L	CGATCTCGATGTC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15794463	15794463	+	Missense_Mutation	SNP	G	G	C	rs57578760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	44	103	0	0.285714	0	G|0.973;C|0.027	0.027	strong	.	CYP4F12	89	.	NM_023944	exon7	c.G808C	p.V270L	GACGCTGTCATCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417731	105417731	+	Missense_Mutation	SNP	G	G	C	rs199870471		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	108	364	0	0.413793	0	.	.	weak	.	AHNAK2	719	.	NM_138420	exon7	c.C4057G	p.L1353V	CAGACAGGTCCAC	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113376452	113376452	+	Silent	SNP	C	C	T	rs1859329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	20	5	0	0.952381	0	T|0.775;C|0.225	0.775	strong	.	OAS3	63	.	NM_006187	exon1	c.C117T	p.A39A	CGCTGCCCTGAGG	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43579642	43579642	+	Silent	SNP	A	A	G	rs1803670	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	136	304	0	0.475524	0	A|0.738;G|0.262	0.262	strong	.	PSG2	84	.	NM_031246	exon3	c.T573C	p.H191H	AAACCTATGAGTC	.	PASS	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209179939	209179939	+	Missense_Mutation	SNP	A	A	G	rs16840913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	98	95	0	1	0	A|0.965;G|0.035	0.035	strong	.	PIKFYVE	223	.	NM_015040	exon15	c.A1849G	p.M617V	CACATGATGGCAC	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818706	55818706	+	Missense_Mutation	SNP	T	T	C	rs3742569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	107	190	0	0.493088	0	T|0.582;C|0.418	0.418	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T1598C	p.L533P	TTGTACTGCCAGC	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	317	144	250	0	0.454259	0	A|0.716;G|0.284	0.284	strong	.	SLC22A16	81	.	NM_033125	exon2	c.T312C	p.N104N	CCTCTTATTCCTG	.	PASS	Atlas-SNP
LOXL2	4017	hgsc.bcm.edu	37	8	23174481	23174481	+	Silent	SNP	G	G	A	rs7357444	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	34	70	0	0.425	0	G|0.949;A|0.051	0.051	strong	.	LOXL2	97	.	NM_002318	exon9	c.C1617T	p.A539A	AACTCCGGCCCCG	.	PASS	Atlas-SNP
VPS9D1	9605	hgsc.bcm.edu	37	16	89778919	89778919	+	Silent	SNP	T	T	C	rs139626173	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	27	42	0	0.710526	0	T|0.989;C|0.011	0.011	strong	.	.	.	.	NM_004913	exon6	c.A555G	p.L185L	CCGCTGTAGAGAG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs71563186		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	37	194	0	0.268116	0	T|0.500;C|0.500	0.500	weak	TYW1,NS,carcinoma,0,1	TYW1	71	1	NM_018264	exon15	c.T1900C	p.L634L	CACGAGTTGGTGG	.	scavenged	Atlas-SNP
CPB2	1361	hgsc.bcm.edu	37	13	46638826	46638826	+	Silent	SNP	G	G	A	rs2277440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	56	102	0	0.513761	0	G|0.890;A|0.110	0.110	strong	CPB2,NS,carcinoma,0,1	CPB2	60	1	NM_001872	exon8	c.C753T	p.I251I	TGTTCCGATGCAA	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26816779	26816779	+	Missense_Mutation	SNP	C	C	T	rs77639758	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	38	68	0	0.513514	0	C|0.998;T|0.002	0.002	strong	.	ITPR2	270	.	NM_002223	exon15	c.G1552A	p.V518I	CAAATACCTATCA	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12315915	12315915	+	Missense_Mutation	SNP	A	A	G	rs1493954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	24	0	0.45614	0	A|0.511;C|0.004	.	strong	.	MICALCL	59	.	NM_032867	exon3	c.A937G	p.S313G	TCATTCAGCCTTC	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240577	39240577	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	16	106	0	0.118519	0	.	.	none	.	KRTAP4-7	49	.	NM_033061	exon1	c.A119G	p.Y40C	CCTGCTACCGCCC	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137707834	137707834	+	Silent	SNP	G	G	A	rs3827848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	76	268	0	0.320675	0	G|0.865;A|0.135	0.135	strong	COL5A1,NS,carcinoma,0,2	COL5A1	323	2	NM_000093	exon52	c.G4122A	p.T1374T	GCAGACGGTGAGT	.	PASS	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50824117	50824117	+	Missense_Mutation	SNP	G	G	A	rs1880676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	67	147	0	0.485507	0	G|0.836;A|0.164	0.164	strong	CHAT_ENST00000395562,NS,meningioma,0,1	CHAT	162	1	NM_001142933	exon2	c.G19A	p.D7N	TGCAGAGATGAAG	.	PASS	Atlas-SNP
C8orf74	203076	hgsc.bcm.edu	37	8	10557760	10557760	+	Missense_Mutation	SNP	A	A	G	rs57041981	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	26	80	0	0.4	0	A|0.822;G|0.178	0.178	strong	.	C8orf74	28	.	NM_001040032	exon4	c.A664G	p.I222V	AGCCTCATCTGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512079	195512079	+	Silent	SNP	C	C	A	rs200031229	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	354	195	632	3	0.550847	0.00474684	C|0.922;A|0.078	0.078	strong	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.G6372T	p.G2124G	GGTGTCCCCTGTG	.	PASS	Atlas-SNP
HRCT1	646962	hgsc.bcm.edu	37	9	35906601	35906601	+	Missense_Mutation	SNP	C	C	A	rs112212538	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	22	37	0	0.611111	0	C|0.846;A|0.154	0.154	strong	.	HRCT1	14	.	NM_001039792	exon1	c.C317A	p.P106H	ACCACCCCCACCG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	100	220	0	0.492611	0	T|0.887;C|0.113	0.113	strong	ULK4_ENST00000301831,colon,carcinoma,+1,2	ULK4	150	2	NM_017886	exon11	c.A1042G	p.S348G	GAGTACTCTTAGG	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75277757	75277757	+	Silent	SNP	C	C	G	rs650241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	66	0	0.477612	0	C|0.668;G|0.332	0.332	strong	SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	NM_001235	exon2	c.C363G	p.S121S	CAACTCCACGGCG	.	PASS	Atlas-SNP
YY1AP1	55249	hgsc.bcm.edu	37	1	155629982	155629982	+	Missense_Mutation	SNP	C	C	T	rs145852062	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	320	162	291	1	0.50625	0.00343643	C|0.981;T|0.019	0.019	strong	.	YY1AP1	104	.	NM_001198903	exon10	c.G2133A	p.M711I	CTGGATCATGTTA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151927070	151927070	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1500	179	1867	4	0.119333	0.00214247	.	.	none	MLL3_ENST00000355193,bladder,carcinoma,+1,4	MLL3	1564	4	NM_170606	exon18	c.G2914A	p.G972R	ATCTTCCTTCTGC	.	scavenged	Atlas-SNP
CAMSAP2	23271	hgsc.bcm.edu	37	1	200776641	200776641	+	Silent	SNP	C	C	T	rs7552353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	36	52	0	0.571429	0	C|0.838;T|0.162	0.162	strong	.	.	.	.	NM_203459	exon3	c.C537T	p.D179D	TGAGGACGCTGTC	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744771	54744771	+	Silent	SNP	A	A	G	rs394983	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	471	124	380	1	0.26327	0.00263158	A|0.570;G|0.430	0.430	strong	.	LILRA6	75	.	NM_024318	exon5	c.T891C	p.Y297Y	TGCACCATAGCAC	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81926702	81926702	+	Missense_Mutation	SNP	G	G	A	rs1049550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	18	39	0	0.461538	0	G|0.630;T|0.004	.	strong	.	ANXA11	32	.	NM_145868	exon7	c.C688T	p.R230C	TGGAGCGACTCCC	.	PASS	Atlas-SNP
MRS2	57380	hgsc.bcm.edu	37	6	24418749	24418749	+	Silent	SNP	G	G	A	rs141564147	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	118	278	0	0.452107	0	G|0.996;A|0.004	0.004	strong	.	MRS2	31	.	NM_020662	exon9	c.G1050A	p.S350S	TCTTTCGCTCTTT	.	PASS	Atlas-SNP
GOPC	57120	hgsc.bcm.edu	37	6	117896421	117896421	+	Missense_Mutation	SNP	C	C	T	rs374207248		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	3	230	0	0.0124481	0	.	.	weak	GOPC,rectum,carcinoma,-1,1	GOPC	29	1	NM_020399	exon4	c.G569A	p.R190H	TGTCTACGAAGGG	.	scavenged	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	37	16	1682281	1682281	+	Silent	SNP	A	A	G	rs3169425	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	89	0	0.52	0	A|0.586;G|0.414	0.414	strong	CRAMP1L,NS,carcinoma,+1,2	CRAMP1L	60	2	NM_020825	exon3	c.A609G	p.A203A	GCCAGCAAGCATG	.	PASS	Atlas-SNP
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882697	143882697	+	Missense_Mutation	SNP	A	A	G	rs77624986	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	754	416	439	4	0.551724	0.00911162	A|0.500;G|0.500	0.500	strong	CTAGE4,right_upper_lobe,carcinoma,-2,1	CTAGE4	10	1	NM_198495	exon1	c.A2101G	p.I701V	GCTCCAATCAGCG	.	scavenged	Atlas-SNP
SRCAP	10847	hgsc.bcm.edu	37	16	30748715	30748715	+	Missense_Mutation	SNP	G	G	A	rs144295177	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	78	144	0	0.52349	0	G|1.000;A|0.000	0.000	weak	.	SRCAP	298	.	NM_006662	exon34	c.G7354A	p.A2452T	GCTCCGGCTGCAA	.	PASS	Atlas-SNP
H6PD	9563	hgsc.bcm.edu	37	1	9322194	9322194	+	Silent	SNP	C	C	T	rs145706807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	126	195	0	0.591549	0	C|0.999;T|0.001	0.001	strong	.	H6PD	71	.	NM_004285	exon4	c.C822T	p.L274L	CACCCTCGTGGCC	.	PASS	Atlas-SNP
METTL3	56339	hgsc.bcm.edu	37	14	21967916	21967916	+	Silent	SNP	A	A	G	rs1139130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	145	172	0	1	0	A|0.488;G|0.512	0.512	strong	.	METTL3	48	.	NM_019852	exon7	c.T1335C	p.N445N	CCAGAGATTTAGA	.	PASS	Atlas-SNP
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	16	46	0	0.333333	0	A|0.939;G|0.061;T|0.000	0.061	strong	.	RAB3D	24	.	NM_004283	exon5	c.T513C	p.N171N	CTTCACATTGATG	.	PASS	Atlas-SNP
CXCR5	643	hgsc.bcm.edu	37	11	118764382	118764382	+	Silent	SNP	G	G	T	rs2230319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	67	97	0	0.587719	0	G|0.952;T|0.048	0.048	strong	.	CXCR5	34	.	NM_001716	exon2	c.G129T	p.G43G	AGAGGGGCCCCTC	.	PASS	Atlas-SNP
NOLC1	9221	hgsc.bcm.edu	37	10	103920255	103920255	+	Silent	SNP	T	T	A	rs145855726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	51	97	0	0.5	0	T|0.997;A|0.003	0.003	strong	.	NOLC1	61	.	NM_004741	exon10	c.T1146A	p.G382G	AGCTGGTACCACC	.	PASS	Atlas-SNP
MEGF10	84466	hgsc.bcm.edu	37	5	126769146	126769146	+	Silent	SNP	T	T	C	rs11950427	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	76	134	0	0.426966	0	T|0.815;C|0.185	0.185	strong	MEGF10,colon,carcinoma,+2,1	MEGF10	152	1	NM_032446	exon15	c.T1785C	p.P595P	CTCCCCTGATGAT	.	PASS	Atlas-SNP
OR2H1	26716	hgsc.bcm.edu	37	6	29429732	29429732	+	Silent	SNP	T	T	C	rs61732184	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	303	139	256	0	0.458746	0	T|0.964;C|0.036	0.036	strong	.	OR2H1	38	.	NM_030883	exon3	c.T186C	p.S62S	CCTCTCTGACCTC	.	PASS	Atlas-SNP
NDOR1	27158	hgsc.bcm.edu	37	9	140108468	140108468	+	Silent	SNP	C	C	T	rs114934623	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	15	36	0	0.217391	0	C|0.994;T|0.006	0.006	strong	.	NDOR1	71	.	NM_001144026	exon5	c.C460T	p.L154L	AGGGTTCTGGGGC	.	PASS	Atlas-SNP
HOXC10	3226	hgsc.bcm.edu	37	12	54379610	54379610	+	Silent	SNP	G	G	C	rs145093077	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	49	72	0	0.462264	0	G|1.000;A|0.000	.	alt	.	HOXC10	42	.	NM_017409	exon1	c.G567C	p.S189S	GGAATCGCCTCAG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036435	33036435	+	Missense_Mutation	SNP	T	T	G	rs1126769	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	444	0	1	0	T|0.815;G|0.185	0.185	strong	.	HLA-DPA1	20	.	NM_033554	exon4	c.A775C	p.T259P	ACAGGGTCCCCTG	.	PASS	Atlas-SNP
DAOA	267012	hgsc.bcm.edu	37	13	106119446	106119446	+	Missense_Mutation	SNP	G	G	A	rs2391191	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	19	74	0	0.372549	0	G|0.570;A|0.430	0.430	strong	.	DAOA	26	.	NM_172370	exon2	c.G89A	p.R30K	TTCAAAGGAGCAT	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23731412	23731412	+	Missense_Mutation	SNP	G	G	A	rs2070856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	81	209	0	0.433155	0	G|0.847;A|0.153	0.153	strong	.	CST1	37	.	NM_001898	exon1	c.C92T	p.P31L	CCACCCGGGATTA	.	PASS	Atlas-SNP
C5orf30	90355	hgsc.bcm.edu	37	5	102612166	102612166	+	Silent	SNP	T	T	C	rs17155192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	45	106	0	0.416667	0	T|0.926;C|0.074	0.074	strong	.	C5orf30	18	.	NM_033211	exon3	c.T546C	p.D182D	AGCTGATACAGAA	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525650	248525650	+	Silent	SNP	C	C	T	rs28602650	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	925	450	893	2	0.486486	0.00223964	C|0.791;T|0.209	0.209	strong	.	OR2T4	126	.	NM_001004696	exon1	c.C768T	p.T256T	CCTCACCATCCAC	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48598823	48598823	+	Missense_Mutation	SNP	A	A	G	rs156631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	57	95	0	0.553398	0	T|0.003;G|0.559	0.559	strong	.	PLA2G4C	76	.	NM_001159322	exon7	c.T637C	p.S213P	GTGCAGAGAAGCC	.	PASS	Atlas-SNP
CD14	929	hgsc.bcm.edu	37	5	140011468	140011468	+	Silent	SNP	C	C	G	rs4914	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	99	208	0	0.535135	0	C|0.905;G|0.095	0.095	strong	.	CD14	20	.	NM_001174105	exon3	c.G1101C	p.L367L	TTGGAGCAGCACC	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89498428	89498428	+	Silent	SNP	G	G	A	rs1398197	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	116	230	0	0.511013	0	G|0.889;A|0.111	0.111	strong	.	EPHA3	501	.	NM_005233	exon14	c.G2400A	p.K800K	CCGCAAGTTCACG	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20766752	20766752	+	Missense_Mutation	SNP	G	G	T	rs35885925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	27	76	0	0.54	0	G|0.979;T|0.021	0.021	strong	.	ABCB5	357	.	NM_001163941	exon22	c.G2715T	p.Q905H	GCTTCAGACTCAA	.	PASS	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46709881	46709881	+	Missense_Mutation	SNP	G	G	A	rs6008622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	34	53	0	0.53125	0	G|0.845;A|0.155	0.155	strong	.	GTSE1	100	.	NM_016426	exon6	c.G1022A	p.S341N	CATCCAGTGCGTG	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	878583	878583	+	Missense_Mutation	SNP	G	G	T	rs114826023	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	16	39	0	0.421053	0	G|0.997;T|0.003	0.003	strong	.	SUN1	157	.	NM_001171945	exon4	c.G289T	p.G97C	GACAGCGGCACCA	.	PASS	Atlas-SNP
ESYT1	23344	hgsc.bcm.edu	37	12	56531154	56531154	+	Silent	SNP	T	T	C	rs2271192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	134	140	0	0.992593	0	T|0.802;C|0.198	0.198	strong	.	ESYT1	84	.	NM_001184796	exon17	c.T1965C	p.T655T	TGGGACTGAGGTG	.	PASS	Atlas-SNP
CPNE4	131034	hgsc.bcm.edu	37	3	131268824	131268824	+	Silent	SNP	T	T	C	rs11915192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	53	123	0	0.449153	0	T|0.840;C|0.160	0.160	strong	.	CPNE4	112	.	NM_130808	exon14	c.A1269G	p.S423S	TGACGCTGACTTG	.	PASS	Atlas-SNP
FOXA2	3170	hgsc.bcm.edu	37	20	22563134	22563134	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	38	107	0	0.345455	0	.	.	none	.	FOXA2	48	.	NM_021784	exon2	c.T746C	p.F249S	TTCTCGAACATGT	.	PASS	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7915912	7915912	+	Missense_Mutation	SNP	C	C	T	rs34598902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	24	31	0	0.631579	0	C|0.956;T|0.044	0.044	strong	.	GUCY2D	82	.	NM_000180	exon10	c.C2101T	p.P701S	GAGCCTCCCAGAG	.	PASS	Atlas-SNP
HIGD2A	192286	hgsc.bcm.edu	37	5	175815874	175815874	+	Silent	SNP	T	T	C	rs1060588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	70	74	0	0.985915	0	T|0.893;C|0.107	0.107	strong	.	HIGD2A	7	.	NM_138820	exon1	c.T54C	p.P18P	GAAGCCTCCAGTC	.	PASS	Atlas-SNP
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	67	89	0	0.567797	0	A|0.561;G|0.439	0.439	strong	TRPV2,right_upper_lobe,carcinoma,+1,2	TRPV2	74	2	NM_016113	exon4	c.A390G	p.G130G	GGACGGAGTCAAT	.	PASS	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43614316	43614316	+	Silent	SNP	C	C	G	rs9620123	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	41	80	0	0.5125	0	C|0.719;G|0.281	0.281	strong	.	SCUBE1	105	.	NM_173050	exon15	c.G1836C	p.A612A	CTCCAGCGCCTTG	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289242	74289242	+	Silent	SNP	T	T	C	rs3803736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	38	78	0	0.493506	0	T|0.916;C|0.084	0.084	strong	.	QRICH2	143	.	NM_032134	exon4	c.A1068G	p.Q356Q	GCCATGTTGATCG	.	PASS	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	37	4	152571711	152571711	+	Missense_Mutation	SNP	C	C	T	rs77993711	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	55	126	0	0.486726	0	C|0.995;T|0.005	0.005	strong	.	FAM160A1	60	.	NM_001109977	exon11	c.C2518T	p.H840Y	AGTCGCCATCCCG	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33371442	33371442	+	Missense_Mutation	SNP	T	T	C	rs150499320	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	55	123	0	0.429688	0	T|0.999;C|0.001	0.001	strong	.	HUNK	74	.	NM_014586	exon11	c.T2090C	p.L697P	AGCCCCTAGCCCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682831	100682831	+	Missense_Mutation	SNP	C	C	G	rs34223735	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	9	120	0	0.0616438	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.C8134G	p.L2712V	AGCACCCTTTCAA	.	PASS	Atlas-SNP
GAL3ST1	9514	hgsc.bcm.edu	37	22	30953295	30953295	+	Missense_Mutation	SNP	C	C	T	rs2267161	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	347	172	307	0	0.495677	0	C|0.671;T|0.329	0.329	strong	.	GAL3ST1	44	.	NM_004861	exon3	c.G85A	p.V29M	AGTACACCAGCAG	.	PASS	Atlas-SNP
OR2AE1	81392	hgsc.bcm.edu	37	7	99473801	99473801	+	Missense_Mutation	SNP	A	A	G	rs73403577	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	74	169	0	0.493333	0	A|0.933;G|0.067	0.067	strong	OR2AE1,rectum,carcinoma,+1,1	OR2AE1	32	1	NM_001005276	exon1	c.T856C	p.S286P	TCAGAGAATTCAA	.	PASS	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	117637	117637	+	Silent	SNP	G	G	A	rs138098441	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	115	219	0	0.504386	0	G|0.974;A|0.026	0.026	strong	.	FOXD4	75	.	NM_207305	exon1	c.C483T	p.C161C	GACGAAGCAGTCG	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25671871	25671871	+	Silent	SNP	A	A	G	rs34028410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	79	117	0	0.523179	0	A|0.980;G|0.020	0.020	strong	.	IFLTD1	121	.	NM_001145728	exon8	c.T1047C	p.P349P	GCGATTAGGGAAA	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs1613931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	75	84	0	0.986842	0	C|0.686;T|0.314	0.314	strong	KRT84,colon,carcinoma,0,1	KRT84	61	1	NM_033045	exon2	c.G551A	p.R184Q	AGGAACCGAACCT	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	20996868	20996868	+	Missense_Mutation	SNP	A	A	T	rs34179606	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	35	79	0	0.530303	0	A|0.989;T|0.011	0.011	strong	.	DNAH3	1142	.	NM_017539	exon48	c.T7196A	p.I2399N	TTGCTGATGTTGT	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166781188	166781188	+	Missense_Mutation	SNP	G	G	A	rs16851307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	44	121	0	0.382609	0	G|0.983;A|0.017	0.017	strong	.	TTC21B	130	.	NM_024753	exon12	c.C1387T	p.P463S	TTGCAGGCTAAAC	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45782903	45782903	+	Silent	SNP	T	T	C	rs6007010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	64	126	0	0.576577	0	T|0.518;C|0.482	0.482	strong	SMC1B_ENST00000357450,NS,carcinoma,-1,4	SMC1B	215	4	NM_148674	exon11	c.A1755G	p.L585L	CTCCCTTAGTCTT	.	PASS	Atlas-SNP
LYSMD1	388695	hgsc.bcm.edu	37	1	151138250	151138250	+	Missense_Mutation	SNP	G	G	T	rs113805704	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	52	121	0	0.530612	0	G|0.994;T|0.006	0.006	strong	.	LYSMD1	23	.	NM_001136543	exon1	c.C9A	p.S3R	AGGTCCGCTCCGC	.	PASS	Atlas-SNP
OR6K2	81448	hgsc.bcm.edu	37	1	158669980	158669980	+	Missense_Mutation	SNP	G	G	A	rs111363268	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	73	0	0.494118	0	G|0.977;A|0.023	0.023	strong	OR6K2,right_upper_lobe,carcinoma,+2,1	OR6K2	104	1	NM_001005279	exon1	c.C463T	p.P155S	GAAGGGGTGTGAT	.	PASS	Atlas-SNP
LMO1	4004	hgsc.bcm.edu	37	11	8246181	8246181	+	Silent	SNP	A	A	G	rs1042359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	68	71	0	0.552846	0	G|0.176;N|0.002	0.176	strong	.	LMO1	14	.	NM_002315	exon4	c.T453C	p.F151F	GGATTCAAAGGTG	.	PASS	Atlas-SNP
GIGYF2	26058	hgsc.bcm.edu	37	2	233708806	233708806	+	Silent	SNP	A	A	G	rs3816334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	234	251	0	0.995745	0	A|0.313;G|0.687	0.687	strong	GIGYF2_ENST00000409451,colon,carcinoma,0,2	GIGYF2	288	2	NM_001103147	exon26	c.A3003G	p.Q1001Q	GCAGCAACAGCAA	.	PASS	Atlas-SNP
PLCD4	84812	hgsc.bcm.edu	37	2	219492924	219492924	+	Silent	SNP	T	T	C	rs612874	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	77	138	0	0.578947	0	T|0.503;C|0.497	0.497	strong	.	PLCD4	51	.	NM_032726	exon7	c.T945C	p.C315C	GCTTTGTGGCCAG	.	PASS	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55183726	55183726	+	Missense_Mutation	SNP	G	G	A	rs61731968	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	49	112	0	0.429825	0	G|0.927;A|0.073	0.073	strong	.	AKAP1	73	.	NM_001242902	exon3	c.G901A	p.E301K	GGTGTCGAGGGAG	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6611560	6611560	+	Missense_Mutation	SNP	G	G	A	rs61733399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	55	103	0	0.55	0	G|0.981;A|0.019	0.019	strong	.	MAN2B2	80	.	NM_015274	exon13	c.G2042A	p.R681H	CAATCCGCTCCCG	.	PASS	Atlas-SNP
PTP4A1	7803	hgsc.bcm.edu	37	6	64289996	64289996	+	Silent	SNP	C	C	T	rs1681943	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	23	45	0	0.547619	0	C|0.980;T|0.020	0.020	strong	.	PTP4A1	13	.	NM_003463	exon6	c.C439T	p.L147L	CAACTTCTGTATT	.	PASS	Atlas-SNP
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410619	32410619	+	Silent	SNP	A	A	G	rs2833198	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	54	106	0	0.461538	0	A|0.811;G|0.188	0.188	strong	.	KRTAP19-8	9	.	NM_001099219	exon1	c.T144C	p.C48C	TCGGCAACAGCTG	.	PASS	Atlas-SNP
ARL4D	379	hgsc.bcm.edu	37	17	41477670	41477670	+	Silent	SNP	G	G	A	rs61749921	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	28	67	0	0.571429	0	G|0.979;A|0.021	0.021	strong	.	ARL4D	16	.	NM_001661	exon2	c.G570A	p.R190R	CAAGAGGAAGAAG	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242066830	242066830	+	Silent	SNP	G	G	A	rs2240544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	93	0	0.45	0	G|0.910;A|0.090	0.090	strong	.	PASK	230	.	NM_015148	exon10	c.C1500T	p.H500H	TTCACCGTGCACT	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13068191	13068191	+	Silent	SNP	C	C	A	rs143595675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	55	76	0	0.5	0	C|0.996;A|0.004	0.004	strong	.	CEP192	340	.	NM_032142	exon23	c.C4713A	p.G1571G	AGCAGGCCCTTCT	.	PASS	Atlas-SNP
PEMT	10400	hgsc.bcm.edu	37	17	17425631	17425631	+	Missense_Mutation	SNP	C	C	T	rs897453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	104	0	0.5	0	T|0.286;G|0.001;C|0.713;N|0.000	0.286	strong	.	PEMT	12	.	NM_001267552	exon3	c.G283A	p.V95I	TGGTGACGCTTAG	.	PASS	Atlas-SNP
CRYL1	51084	hgsc.bcm.edu	37	13	21086599	21086599	+	Silent	SNP	G	G	A	rs7139733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	73	70	0	1	0	G|0.896;A|0.104	0.104	strong	.	CRYL1	28	.	NM_015974	exon2	c.C132T	p.N44N	CAGGGCGTTCCTT	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994763	45994763	+	Silent	SNP	C	C	T	rs115169164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	52	127	0	0.5	0	C|0.980;T|0.020	0.020	strong	.	KRTAP10-4	44	.	NM_198687	exon1	c.C1128T	p.P376P	CGTGCCCGTCCCT	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	32	127	0	0.296296	0	T|0.000;G|0.240;C|0.000;A|0.760	0.240	strong	.	COL4A1	372	.	NM_001845	exon21	c.T1257C	p.P419P	GGGCCCAGGGGAA	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13506	13506	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	8	20	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.C1170T	p.Y390Y	TTTCTACTCCAAA	.	PASS	Atlas-SNP
STK38L	23012	hgsc.bcm.edu	37	12	27450671	27450671	+	Silent	SNP	G	G	T	rs56140810	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	32	56	0	0.470588	0	G|0.972;T|0.028	0.028	strong	.	STK38L	44	.	NM_015000	exon2	c.G18T	p.G6G	GGCAGGGACTACA	.	PASS	Atlas-SNP
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19316086	19316086	+	Silent	SNP	G	G	A	rs12155539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	351	149	332	1	0.424501	0.00301205	G|0.616;A|0.384	0.384	strong	CSGALNACT1,colon,carcinoma,0,1	CSGALNACT1	72	1	NM_018371	exon5	c.C702T	p.H234H	GAATTCGTGTTTG	.	PASS	Atlas-SNP
TMEM187	8269	hgsc.bcm.edu	37	X	153247745	153247745	+	Missense_Mutation	SNP	A	A	G	rs7350355	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	49	146	0	0.355072	0	A|0.587;0|0.003	.	strong	.	TMEM187	21	.	NM_003492	exon2	c.A232G	p.M78V	GGCGCGATGGGGC	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3647692	3647692	+	Missense_Mutation	SNP	A	A	C	rs74319927	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	29	49	0	0.537037	0	A|0.941;C|0.059	0.059	strong	.	SLX4	173	.	NM_032444	exon7	c.T1371G	p.N457K	ACTTTTATTCTCT	.	PASS	Atlas-SNP
SHROOM4	57477	hgsc.bcm.edu	37	X	50350782	50350782	+	Silent	SNP	C	C	T	rs113799046		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	7	141	0	0.0721649	0	C|0.500;T|0.500	0.500	weak	.	SHROOM4	171	.	NM_020717	exon6	c.G3360A	p.Q1120Q	CTTCTGCTGCTGG	.	PASS	Atlas-SNP
NOP14	8602	hgsc.bcm.edu	37	4	2955361	2955361	+	Missense_Mutation	SNP	T	T	G	rs111987238	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	55	117	0	0.478261	0	T|0.995;G|0.005	0.005	strong	.	NOP14	69	.	NM_003703	exon5	c.A624C	p.Q208H	TTGAGCTTGTCTC	.	PASS	Atlas-SNP
SOWAHB	345079	hgsc.bcm.edu	37	4	77817362	77817362	+	Silent	SNP	T	T	C	rs2703131	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	101	0	1	0	T|0.804;C|0.196	0.196	strong	.	.	.	.	NM_001029870	exon1	c.A1641G	p.L547L	TAGTGATAAACCT	.	PASS	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	744570	744570	+	Silent	SNP	G	G	A	rs6054605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	49	80	0	0.471154	0	G|0.908;A|0.092	0.092	strong	.	.	.	.	NM_033409	exon3	c.C645T	p.P215P	GTGGGCGGGAAGG	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	26	564	0	0.0718232	0	.	.	weak	SIRPA,brain,glioma,0,4	SIRPA	83	4	NM_001040022	exon3	c.C300A	p.N100K	GAGAAACAACATG	.	scavenged	Atlas-SNP
ABCB1	5243	hgsc.bcm.edu	37	7	87179256	87179256	+	Missense_Mutation	SNP	G	G	A	rs142600685	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	57	139	0	0.419118	0	G|0.999;A|0.001	0.001	strong	ABCB1,NS,carcinoma,0,2	ABCB1	263	2	NM_000927	exon14	c.C1465T	p.R489C	CATAGCGAATGTT	.	PASS	Atlas-SNP
TATDN2	9797	hgsc.bcm.edu	37	3	10311949	10311949	+	Silent	SNP	T	T	C	rs145595744	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	80	83	0	0.610687	0	T|0.997;C|0.003	0.003	strong	.	TATDN2	59	.	NM_014760	exon4	c.T1083C	p.S361S	GCCTTCTTCCTTC	.	PASS	Atlas-SNP
MAN1C1	57134	hgsc.bcm.edu	37	1	26080052	26080052	+	Silent	SNP	C	C	T	rs12073358	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	59	99	0	0.453846	0	C|0.953;T|0.047	0.047	strong	MAN1C1,NS,carcinoma,0,1	MAN1C1	48	1	NM_020379	exon5	c.C912T	p.G304G	AAAGGGCGTGGTG	.	PASS	Atlas-SNP
NUDT18	79873	hgsc.bcm.edu	37	8	21965113	21965113	+	Missense_Mutation	SNP	T	T	C	rs3739435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	37	83	0	0.544118	0	T|0.476;C|0.524	0.524	strong	.	NUDT18	13	.	NM_024815	exon5	c.A670G	p.M224V	GCTCCATAGGGTC	.	PASS	Atlas-SNP
RNF122	79845	hgsc.bcm.edu	37	8	33416189	33416189	+	Silent	SNP	G	G	A	rs3735950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	34	70	0	0.515152	0	G|0.454;A|0.546	0.546	strong	.	RNF122	17	.	NM_024787	exon2	c.C126T	p.F42F	TGTGCCGAAGATG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76464916	76464916	+	Missense_Mutation	SNP	G	G	A	rs635874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	61	68	0	0.983871	0	G|0.874;A|0.126	0.126	strong	.	DNAH17	347	.	NM_173628	exon55	c.C8561T	p.S2854L	AACACCGAGGGAA	.	PASS	Atlas-SNP
DNMT1	1786	hgsc.bcm.edu	37	19	10267077	10267077	+	Silent	SNP	T	T	C	rs2228611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	41	97	0	0.42268	0	T|0.475;C|0.525	0.525	strong	.	DNMT1	148	.	NM_001130823	exon18	c.A1389G	p.P463P	AAGAGATGGGTCA	.	PASS	Atlas-SNP
FGFR2	2263	hgsc.bcm.edu	37	10	123310871	123310871	+	Missense_Mutation	SNP	A	A	G	rs755793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	37	70	0	0.397849	0	A|0.878;G|0.122	0.122	strong	.	FGFR2	758	.	NM_022970	exon5	c.T557C	p.M186T	GTTGGCATTGGGT	.	PASS	Atlas-SNP
ZNF658	26149	hgsc.bcm.edu	37	9	40784132	40784132	+	Silent	SNP	A	A	G	rs79131704		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	93	233	0	0.352273	0	.	.	weak	.	ZNF658	100	.	NM_033160	exon4	c.T213C	p.D71D	GAATTCATCTTCT	.	PASS	Atlas-SNP
OR6C76	390326	hgsc.bcm.edu	37	12	55820927	55820927	+	Missense_Mutation	SNP	C	C	T	rs73327795	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	31	70	0	0.574074	0	C|0.983;T|0.017	0.017	strong	.	OR6C76	98	.	NM_001005183	exon1	c.C890T	p.A297V	AACAAGCATTTAA	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125441347	125441347	+	Silent	SNP	T	T	C	rs12300199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	43	160	0	0.394495	0	T|0.943;C|0.057	0.057	strong	.	DHX37	114	.	NM_032656	exon18	c.A2343G	p.A781A	GCGGGGTGCCACG	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94335037	94335037	+	Missense_Mutation	SNP	C	C	A	rs35885673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	66	194	0	0.458333	0	C|0.975;A|0.025	0.025	strong	.	PIWIL4	70	.	NM_152431	exon12	c.C1457A	p.T486N	TGAATACCTGGTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509559	195509559	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	24	261	0	0.128342	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	NM_018406	exon2	c.C8892T	p.T2964T	AGTGTCGGTGACA	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91532574	91532574	+	Missense_Mutation	SNP	A	A	G	rs150021584	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	389	182	407	1	0.467866	0.002457	A|0.999;G|0.001	0.001	strong	.	KIF20B	191	.	NM_016195	exon32	c.A5251G	p.I1751V	ATTGATATATCAG	.	PASS	Atlas-SNP
KLHDC4	54758	hgsc.bcm.edu	37	16	87743072	87743072	+	Missense_Mutation	SNP	C	C	T	rs61735154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	32	34	0	0.516129	0	C|0.978;T|0.022	0.022	strong	.	KLHDC4	45	.	NM_017566	exon10	c.G1246A	p.E416K	TGTCTTCGTCCTC	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44378063	44378063	+	Silent	SNP	T	T	C	rs79324499	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	52	164	0	0.440678	0	T|0.939;C|0.061	0.061	strong	.	ZNF404	46	.	NM_001033719	exon2	c.A294G	p.R98R	TTTAGGTCTCTGT	.	PASS	Atlas-SNP
KCNJ11	3767	hgsc.bcm.edu	37	11	17408630	17408630	+	Missense_Mutation	SNP	C	C	T	rs5215	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	227	207	0	0.991266	0	C|0.272;T|0.728	0.728	strong	.	KCNJ11	39	.	NM_000525	exon1	c.G1009A	p.V337I	CTTTGACGGTGTT	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007743	6007743	+	Missense_Mutation	SNP	A	A	G	rs61750887	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	39	105	0	0.375	0	A|0.286;G|0.714	0.714	strong	.	OR52L1	100	.	NM_001005173	exon1	c.T418C	p.C140R	CATAGCAATCCAG	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17531057	17531057	+	Missense_Mutation	SNP	C	C	A	rs139996942	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	64	100	1	0.516129	0.01	C|0.988;A|0.012	0.012	strong	USH1C,NS,carcinoma,-1,2	USH1C	157	2	NM_153676	exon18	c.G1859T	p.R620L	AGTGGGCGGGTGG	.	scavenged	Atlas-SNP
TACC1	6867	hgsc.bcm.edu	37	8	38684853	38684853	+	Silent	SNP	T	T	C	rs2037204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	117	296	0	0.391304	0	T|0.626;C|0.374	0.374	strong	.	TACC1	98	.	NM_006283	exon5	c.T1620C	p.P540P	TGTTCCTGTGTCT	.	PASS	Atlas-SNP
GPR78	27201	hgsc.bcm.edu	37	4	8589023	8589023	+	Missense_Mutation	SNP	G	G	A	rs9685931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	125	215	1	0.531915	0.00465116	G|0.871;A|0.129	0.129	strong	GPR78,NS,carcinoma,0,3	GPR78	58	3	NM_080819	exon3	c.G1025A	p.R342H	CCCCGCGCCCAGC	.	PASS	Atlas-SNP
SNX31	169166	hgsc.bcm.edu	37	8	101648164	101648164	+	Missense_Mutation	SNP	C	C	G	rs2187016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	43	120	0	0.387387	0	C|0.720;G|0.280	0.280	strong	.	SNX31	66	.	NM_152628	exon3	c.G217C	p.D73H	TCTCATCAGCCAT	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32612837	32612837	+	Silent	SNP	T	T	C	rs138053039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	53	116	0	0.46087	0	T|0.988;C|0.012	0.012	strong	.	AVL9	66	.	NM_015060	exon12	c.T1377C	p.H459H	GATCCATGATCCA	.	PASS	Atlas-SNP
SIGLEC8	27181	hgsc.bcm.edu	37	19	51957556	51957556	+	Missense_Mutation	SNP	T	T	C	rs3829659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	101	221	0	0.480952	0	T|0.647;C|0.353	0.353	strong	SIGLEC8,NS,carcinoma,0,1	SIGLEC8	130	1	NM_014442	exon6	c.A1162G	p.R388G	TCTTCCTGCAGGA	.	PASS	Atlas-SNP
ENDOV	284131	hgsc.bcm.edu	37	17	78395734	78395734	+	Missense_Mutation	SNP	G	G	A	rs34933300	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	14	59	0	0.297872	0	G|0.855;A|0.145	0.145	strong	.	ENDOV	26	.	NM_173627	exon3	c.G335A	p.R112Q	AGCTGCGGGAGAA	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191116	152191116	+	Missense_Mutation	SNP	C	C	T	rs138107632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	124	221	1	0.466165	0.00452489	C|0.985;T|0.015	0.015	strong	.	HRNR	403	.	NM_001009931	exon3	c.G2989A	p.G997S	GTTGGCCGTGGCC	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346236	116346236	+	Silent	SNP	G	G	A	rs41301525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	68	70	0	0.647619	0	G|0.886;A|0.114	0.114	strong	.	RGS3	251	.	NM_144488	exon21	c.G2544A	p.A848A	ACCTGCGGCCCCC	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234386134	234386134	+	Silent	SNP	A	A	G	rs2971863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	29	70	0	0.318681	0	A|0.746;G|0.254	0.254	strong	.	USP40	174	.	NM_018218	exon31	c.T3648C	p.H1216H	CTGCTCATGGAGG	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	37	15	70959576	70959576	+	Silent	SNP	C	C	T	rs61746327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	68	149	0	0.42236	0	C|0.989;T|0.011	0.011	strong	.	UACA	235	.	NM_018003	exon16	c.G3447A	p.V1149V	TTTGGTCACTGTC	.	PASS	Atlas-SNP
GPRIN3	285513	hgsc.bcm.edu	37	4	90169925	90169925	+	Missense_Mutation	SNP	A	A	G	rs7653897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	64	141	0	0.423841	0	A|0.398;G|0.602	0.602	strong	.	GPRIN3	90	.	NM_198281	exon2	c.T1337C	p.V446A	TCCCTCACTGGAG	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85993923	85993923	+	Silent	SNP	C	C	T	rs149121025	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	59	0	0.43617	0	C|0.998;T|0.002	0.002	strong	LRIT1,NS,haematopoietic_neoplasm,0,1	LRIT1	73	1	NM_015613	exon3	c.G801A	p.L267L	GCCACCCAAAAGG	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25356053	25356053	+	Silent	SNP	T	T	C	rs9707144	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	77	0	1	0	T|0.556;C|0.444	0.444	strong	.	RNF17	259	.	NM_001184993	exon6	c.T582C	p.F194F	ACAGTTTGACCAA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12920067	12920067	+	Silent	SNP	C	C	G	rs17038709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	123	202	0	0.504098	0	C|0.887;G|0.113	0.113	strong	PRAMEF2,NS,carcinoma,+2,1	PRAMEF2	85	1	NM_023014	exon3	c.C807G	p.L269L	ACACCTCCAGTTG	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43529026	43529026	+	Missense_Mutation	SNP	C	C	T	rs34787457	bycluster;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	78	198	0	0.443182	0	CA|0.500;TG|0.500	.	alt	.	PSG11	57	.	NM_002785	exon2	c.G247A	p.V83I	CTACTACATATGA	.	PASS	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2752487	2752487	+	Missense_Mutation	SNP	G	G	A	rs7776970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	51	152	0	0.495146	0	G|0.664;A|0.336	0.336	strong	.	AMZ1	41	.	NM_133463	exon7	c.G1472A	p.R491H	CCCCCCGTCCCTG	.	PASS	Atlas-SNP
GDNF	2668	hgsc.bcm.edu	37	5	37835752	37835752	+	Silent	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	50	141	0	0.390625	0	.	.	none	.	GDNF	56	.	NM_001190468	exon1	c.T9G	p.S3S	AGGCAAAGACTGC	.	PASS	Atlas-SNP
MAP2K1	5604	hgsc.bcm.edu	37	15	66779597	66779597	+	Silent	SNP	A	A	T	rs146869577	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	51	133	0	0.443478	0	A|0.995;T|0.005	0.005	strong	.	MAP2K1	115	.	NM_002755	exon8	c.A927T	p.A309A	CATGGCAATTTTT	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43161766	43161766	+	Silent	SNP	C	C	T	rs61740546	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	31	53	0	0.43662	0	C|0.980;G|0.000	.	strong	.	RIPK4	151	.	NM_020639	exon8	c.G1587A	p.S529S	GTTGACCGAGGCG	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49442735	49442735	+	Silent	SNP	C	C	T	rs2270940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	55	104	0	0.491071	0	C|0.924;T|0.076	0.076	strong	.	DHDH	35	.	NM_014475	exon4	c.C396T	p.S132S	TGCCTCCGAGGCT	.	PASS	Atlas-SNP
TAC3	6866	hgsc.bcm.edu	37	12	57406234	57406234	+	Missense_Mutation	SNP	A	A	G	rs73334764	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	77	0	0.506024	0	A|0.971;G|0.029	0.029	strong	.	TAC3	11	.	NM_013251	exon6	c.T295C	p.S99P	TAGGAGAGTCTAG	.	PASS	Atlas-SNP
ARL14	80117	hgsc.bcm.edu	37	3	160395483	160395483	+	Missense_Mutation	SNP	C	C	A	rs35633732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	122	118	0	0.99187	0	C|0.942;A|0.058	0.058	strong	.	ARL14	16	.	NM_025047	exon1	c.C349A	p.P117T	AATGTGCCTGTTG	.	PASS	Atlas-SNP
SLC40A1	30061	hgsc.bcm.edu	37	2	190437572	190437572	+	Silent	SNP	G	G	A	rs11568344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	98	186	0	0.5	0	G|0.960;A|0.040	0.040	strong	.	SLC40A1	51	.	NM_014585	exon4	c.C387T	p.L129L	ACTTACGAGAACC	.	PASS	Atlas-SNP
TLL2	7093	hgsc.bcm.edu	37	10	98240156	98240156	+	Missense_Mutation	SNP	T	T	A	rs61738802	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	118	250	0	0.460938	0	T|0.986;A|0.014	0.014	strong	.	TLL2	122	.	NM_012465	exon2	c.A236T	p.K79I	CTGGCTTTGTCAA	.	PASS	Atlas-SNP
NDUFS4	4724	hgsc.bcm.edu	37	5	52856572	52856572	+	Missense_Mutation	SNP	T	T	A	rs145347909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	39	63	0	0.4875	0	T|0.999;A|0.001	0.001	strong	.	NDUFS4	17	.	NM_002495	exon1	c.T80A	p.V27D	TTTCCGTTTCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505811	195505811	+	Missense_Mutation	SNP	T	T	C	rs201373238		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	30	237	4	0.120968	0.0168776	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A12640G	p.T4214A	AGGAAGTGTCGGT	.	scavenged	Atlas-SNP
SIDT2	51092	hgsc.bcm.edu	37	11	117062989	117062989	+	Missense_Mutation	SNP	C	C	T	rs12285035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	98	0	1	0	C|0.978;T|0.022	0.022	strong	.	SIDT2	82	.	NM_001040455	exon20	c.C1892T	p.T631M	GGAACACGGCGTT	.	PASS	Atlas-SNP
IQCG	84223	hgsc.bcm.edu	37	3	197665599	197665599	+	Missense_Mutation	SNP	G	G	T	rs9880989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	257	279	1	1	0.00358423	G|0.736;T|0.264	0.264	strong	.	IQCG	44	.	NM_032263	exon5	c.C335A	p.A112D	GTTGAGGCCATTG	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12409209	12409209	+	Missense_Mutation	SNP	G	G	A	rs77088407	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	81	178	0	0.503106	0	G|0.985;A|0.015	0.015	strong	.	VWDE	123	.	NM_001135924	exon12	c.C2723T	p.S908F	CTTGGGGAACACG	.	PASS	Atlas-SNP
MCRS1	10445	hgsc.bcm.edu	37	12	49952668	49952668	+	Silent	SNP	G	G	A	rs2303305	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	21	23	0	0.5	0	G|0.892;A|0.108	0.108	strong	.	MCRS1	40	.	NM_001012300	exon13	c.C1299T	p.L433L	GCCACAGAGCACC	.	PASS	Atlas-SNP
CLEC4A	50856	hgsc.bcm.edu	37	12	8290881	8290881	+	Missense_Mutation	SNP	T	T	C	rs74810750	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	72	127	0	0.444444	0	T|0.994;C|0.006	0.006	strong	.	CLEC4A	28	.	NM_016184	exon6	c.T712C	p.X238R	CACTTATGAACTG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79029288	79029288	+	Missense_Mutation	SNP	C	C	A	rs1428223	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	116	124	0	1	0	C|0.752;A|0.248	0.248	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.C4700A	p.A1567E	AAACAGCAAGTTC	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13323261	13323261	+	Silent	SNP	C	C	T	rs7249722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	49	106	0	0.449541	0	C|0.996;T|0.004	0.004	strong	.	CACNA1A	715	.	NM_001127221	exon42	c.G6129A	p.T2043T	TGTGCCCGTCTTC	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	3	6	0	0.25	0	C|0.643;T|0.357	0.357	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon12	c.C1531T	p.P511S	CGAGGCCCCTCCC	.	scavenged	Atlas-SNP
APOBEC3C	27350	hgsc.bcm.edu	37	22	39413957	39413957	+	Missense_Mutation	SNP	G	G	A	rs141108460		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	114	281	0	0.413043	0	G|1.000;A|0.000	0.000	weak	.	APOBEC3C	21	.	NM_014508	exon3	c.G361A	p.A121T	TTCACCGCCCGCC	.	PASS	Atlas-SNP
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628395	51628395	+	Missense_Mutation	SNP	C	C	T	rs144549146	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	108	210	0	0.475771	0	C|1.000;T|0.000	0.000	strong	.	SIGLEC9	85	.	NM_001198558	exon1	c.C164T	p.P55L	CTGGCCCAGTAGT	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7950952	7950952	+	Silent	SNP	C	C	A	rs9898751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	45	92	1	0.48913	0.0108696	C|0.565;A|0.435	0.435	strong	ALOX15B,NS,carcinoma,0,2	ALOX15B	66	2	NM_001141	exon12	c.C1650A	p.S550S	CTGCTCCGCCAAG	.	scavenged	Atlas-SNP
ZNF714	148206	hgsc.bcm.edu	37	19	21300142	21300142	+	Silent	SNP	A	A	C	rs112722125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	17	47	0	0.472222	0	A|0.933;C|0.067	0.067	strong	.	ZNF714	121	.	NM_182515	exon5	c.A672C	p.G224G	TACTGGAGAGAAA	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	111	0	0.990291	0	T|0.682;C|0.318	0.318	strong	IQUB,colon,carcinoma,0,2	IQUB	117	2	NM_178827	exon12	c.A2160G	p.A720A	AGCAGCTGCTTCA	.	PASS	Atlas-SNP
PIGR	5284	hgsc.bcm.edu	37	1	207106444	207106444	+	Silent	SNP	A	A	G	rs172361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	86	2	0.487805	0.0232558	A|0.773;G|0.227	0.227	strong	PIGR,NS,carcinoma,0,1	PIGR	98	1	NM_002644	exon7	c.T1773C	p.F591F	CTCCCGAAAACCA	.	scavenged	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19058425	19058425	+	Silent	SNP	G	G	A	rs62563591	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	123	240	0	0.984	0	G|0.250;A|0.750	0.750	weak	.	HAUS6	66	.	NM_017645	exon16	c.C2340T	p.L780L	TTCCGGGAGAGTT	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88781040	88781040	+	Missense_Mutation	SNP	A	A	G	rs8059048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	76	178	0	0.457831	0	A|0.751;G|0.249	0.249	strong	CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	NM_001012759	exon12	c.A1247G	p.Q416R	TCTCCCAGATGCA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1250488	1250488	+	Silent	SNP	C	C	T	rs2075859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	74	165	0	0.544118	0	C|0.604;T|0.396	0.396	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon9	c.C1065T	p.C355C	GCTCTGCGAGGAC	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119659518	119659518	+	Silent	SNP	G	G	A	rs1128403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	75	170	0	0.421348	0	G|0.956;A|0.044	0.044	strong	.	SEC24D	96	.	NM_014822	exon19	c.C2394T	p.L798L	CTGGTGGAGAACT	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55148031	55148031	+	Silent	SNP	T	T	C	rs637515		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	409	6	335	6	0.0146699	0.0179104	.	.	weak	LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	NM_001081637	exon14	c.T1740C	p.P580P	TCCTCCTTCCCCA	.	scavenged	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101730064	101730064	+	Missense_Mutation	SNP	G	G	A	rs72681442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	427	22	448	0	0.0515222	0	G|0.823;A|0.177	0.177	strong	PABPC1,NS,carcinoma,0,1	PABPC1	76	1	NM_002568	exon3	c.C440T	p.T147M	TCCTGCGTCTCAA	.	scavenged	Atlas-SNP
FAM194A	131831	hgsc.bcm.edu	37	3	150391789	150391789	+	Missense_Mutation	SNP	C	C	T	rs11919896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	30	78	0	0.483871	0	C|0.970;T|0.030	0.030	strong	.	FAM194A	91	.	NM_152394	exon11	c.G1297A	p.G433R	TGCTCCCATGTTT	.	PASS	Atlas-SNP
TAS2R16	50833	hgsc.bcm.edu	37	7	122635386	122635386	+	Silent	SNP	C	C	G	rs2692396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	53	128	0	0.420635	0	C|0.916;G|0.084	0.084	strong	.	TAS2R16	57	.	NM_016945	exon1	c.G303C	p.V101V	GTAGAACACGGTA	.	PASS	Atlas-SNP
MCEE	84693	hgsc.bcm.edu	37	2	71351641	71351641	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	55	0	0.490196	0	.	.	none	.	MCEE	19	.	NM_032601	exon2	c.A73G	p.T25A	TTACTGTTGGAAT	.	PASS	Atlas-SNP
SLC25A46	91137	hgsc.bcm.edu	37	5	110097208	110097208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	3	110	0	0.0280374	0	.	.	none	SLC25A46,NS,carcinoma,-1,1	SLC25A46	33	1	NM_138773	exon8	c.A983G	p.D328G	GTTCTGACGTTAT	.	scavenged	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55790053	55790053	+	Missense_Mutation	SNP	T	T	C	rs61733359	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	19	50	0	0.513514	0	T|0.995;C|0.005	0.005	strong	.	DYX1C1	54	.	NM_001033560	exon3	c.A128G	p.N43S	GGAAAGTTGACCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281172	152281172	+	Missense_Mutation	SNP	T	T	G	rs74129455	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	740	360	396	0	0.486486	0	T|0.500;G|0.500	0.500	strong	FLG,lower_third,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.A6190C	p.K2064Q	CAGCTTTTCCCTG	.	PASS	Atlas-SNP
C4BPB	725	hgsc.bcm.edu	37	1	207269919	207269919	+	Silent	SNP	C	C	T	rs8942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	55	88	0	0.514019	0	C|0.623;T|0.377	0.377	strong	.	C4BPB	19	.	NM_001017365	exon5	c.C462T	p.N154N	AAATAACTTCACC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1267325	1267325	+	Missense_Mutation	SNP	T	T	C	rs55813014	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	113	224	0	0.455645	0	T|0.574;C|0.426	0.426	strong	.	MUC5B	473	.	NM_002458	exon31	c.T9215C	p.F3072S	CCTCCTTCACCCT	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39166887	39166887	+	Missense_Mutation	SNP	C	C	T	rs74824603	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	61	129	0	0.469231	0	A|0.004;C|0.994;T|0.001	0.001	strong	.	TTC21A	96	.	NM_145755	exon11	c.C1280T	p.A427V	CCACAGCGCTCCT	.	PASS	Atlas-SNP
PDE11A	50940	hgsc.bcm.edu	37	2	178592452	178592452	+	Silent	SNP	C	C	A	rs77341035	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	54	105	0	0.482143	0	C|0.989;A|0.011	0.011	strong	.	PDE11A	283	.	NM_016953	exon12	c.G1977T	p.R659R	AACCATCCGATAG	.	PASS	Atlas-SNP
KLK7	5650	hgsc.bcm.edu	37	19	51480840	51480840	+	Silent	SNP	C	C	G	rs1654528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	160	0	0.480263	0	C|0.884;G|0.116	0.116	strong	.	KLK7	40	.	NM_139277	exon6	c.G714C	p.V238V	CTTGCACACTTGA	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232575051	232575051	+	Silent	SNP	G	G	A	rs189356281	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	61	106	1	0.495935	0.00943396	G|0.996;A|0.004	0.004	strong	SIPA1L2,colon,carcinoma,-2,1	SIPA1L2	218	1	NM_020808	exon13	c.C3834T	p.L1278L	AGGGCCGAGGATG	.	scavenged	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167674472	167674472	+	Silent	SNP	G	G	A	rs17070023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	70	144	0	0.56	0	G|0.910;A|0.090	0.090	strong	ODZ2_ENST00000519204,NS,carcinoma,+1,6	.	.	6	NM_001122679	exon27	c.G6501A	p.T2167T	GATGACGGTGCAA	.	PASS	Atlas-SNP
PCDHA9	9752	hgsc.bcm.edu	37	5	140229581	140229581	+	Missense_Mutation	SNP	G	G	C	rs59056023	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	173	300	1	0.5	0.00333333	G|0.939;C|0.061	0.061	strong	.	PCDHA9	373	.	NM_031857	exon1	c.G1501C	p.E501Q	TTGGGCGAGCGCT	.	PASS	Atlas-SNP
TSGA10	80705	hgsc.bcm.edu	37	2	99722135	99722135	+	Missense_Mutation	SNP	C	C	T	rs146207401	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	30	73	0	0.454545	0	C|0.999;T|0.001	0.001	strong	.	TSGA10	81	.	NM_182911	exon7	c.G236A	p.R79Q	TCTCGTCGAAGTC	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854428	12854428	+	Missense_Mutation	SNP	C	C	T	rs1769774	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	666	251	618	1	0.376877	0.00161812	C|0.713;T|0.287	0.287	strong	.	PRAMEF1	78	.	NM_023013	exon3	c.C652T	p.P218S	TCCTGGCCACGTC	.	PASS	Atlas-SNP
HEPHL1	341208	hgsc.bcm.edu	37	11	93844722	93844722	+	Silent	SNP	C	C	T	rs76467816	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	193	205	0	0.994845	0	C|0.979;T|0.021	0.021	strong	.	HEPHL1	144	.	NM_001098672	exon19	c.C3228T	p.S1076S	TTACTCCACCACA	.	PASS	Atlas-SNP
SMPD2	6610	hgsc.bcm.edu	37	6	109764535	109764535	+	Missense_Mutation	SNP	G	G	T	rs1476387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	188	176	0	1	0	A|0.000;G|0.469;T|0.531	0.531	strong	SMPD2,NS,carcinoma,0,1	SMPD2	25	1	NM_003080	exon9	c.G795T	p.R265S	TCACAGGGGCACC	.	PASS	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226074635	226074635	+	Missense_Mutation	SNP	C	C	T	rs61739581	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	285	134	293	0	0.470175	0	C|0.939;T|0.061	0.061	strong	.	LEFTY1	30	.	NM_020997	exon4	c.G893A	p.R298Q	GGCTGCCGGCAGG	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133906136	133906136	+	Missense_Mutation	SNP	G	G	C	rs16893332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	82	150	0	0.473988	0	A|0.002;C|0.049;G|0.950	0.049	strong	.	TG	416	.	NM_003235	exon11	c.G2963C	p.R988P	TTCTGCGTGGGAG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88534065	88534065	+	Missense_Mutation	SNP	G	G	A	rs3750025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	79	128	0	0.503185	0	G|0.906;A|0.094	0.094	strong	.	DSPP	174	.	NM_014208	exon4	c.G727A	p.D243N	AATTCCGATGGGA	.	PASS	Atlas-SNP
RBPJL	11317	hgsc.bcm.edu	37	20	43945377	43945377	+	Missense_Mutation	SNP	C	C	A	rs35220957	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	25	45	0	0.641026	0	C|0.988;A|0.012	0.012	strong	.	RBPJL	67	.	NM_014276	exon12	c.C1332A	p.S444R	CTGCAGCGACTGG	.	PASS	Atlas-SNP
ZNF213	7760	hgsc.bcm.edu	37	16	3190767	3190767	+	Missense_Mutation	SNP	G	G	A	rs143851164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	20	33	0	0.606061	0	G|1.000;A|0.000	0.000	weak	.	ZNF213	36	.	NM_004220	exon6	c.G799A	p.D267N	GGCAGCGACGTGA	.	PASS	Atlas-SNP
C5orf55	116349	hgsc.bcm.edu	37	5	442675	442675	+	Missense_Mutation	SNP	C	C	T	rs139173233	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	29	58	0	0.617021	0	C|0.966;T|0.034	0.034	strong	.	C5orf55	11	.	NM_138464	exon1	c.G263A	p.G88D	CGGTGGCCACCCA	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	37	11	118773204	118773204	+	Silent	SNP	G	G	A	rs7119065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	19	21	0	0.633333	0	G|0.949;A|0.051	0.051	strong	BCL9L_ENST00000392849,right_upper_lobe,carcinoma,-1,2	BCL9L	254	2	NM_182557	exon6	c.C1248T	p.D416D	CTCAATGTCTCGC	.	PASS	Atlas-SNP
GZF1	64412	hgsc.bcm.edu	37	20	23350790	23350790	+	Silent	SNP	C	C	T	rs10485644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	100	184	0	0.497512	0	C|0.893;T|0.107	0.107	strong	.	GZF1	61	.	NM_022482	exon5	c.C1848T	p.N616N	CAAGAACGATGAC	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170097707	170097707	+	Missense_Mutation	SNP	T	T	G	rs17848149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	63	160	0	0.39375	0	T|0.963;G|0.037	0.037	strong	.	LRP2	751	.	NM_004525	exon25	c.A3836C	p.D1279A	CCGTTGTCACAGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149481205	149481205	+	Missense_Mutation	SNP	T	T	C	rs73727609	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	28	55	0	0.430769	0	T|0.986;C|0.014	0.014	strong	.	.	.	.	NM_198455	exon18	c.T2687C	p.M896T	CCACCATGAAGGA	.	PASS	Atlas-SNP
USP11	8237	hgsc.bcm.edu	37	X	47107038	47107038	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	111	256	0	0.4625	0	.	.	none	.	USP11	93	.	NM_004651	exon20	c.C2694T	p.S898S	GGACAGCGGCCAG	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53298699	53298699	+	Missense_Mutation	SNP	G	G	A	rs201807576	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	6	104	0	0.0491803	0	G|0.944;A|0.055	0.055	strong	KRT8,colon,carcinoma,0,2	KRT8	41	2	NM_001256282	exon2	c.C151T	p.R51C	AGGAGCGGCTGCT	.	scavenged	Atlas-SNP
ARL5C	390790	hgsc.bcm.edu	37	17	37316988	37316988	+	Missense_Mutation	SNP	T	T	C	rs16522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	27	51	0	0.45	0	A|0.012;C|0.144	0.144	strong	.	ARL5C	3	.	NM_001143968	exon5	c.A347G	p.Q116R	GCATCCTGTAGAG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	108	166	0	0.606742	0	T|0.432;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.T4179C	p.T1393T	CAGGACTGTGGAA	.	PASS	Atlas-SNP
DSEL	92126	hgsc.bcm.edu	37	18	65180706	65180706	+	Silent	SNP	T	T	C	rs9959648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	67	0	1	0	T|0.949;C|0.051	0.051	strong	.	DSEL	196	.	NM_032160	exon2	c.A1170G	p.Q390Q	CCACCTTTGGGCA	.	PASS	Atlas-SNP
FASTKD1	79675	hgsc.bcm.edu	37	2	170413700	170413700	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	46	107	0	0.554217	0	.	.	none	.	FASTKD1	86	.	NM_024622	exon6	c.A1079G	p.K360R	TACCTTTTAATCA	.	PASS	Atlas-SNP
OR52B6	340980	hgsc.bcm.edu	37	11	5602275	5602275	+	Missense_Mutation	SNP	A	A	G	rs1077126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	237	204	1	1	0.00490196	A|0.482;G|0.518	0.518	strong	.	OR52B6	37	.	NM_001005162	exon1	c.A169G	p.T57A	TACATCACTGCCC	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	37	11	82875359	82875359	+	Silent	SNP	G	G	A	rs7130527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	52	89	0	0.981132	0	G|0.905;A|0.095	0.095	strong	.	PCF11	220	.	NM_015885	exon4	c.G618A	p.Q206Q	AAGGCAGCAGTTA	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52369086	52369086	+	Silent	SNP	G	G	A	rs3213805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	94	215	0	0.465347	0	G|0.883;A|0.117	0.117	strong	ITGA2_ENST00000296585,NS,carcinoma,0,1	ITGA2	211	1	NM_002203	exon20	c.G2568A	p.L856L	CTCCCTGCCGGTA	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88779739	88779739	+	Missense_Mutation	SNP	A	A	G	rs11549837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	79	0	1	0	A|0.607;G|0.393	0.393	strong	.	CTU2	66	.	NM_001012759	exon8	c.A757G	p.M253V	CTCCACATGGCCC	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6103072	6103072	+	Missense_Mutation	SNP	C	C	T	rs2229446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	23	72	0	0.479167	0	C|0.939;T|0.061	0.061	strong	VWF,rectum,carcinoma,-1,1	VWF	338	1	NM_000552	exon37	c.G6554A	p.R2185Q	TTGGTCCGACAGA	.	PASS	Atlas-SNP
TNFAIP3	7128	hgsc.bcm.edu	37	6	138196066	138196066	+	Missense_Mutation	SNP	T	T	G	rs2230926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	94	164	0	0.522222	0	T|0.857;G|0.143	0.143	strong	TNFAIP3,eye,lymphoid_neoplasm,0,1	TNFAIP3	340	1	NM_001270507	exon3	c.T380G	p.F127C	CGCTGTTCAGCAC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103383417	103383417	+	Missense_Mutation	SNP	T	T	C	rs9554897	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	130	212	0	0.548523	0	C|0.312;N|0.000	0.312	strong	.	.	.	.	NM_001146197	exon4	c.A19630G	p.K6544E	TTTCTTTTACTGA	.	PASS	Atlas-SNP
PCDH12	51294	hgsc.bcm.edu	37	5	141336858	141336858	+	Missense_Mutation	SNP	C	C	T	rs140883612	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	106	220	0	0.471111	0	C|0.991;T|0.009	0.009	strong	.	PCDH12	133	.	NM_016580	exon1	c.G559A	p.G187S	CAGGGCCCACAAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Missense_Mutation	SNP	C	C	T	rs56021350	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	12	24	0	0.363636	0	C|0.825;T|0.175	0.175	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon49	c.C13196T	p.T4399M	CGGCCACGCTCAC	.	PASS	Atlas-SNP
MDH2	4191	hgsc.bcm.edu	37	7	75677504	75677504	+	Missense_Mutation	SNP	C	C	T	rs6720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	16	13	0	0.666667	0	C|0.494;T|0.506	0.506	strong	MDH2,NS,carcinoma,0,1	MDH2	35	1	NM_005918	exon1	c.C26T	p.A9V	GGCCTGCCAGCGC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	38	86	0	0.383838	0	A|0.862;C|0.138	0.138	strong	.	DNHD1	198	.	NM_173589	exon3	c.A836C	p.Q279P	ATAGCCAGGTGAT	.	PASS	Atlas-SNP
CBLC	23624	hgsc.bcm.edu	37	19	45285734	45285734	+	Silent	SNP	G	G	A	rs10416628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	62	118	0	0.521008	0	G|0.958;A|0.042	0.042	strong	.	CBLC	41	.	NM_001130852	exon4	c.G765A	p.R255R	CTGCAGGGACAAG	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116930100	116930100	+	Missense_Mutation	SNP	G	G	A	rs2567707	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	52	80	0	0.675325	0	G|0.811;A|0.189	0.189	strong	.	COL27A1	200	.	NM_032888	exon3	c.G265A	p.V89I	GGCACCGTCATTC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124387586	124387586	+	Silent	SNP	A	A	G	rs61587964	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	81	0	1	0	A|0.680;G|0.320	0.320	strong	.	DNAH10	888	.	NM_207437	exon56	c.A9387G	p.A3129A	CCTGGCAGAGGTC	.	PASS	Atlas-SNP
BRD7	29117	hgsc.bcm.edu	37	16	50368626	50368626	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	8	71	0	0.0952381	0	.	.	none	.	BRD7	61	.	NM_013263	exon7	c.A883G	p.K295E	ACTTTTTATTTTC	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253931	39253931	+	Missense_Mutation	SNP	G	G	A	rs150613353	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	54	84	0	0.439024	0	G|0.966;A|0.034	0.034	strong	.	KRTAP4-8	57	.	NM_031960	exon1	c.C406T	p.R136C	AGGGGCGGCAGCA	.	PASS	Atlas-SNP
ERN2	10595	hgsc.bcm.edu	37	16	23721865	23721865	+	Missense_Mutation	SNP	C	C	T	rs9932495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	156	0	0.515152	0	C|0.981;T|0.019	0.019	strong	.	ERN2	131	.	NM_033266	exon3	c.G349A	p.V117I	CGATGACGGGATC	.	PASS	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109496813	109496813	+	Missense_Mutation	SNP	T	T	C	rs16973313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	93	0	0.431193	0	T|0.882;C|0.118	0.118	strong	.	MYO16	285	.	NM_001198950	exon10	c.T1220C	p.M407T	ACCCCATGATGAG	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33587298	33587298	+	Silent	SNP	C	C	T	rs114017497	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	167	0	0.480263	0	C|0.991;T|0.009	0.009	strong	.	GPATCH1	79	.	NM_018025	exon7	c.C798T	p.G266G	AGCTGGCGATCTT	.	PASS	Atlas-SNP
LAMP1	3916	hgsc.bcm.edu	37	13	113973832	113973832	+	Missense_Mutation	SNP	C	C	T	rs9577229	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	62	0	0.467742	0	C|0.947;T|0.053	0.053	strong	LAMP1,NS,carcinoma,0,1	LAMP1	41	1	NM_005561	exon5	c.C611T	p.A204V	CCCCTGCGCCACC	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	12950315	12950315	+	Silent	SNP	G	G	T	rs568182	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	34	62	0	0.539683	0	G|0.887;T|0.113	0.113	strong	DLC1,NS,carcinoma,-1,2	DLC1	411	2	NM_182643	exon13	c.C3546A	p.R1182R	CTGCAGGCGCTGG	.	PASS	Atlas-SNP
DOPEY1	23033	hgsc.bcm.edu	37	6	83850049	83850049	+	Missense_Mutation	SNP	A	A	T	rs9444039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	88	0	0.520548	0	A|0.968;T|0.032	0.032	strong	.	DOPEY1	190	.	NM_015018	exon23	c.A5342T	p.Q1781L	TGCATCAAGCTGA	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34111969	34111969	+	Silent	SNP	C	C	T	rs58745096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	87	168	0	0.5	0	C|0.984;T|0.016	0.016	strong	RYR3,NS,carcinoma,0,1	RYR3	760	1	NM_001036	exon77	c.C10719T	p.D3573D	GGAAGACGACCCT	.	PASS	Atlas-SNP
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914013	31914013	+	Missense_Mutation	SNP	G	G	A	rs115563631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	42	94	0	0.446809	0	G|0.985;A|0.015	0.015	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.C140T	p.S47L	CGGCATGATGGGC	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	63119442	63119442	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	45	129	0	0.302013	0	.	.	none	.	DOCK7	184	.	NM_001271999	exon4	c.G343A	p.D115N	TACAGTCTCTAAC	.	PASS	Atlas-SNP
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	66	96	0	1	0	T|0.686;C|0.314	0.314	strong	.	HSPA9	49	.	NM_004134	exon9	c.A948G	p.K316K	TTCACATTTAGCC	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782731	54782731	+	Silent	SNP	G	G	A	rs10404685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	153	215	1	0.640167	0.00465116	G|0.904;A|0.096	0.096	strong	.	LILRB2	94	.	NM_005874	exon6	c.C891T	p.Y297Y	TGCACCGTAGCAT	.	PASS	Atlas-SNP
EFHC1	114327	hgsc.bcm.edu	37	6	52343899	52343899	+	Missense_Mutation	SNP	T	T	C	rs1266787	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	49	101	0	0.471154	0	A|0.004;C|0.085	0.085	strong	.	EFHC1	68	.	NM_018100	exon8	c.T1343C	p.M448T	CCGACATGATCAG	.	PASS	Atlas-SNP
PHYHIPL	84457	hgsc.bcm.edu	37	10	61005244	61005244	+	Missense_Mutation	SNP	G	G	C	rs2452505	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	76	135	0	0.589147	0	G|0.259;C|0.741	0.741	strong	.	PHYHIPL	44	.	NM_032439	exon5	c.G1024C	p.V342L	CTTTCTGTGGGCA	.	PASS	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98558922	98558922	+	Silent	SNP	G	G	A	rs34983214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	46	81	0	0.489362	0	G|0.993;A|0.007	0.007	strong	.	TRRAP	863	.	NM_001244580	exon45	c.G6507A	p.T2169T	CTGCACGGGCCTA	.	PASS	Atlas-SNP
GFRA4	64096	hgsc.bcm.edu	37	20	3640568	3640568	+	Silent	SNP	C	C	T	rs74740423	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	23	37	0	0.560976	0	C|0.968;T|0.032	0.032	strong	.	GFRA4	10	.	NM_145762	exon5	c.G888A	p.P296P	CAGGGCCGGGAGA	.	PASS	Atlas-SNP
PEX11G	92960	hgsc.bcm.edu	37	19	7547074	7547074	+	Missense_Mutation	SNP	A	A	C	rs2303146	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	34	44	0	1	0	A|0.557;C|0.443	0.443	strong	.	PEX11G	16	.	NM_001270539	exon3	c.T273G	p.C91W	GGAGACACAGCGG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56087423	56087423	+	Missense_Mutation	SNP	G	G	A	rs79451216	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	6	43	1	0.130435	0.0232558	G|0.913;A|0.086	0.086	strong	PSPH,NS,lymphoid_neoplasm,0,1	PSPH	23	1	NM_004577	exon5	c.C145T	p.R49W	CTCGCCGTGTCCT	.	scavenged	Atlas-SNP
ACOT1	641371	hgsc.bcm.edu	37	14	74009937	74009937	+	Missense_Mutation	SNP	A	A	G	rs377598014		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	906	319	659	0	0.352097	0	.	.	weak	.	ACOT1	12	.	NM_001037161	exon3	c.A844G	p.I282V	AATCGCATCAAGG	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32370859	32370859	+	Missense_Mutation	SNP	C	C	T	rs9461742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	92	168	0	0.474227	0	C|0.992;T|0.008	0.008	strong	.	BTNL2	50	.	NM_019602	exon3	c.G562A	p.V188M	CAGACACGGCCAG	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6711070	6711070	+	Missense_Mutation	SNP	C	C	G	rs11569422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	90	177	0	0.48913	0	C|0.980;G|0.020	0.020	strong	.	C3	192	.	NM_000064	exon12	c.G1407C	p.E469D	GAGGGTCTCCCCG	.	PASS	Atlas-SNP
MPZL2	10205	hgsc.bcm.edu	37	11	118133334	118133334	+	Silent	SNP	T	T	C	rs17122002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	70	167	0	0.583333	0	T|0.954;C|0.046	0.046	strong	.	MPZL2	20	.	NM_005797	exon3	c.A255G	p.Q85Q	CATGGGTTGGAAG	.	PASS	Atlas-SNP
SHMT2	6472	hgsc.bcm.edu	37	12	57627074	57627074	+	Silent	SNP	G	G	T	rs2229717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	89	164	0	0.566879	0	G|0.952;T|0.048	0.048	strong	.	SHMT2	40	.	NM_005412	exon8	c.G969T	p.L323L	ATCCCTGCAGGGG	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	96012108	96012108	+	Silent	SNP	C	C	T	rs61732522	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	75	190	0	0.371287	0	C|0.983;T|0.017	0.017	strong	.	PLCE1	543	.	NM_016341	exon9	c.C3132T	p.H1044H	GGCTCACGCTGTG	.	PASS	Atlas-SNP
WAS	7454	hgsc.bcm.edu	37	X	48546837	48546837	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	68	238	0	0.266667	0	.	.	none	.	WAS	51	.	NM_000377	exon9	c.G926A	p.R309H	TGAGGCGCCAGGG	.	PASS	Atlas-SNP
DMBX1	127343	hgsc.bcm.edu	37	1	46978076	46978076	+	Silent	SNP	C	C	A	rs11211298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	86	0	0.528571	0	C|0.938;A|0.062	0.062	strong	.	DMBX1	50	.	NM_147192	exon4	c.C1059A	p.T353T	AGCTACCCTGAAC	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62173925	62173925	+	Silent	SNP	T	T	G	rs404613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	141	145	0	0.986014	0	T|0.680;G|0.320	0.320	strong	SRMS,NS,lymphoid_neoplasm,0,1	SRMS	48	1	NM_080823	exon4	c.A655C	p.R219R	CCTGCCTCGGGGC	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	8	15	0	0.421053	0	G|0.476;A|0.524	0.524	strong	LRWD1,NS,carcinoma,0,1	LRWD1	41	1	NM_152892	exon13	c.G1614A	p.T538T	GTCCACGGTGGCA	.	PASS	Atlas-SNP
CYP27A1	1593	hgsc.bcm.edu	37	2	219674482	219674482	+	Silent	SNP	G	G	A	rs692003	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	32	82	0	0.438356	0	G|0.935;A|0.065	0.065	strong	.	CYP27A1	52	.	NM_000784	exon2	c.G438A	p.P146P	TGGGCCGTTCACC	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23874523	23874523	+	Silent	SNP	C	C	T	rs2277474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	93	173	0	0.525424	0	C|0.794;A|0.002	.	strong	.	MYH6	274	.	NM_002471	exon5	c.G411A	p.E137E	CACCACCTCGGCA	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120057163	120057163	+	Silent	SNP	G	G	A	rs33913717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	127	233	0	0.508	0	G|0.990;A|0.010	0.010	strong	HSD3B1,caecum,carcinoma,+1,1	HSD3B1	53	1	NM_000862	exon4	c.G1017A	p.A339A	TCTGGCGTATAAG	.	PASS	Atlas-SNP
C6orf52	347744	hgsc.bcm.edu	37	6	10687746	10687746	+	Missense_Mutation	SNP	G	G	T	rs7749306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	36	58	0	0.455696	0	A|0.000;G|0.781;T|0.219	0.219	strong	.	C6orf52	9	.	NM_001145020	exon2	c.C38A	p.A13D	TGTTGAGCTATGC	.	PASS	Atlas-SNP
CD1E	913	hgsc.bcm.edu	37	1	158325819	158325819	+	Silent	SNP	G	G	A	rs61734678	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	114	219	0	0.457831	0	G|0.988;A|0.012	0.012	strong	CD1E,colon,carcinoma,+1,2	CD1E	129	2	NM_030893	exon4	c.G828A	p.A276A	TGTGGCGGCTGGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228547691	228547691	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	83	128	0	0.506098	0	.	.	none	.	OBSCN	2142	.	NM_052843	exon81	c.C19098T	p.P6366P	GACCCCCGGAGGG	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	37	17	66928460	66928460	+	Missense_Mutation	SNP	T	T	C	rs16973446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	40	76	0	0.43956	0	T|0.915;C|0.085	0.085	strong	.	ABCA8	213	.	NM_007168	exon6	c.A766G	p.T256A	TCATTGTCATCAA	.	PASS	Atlas-SNP
ISLR2	57611	hgsc.bcm.edu	37	15	74425410	74425410	+	Silent	SNP	T	T	C	rs3743207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	28	52	0	0.491228	0	T|0.898;C|0.102	0.102	strong	.	ISLR2	78	.	NM_001130138	exon4	c.T315C	p.D105D	CCTCGATCTGAGC	.	PASS	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42438380	42438380	+	Silent	SNP	G	G	A	rs80108792	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	47	109	0	0.522222	0	G|0.988;A|0.012	0.012	strong	.	PLA2G4F	75	.	NM_213600	exon14	c.C1479T	p.Y493Y	AATGGGGTAAGGG	.	PASS	Atlas-SNP
CLRN2	645104	hgsc.bcm.edu	37	4	17517141	17517141	+	Silent	SNP	G	G	A	rs201838208	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	80	164	0	0.540541	0	.	.	weak	.	CLRN2	40	.	NM_001079827	exon1	c.G252A	p.T84T	ATTCACGAGTGAG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79029749	79029749	+	Missense_Mutation	SNP	A	A	G	rs1428225	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	64	56	1	1	0.0178571	A|0.752;G|0.248	0.248	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.A5161G	p.I1721V	AAGATCATCAGCC	.	scavenged	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3645607	3645607	+	Missense_Mutation	SNP	A	A	G	rs77985244	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	21	51	0	0.466667	0	A|0.932;G|0.068	0.068	strong	.	SLX4	173	.	NM_032444	exon9	c.T2012C	p.L671S	CTTACCAAGGTGC	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30673013	30673013	+	Missense_Mutation	SNP	A	A	G	rs61733213	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	363	186	322	1	0.512397	0.00310559	A|0.958;G|0.042	0.042	strong	.	MDC1	218	.	NM_014641	exon10	c.T3947C	p.M1316T	GAGGACATATTTG	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6209363	6209363	+	Silent	SNP	T	T	C	rs12565328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	57	112	0	0.463415	0	T|0.543;C|0.457	0.457	strong	.	CHD5	267	.	NM_015557	exon8	c.A1104G	p.V368V	CAGGCATACGAGA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512939	4512939	+	Missense_Mutation	SNP	T	T	C	rs201080851	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	78	381	0	0.3	0	T|0.984;C|0.016	0.016	strong	.	PLIN4	191	.	NM_001080400	exon3	c.A991G	p.M331V	CATTCATGGCACC	.	PASS	Atlas-SNP
KRTAP1-5	83895	hgsc.bcm.edu	37	17	39183304	39183304	+	Missense_Mutation	SNP	C	C	T	rs62623375	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	74	153	0	0.406593	0	C|0.882;T|0.118	0.118	strong	.	KRTAP1-5	33	.	NM_031957	exon1	c.G104A	p.C35Y	GGCTGGCAGCAGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100675376	100675376	+	Missense_Mutation	SNP	A	A	C	rs10229731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	61	103	0	0.54955	0	A|0.825;C|0.175	0.175	strong	.	MUC17	804	.	NM_001040105	exon3	c.A679C	p.K227Q	ACCATGAAGGTGG	.	PASS	Atlas-SNP
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73932560	73932560	+	Silent	SNP	A	A	G	rs17851629	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	146	0	1	0	A|0.744;G|0.256	0.256	strong	.	GTF2IRD1	91	.	NM_001199207	exon5	c.A609G	p.E203E	GCCCGAAGGCCTG	.	PASS	Atlas-SNP
TRIM64C	646754	hgsc.bcm.edu	37	11	49080616	49080616	+	Missense_Mutation	SNP	T	T	C	rs60452246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	113	273	0	0.463115	0	T|0.586;C|0.414	0.414	strong	.	TRIM64C	18	.	NM_001206631	exon1	c.A49G	p.I17V	CGCAAATGCAGCA	.	PASS	Atlas-SNP
PTPN23	25930	hgsc.bcm.edu	37	3	47454398	47454398	+	Missense_Mutation	SNP	C	C	T	rs140165828	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	116	237	0	0.469636	0	C|0.998;T|0.002	0.002	strong	PTPN23,NS,carcinoma,-1,1	PTPN23	85	1	NM_015466	exon25	c.C4634T	p.P1545L	CCTCCCCGCCCCC	.	PASS	Atlas-SNP
CHST12	55501	hgsc.bcm.edu	37	7	2472662	2472662	+	Missense_Mutation	SNP	G	G	C	rs11537796	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	21	10	17	0	0.47619	0	G|0.970;C|0.030	0.030	strong	.	CHST12	39	.	NM_018641	exon2	c.G388C	p.G130R	CTGCGGGGCTTCT	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714168	32714168	+	Silent	SNP	A	A	G	rs9276437	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	454	250	385	2	0.550661	0.00519481	A|0.848;G|0.152	0.152	strong	.	HLA-DQA2	27	.	NM_020056	exon4	c.A765G	p.L255L	GCTCTTATGAATC	.	PASS	Atlas-SNP
XCL1	6375	hgsc.bcm.edu	37	1	168549321	168549321	+	Missense_Mutation	SNP	G	G	C	rs56148248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	68	281	0	0.42236	0	G|0.982;C|0.018	0.018	strong	.	XCL1	16	.	NM_002995	exon2	c.G82C	p.D28H	GTCTCAGATAAGA	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70928616	70928616	+	Silent	SNP	G	G	A	rs3752703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	28	95	0	0.373333	0	G|0.613;A|0.387	0.387	strong	PTPRB_ENST00000334414,colon,carcinoma,0,3	PTPRB	676	3	NM_001109754	exon30	c.C6201T	p.C2067C	TACACCGCATATC	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52676392	52676392	+	Missense_Mutation	SNP	A	A	G	rs16964944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	119	247	0	0.406143	0	A|0.942;G|0.058	0.058	strong	.	MYO5A	145	.	NM_000259	exon15	c.T1880C	p.M627T	TTGGCCATTTGGC	.	PASS	Atlas-SNP
PLXNA3	55558	hgsc.bcm.edu	37	X	153689893	153689893	+	Missense_Mutation	SNP	G	G	A	rs35285799	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	29	46	0	0.674419	0	G|0.967;A|0.033	0.033	strong	.	PLXNA3	156	.	NM_017514	exon3	c.G1049A	p.R350Q	ACATCCGGCGCCG	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134851605	134851605	+	Silent	SNP	C	C	T	rs56401137	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	95	178	0	0.463415	0	C|0.967;T|0.033	0.033	strong	.	EPHB1	519	.	NM_004441	exon5	c.C1011T	p.S337S	GACGTCCATCATT	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47985655	47985655	+	Silent	SNP	C	C	T	rs2248636	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	74	106	0	0.540146	0	C|0.861;T|0.139	0.139	strong	.	DIP2A	332	.	NM_015151	exon36	c.C4194T	p.T1398T	TGCCACCGGGTAC	.	PASS	Atlas-SNP
DLG2	1740	hgsc.bcm.edu	37	11	83182726	83182726	+	Silent	SNP	G	G	T	rs34857356	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	60	144	0	0.540541	0	G|0.984;T|0.016	0.016	strong	DLG2_ENST00000418306,colon,carcinoma,+2,9	DLG2	448	9	NM_001142699	exon24	c.C2389A	p.R797R	TGATCCGATCCTT	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	108	100	0	0.981818	0	C|0.372;T|0.628	0.628	strong	.	HMCN1	797	.	NM_031935	exon47	c.C7371T	p.C2457C	TACTTGCGTTGTA	.	PASS	Atlas-SNP
FRMD6	122786	hgsc.bcm.edu	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	44	66	0	0.517647	0	G|0.751;C|0.000;A|0.249	0.249	strong	.	FRMD6	100	.	NM_001267046	exon11	c.G1218A	p.T406T	GGACACGGGGCCA	.	PASS	Atlas-SNP
C22orf24	25775	hgsc.bcm.edu	37	22	32334021	32334021	+	Missense_Mutation	SNP	T	T	A	rs1984388	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	101	106	0	0.971154	0	T|0.774;A|0.226	0.226	strong	C22orf24_ENST00000248984,NS,carcinoma,0,1	C22orf24	21	1	NM_015372	exon2	c.A32T	p.H11L	TTTTGATGCAGCC	.	PASS	Atlas-SNP
DPEP3	64180	hgsc.bcm.edu	37	16	68011867	68011867	+	Missense_Mutation	SNP	C	C	T	rs16957670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	79	152	0	0.530201	0	C|0.936;T|0.064	0.064	strong	.	DPEP3	48	.	NM_001129758	exon5	c.G805A	p.V269I	CGCTGACGTTGGT	.	PASS	Atlas-SNP
FAM174A	345757	hgsc.bcm.edu	37	5	99897880	99897880	+	Missense_Mutation	SNP	A	A	G	rs76060686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	117	206	0	0.483471	0	A|0.992;G|0.008	0.008	strong	.	FAM174A	13	.	NM_198507	exon2	c.A557G	p.N186S	ATGCCAATCATCC	.	PASS	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44189166	44189166	+	Silent	SNP	T	T	C	rs1045382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	155	168	0	0.99359	0	T|0.555;C|0.445	0.445	strong	.	PDE9A	69	.	NM_002606	exon17	c.T1491C	p.P497P	CCTTCCTGTGGCA	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47274733	47274733	+	Missense_Mutation	SNP	T	T	C	rs62621889	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	68	155	0	0.42236	0	T|0.989;C|0.011	0.011	strong	.	PREX1	441	.	NM_020820	exon17	c.A1915G	p.I639V	CCTCGATGTCAAA	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112512905	112512905	+	Silent	SNP	G	G	A	rs2072021	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	45	80	0	0.45	0	G|0.735;A|0.265	0.265	strong	.	LAMA4	227	.	NM_001105206	exon6	c.C651T	p.T217T	GAATCCGGTGGTG	.	PASS	Atlas-SNP
PEX11G	92960	hgsc.bcm.edu	37	19	7542118	7542118	+	Silent	SNP	G	G	A	rs7256275	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	32	58	0	0.52459	0	G|0.870;A|0.130	0.130	strong	.	PEX11G	16	.	NM_080662	exon5	c.C696T	p.A232A	GCCGCCGGCCCGG	.	PASS	Atlas-SNP
HOXD8	3234	hgsc.bcm.edu	37	2	176995146	176995146	+	Missense_Mutation	SNP	G	G	A	rs192755857	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	7	2	0	0.777778	0	G|0.966;A|0.034	0.034	strong	.	HOXD8	24	.	NM_001199746	exon1	c.G52A	p.A18T	GCGGCTGCGGCGG	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97852399	97852399	+	Missense_Mutation	SNP	G	G	A	rs11762014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	71	83	0	0.577236	0	G|0.777;A|0.223	0.223	strong	TECPR1,NS,carcinoma,0,1	TECPR1	77	1	NM_015395	exon21	c.C2831T	p.P944L	GCACCCGGGCTCT	.	PASS	Atlas-SNP
RGS9	8787	hgsc.bcm.edu	37	17	63221136	63221136	+	Missense_Mutation	SNP	C	C	T	rs116395890	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	49	95	0	0.510417	0	C|0.994;T|0.006	0.006	strong	.	RGS9	82	.	NM_003835	exon18	c.C1424T	p.A475V	ACATGGCTCCCAG	.	PASS	Atlas-SNP
PDCD1LG2	80380	hgsc.bcm.edu	37	9	5557708	5557708	+	Missense_Mutation	SNP	T	T	C	rs7854413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	293	293	297	0	1	0	T|0.745;C|0.255	0.255	strong	.	PDCD1LG2	16	.	NM_025239	exon5	c.T722C	p.I241T	CAGTGATAGCCCT	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153421912	153421912	+	Silent	SNP	T	T	C	rs1065439	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1069	577	763	2	0.539757	0.00262123	0|0.004;C|0.185	0.185	strong	.	OPN1LW	87	.	NM_020061	exon5	c.T888C	p.G296G	CCCTGGTTACGCC	.	PASS	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8662516	8662516	+	Missense_Mutation	SNP	T	T	C	rs11042023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	147	159	1	0.993243	0.00628931	T|0.470;C|0.530	0.530	strong	TRIM66,rectum,carcinoma,0,1	TRIM66	45	1	NM_014818	exon9	c.A971G	p.H324R	GAGCAGTGGGAGC	.	PASS	Atlas-SNP
LBH	81606	hgsc.bcm.edu	37	2	30457288	30457288	+	Missense_Mutation	SNP	C	C	T	rs144194149	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	98	171	0	0.526882	0	C|0.996;T|0.004	0.004	strong	.	LBH	14	.	NM_030915	exon2	c.C44T	p.S15L	TGAGATCGGCCAA	.	PASS	Atlas-SNP
LPHN3	23284	hgsc.bcm.edu	37	4	62800728	62800728	+	Silent	SNP	T	T	C	rs734644	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	131	126	0	0.992424	0	T|0.303;C|0.697	0.697	strong	.	LPHN3	800	.	NM_015236	exon11	c.T2079C	p.N693N	GGAGAATACAGAC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228560700	228560700	+	Silent	SNP	T	T	C	rs512253	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	62	88	0	0.984127	0	T|0.442;C|0.558	0.558	strong	OBSCN_ENST00000570156,rectum,carcinoma,0,5	OBSCN	2142	5	NM_001271223	exon105	c.T25092C	p.D8364D	GCTGGATGAGCCT	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	65	142	1	0.439189	0.00704225	A|0.796;G|0.204	0.204	strong	FSCB,NS,carcinoma,0,1	FSCB	173	1	NM_032135	exon1	c.T1139C	p.L380P	CCAAGAAGCTCTA	.	scavenged	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158368541	158368541	+	Missense_Mutation	SNP	A	A	G	rs34465440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	74	154	0	0.524823	0	A|0.662;G|0.338	0.338	strong	OR10T2,colon,carcinoma,-1,1	OR10T2	76	1	NM_001004475	exon1	c.T716C	p.V239A	CAGGTGACAAAGG	.	PASS	Atlas-SNP
IRS2	8660	hgsc.bcm.edu	37	13	110435231	110435231	+	Missense_Mutation	SNP	C	C	T	rs1805097	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	14	9	0	0.823529	0	C|0.663;T|0.337	0.337	strong	.	IRS2	44	.	NM_003749	exon1	c.G3170A	p.G1057D	GCGGCGCCCGGGC	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1425700	1425700	+	Silent	SNP	T	T	C	rs819980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	75	149	0	0.441176	0	T|0.629;C|0.371	0.371	strong	ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	NM_031921	exon14	c.T1401C	p.I467I	CCGCATTGACGTG	.	PASS	Atlas-SNP
ATAD3A	55210	hgsc.bcm.edu	37	1	1458944	1458944	+	Silent	SNP	C	C	T	rs112145664	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	106	139	0	0.569892	0	C|0.974;T|0.026	0.026	strong	.	ATAD3A	35	.	NM_018188	exon9	c.C1104T	p.L368L	TGTGCTCAGTGTA	.	PASS	Atlas-SNP
NANS	54187	hgsc.bcm.edu	37	9	100819192	100819192	+	Silent	SNP	C	C	T	rs3739670	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	56	110	0	0.615385	0	C|0.679;T|0.321	0.321	strong	.	NANS	24	.	NM_018946	exon1	c.C102T	p.D34D	CCTGGACGTAGCC	.	PASS	Atlas-SNP
TRMT12	55039	hgsc.bcm.edu	37	8	125463250	125463250	+	Missense_Mutation	SNP	T	T	C	rs3812475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	59	114	0	0.472	0	T|0.442;C|0.558	0.558	strong	.	TRMT12	28	.	NM_017956	exon1	c.T82C	p.W28R	GAGCCTTGGTTTA	.	PASS	Atlas-SNP
F11	2160	hgsc.bcm.edu	37	4	187209702	187209702	+	Silent	SNP	G	G	T	rs5971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	148	257	0	0.522968	0	G|0.914;T|0.086	0.086	strong	F11,NS,carcinoma,0,1	F11	65	1	NM_000128	exon15	c.G1812T	p.R604R	GGAGCGGCCAGGT	.	PASS	Atlas-SNP
ATP1A2	477	hgsc.bcm.edu	37	1	160104950	160104950	+	Silent	SNP	C	C	T	rs61734529	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	414	216	356	0	0.521739	0	C|0.978;T|0.022	0.022	strong	.	ATP1A2	167	.	NM_000702	exon15	c.C1980T	p.C660C	GGCATGCGTGGTG	.	PASS	Atlas-SNP
SF3A3	10946	hgsc.bcm.edu	37	1	38433762	38433762	+	Silent	SNP	G	G	A	rs59294668	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	500	294	478	2	0.588	0.0041841	G|0.983;A|0.017	0.017	strong	.	SF3A3	37	.	NM_006802	exon15	c.C1326T	p.N442N	AGCAGTGTTTGGG	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15850204	15850204	+	Silent	SNP	A	A	G	rs2272554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	148	132	0	0.986667	0	A|0.465;G|0.535	0.535	strong	.	MYH11	520	.	NM_001040114	exon15	c.T1764C	p.A588A	CTTCCCAGCATAA	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	42	104	0	0.42	0	T|0.905;A|0.095	0.095	strong	.	C5orf20	16	.	NM_130848	exon1	c.A403T	p.S135C	TGAAACTACAAAC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144946271	144946271	+	Missense_Mutation	SNP	C	C	T	rs58368323	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	34	95	0	0.472222	0	C|0.961;T|0.039	0.039	strong	.	EPPK1	199	.	NM_031308	exon1	c.G1151A	p.G384E	ACTAGCCCCTTCT	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132192295	132192295	+	Silent	SNP	G	G	A	rs156961	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	82	0	0.480519	0	G|0.594;A|0.406	0.406	strong	.	PLXNA4	873	.	NM_001105543	exon2	c.C1158T	p.L386L	CACCTTGAGCCAG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151949068	151949068	+	Missense_Mutation	SNP	C	C	G	rs3735156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	32	110	0	0.313726	0	C|0.828;G|0.172	0.172	strong	.	MLL3	1564	.	NM_170606	exon11	c.G1577C	p.R526P	TGTAAACGATCCA	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4712395	4712395	+	Silent	SNP	A	A	T	rs1132446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	43	53	0	0.544304	0	A|0.682;T|0.318	0.318	strong	.	PLD2	138	.	NM_001243108	exon5	c.A384T	p.R128R	CCACAGATTTGCC	.	PASS	Atlas-SNP
CC2D1A	54862	hgsc.bcm.edu	37	19	14023191	14023191	+	Silent	SNP	G	G	A	rs7250180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	72	91	0	1	0	G|0.919;A|0.081	0.081	strong	.	CC2D1A	67	.	NM_017721	exon3	c.G252A	p.P84P	AGACCCGGATGAG	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125484044	125484044	+	Silent	SNP	A	A	G	rs12276729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	82	235	0	0.388626	0	A|0.956;G|0.044	0.044	strong	.	STT3A	52	.	NM_152713	exon14	c.A1617G	p.T539T	CCGAACAATTTTA	.	PASS	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	562421	562421	+	Missense_Mutation	SNP	G	G	A	rs2242182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	55	101	0	0.423077	0	G|0.923;A|0.077	0.077	strong	.	RASSF7	22	.	NM_001143994	exon3	c.G467A	p.R156Q	ACCTGCGGGGCCT	.	PASS	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55119466	55119466	+	Silent	SNP	C	C	T	rs2304315	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	51	84	0	0.525773	0	C|0.935;T|0.065	0.065	strong	HEATR8_ENST00000421030,caecum,carcinoma,0,2	.	.	2	NM_001039464	exon3	c.C867T	p.S289S	TTTGAGCGTGACC	.	PASS	Atlas-SNP
ENDOU	8909	hgsc.bcm.edu	37	12	48110150	48110150	+	Silent	SNP	G	G	A	rs61734364	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	93	193	0	0.455882	0	A|0.024;G|0.975;T|0.000	0.024	strong	.	ENDOU	39	.	NM_001172439	exon6	c.C684T	p.D228D	GAAGGCGTCCTGC	.	PASS	Atlas-SNP
OR1D2	4991	hgsc.bcm.edu	37	17	2995994	2995994	+	Silent	SNP	T	T	C	rs769424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	532	263	490	1	0.494361	0.00204082	T|0.754;C|0.246	0.246	strong	.	OR1D2	39	.	NM_002548	exon1	c.A297G	p.T99T	GAGCTGTGTCAGA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62212781	62212781	+	Silent	SNP	T	T	C	rs17238189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	112	255	0	0.472574	0	T|0.930;C|0.070	0.070	strong	.	VPS13C	506	.	NM_020821	exon56	c.A7128G	p.Q2376Q	TGCCATTTGTGGC	.	PASS	Atlas-SNP
ANGPT4	51378	hgsc.bcm.edu	37	20	861853	861853	+	Silent	SNP	G	G	A	rs6086328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	48	121	0	0.432432	0	A|0.066;G|0.934	0.066	strong	.	ANGPT4	77	.	NM_015985	exon5	c.C912T	p.V304V	GGTGTAGACACCA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101719121	101719121	+	Missense_Mutation	SNP	G	G	A	rs79986761	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	16	84	0	0.183908	0	G|0.871;A|0.129	0.129	strong	.	PABPC1	76	.	NM_002568	exon10	c.C1441T	p.R481C	CAACACGCTGTGT	.	PASS	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	37	22	44594584	44594584	+	Silent	SNP	C	C	G	rs139152	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	86	177	0	0.457447	0	C|0.712;G|0.288	0.288	strong	.	PARVG	41	.	NM_001137606	exon12	c.C795G	p.P265P	CACTCCCAACTCT	.	PASS	Atlas-SNP
PECR	55825	hgsc.bcm.edu	37	2	216923679	216923679	+	Missense_Mutation	SNP	C	C	T	rs1429148	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	64	150	0	0.421053	0	C|0.862;T|0.138	0.138	strong	.	PECR	22	.	NM_018441	exon4	c.G445A	p.E149K	CATGCTCTTTCAT	.	PASS	Atlas-SNP
RGMA	56963	hgsc.bcm.edu	37	15	93588309	93588309	+	Silent	SNP	C	C	G	rs62021480	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	13	15	0	0.65	0	C|0.928;G|0.072	0.072	strong	RGMA_ENST00000557301,NS,carcinoma,0,4	RGMA	49	4	NM_001166283	exon4	c.G1296C	p.A432A	CGCAGCCGCCCTG	.	scavenged	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	37	1	55060362	55060362	+	Missense_Mutation	SNP	G	G	A	rs1702003	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	55	126	0	0.419847	0	G|0.813;A|0.187	0.187	strong	ACOT11_ENST00000371316,colon,carcinoma,+1,2	ACOT11	105	2	NM_147161	exon6	c.G605A	p.G202D	TTCAGGGCGGTGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505828	195505828	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	24	246	0	0.0821918	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.C12623A	p.P4208H	GGAAGAGGGGTGG	.	PASS	Atlas-SNP
DIS3	22894	hgsc.bcm.edu	37	13	73349359	73349359	+	Missense_Mutation	SNP	G	G	C	rs7332388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	241	287	1	0.99177	0.00348432	G|0.526;C|0.474	0.474	strong	DIS3,colon,carcinoma,+1,1	DIS3	103	1	NM_014953	exon6	c.C977G	p.T326R	CGTTCTGTCTCTT	.	PASS	Atlas-SNP
COTL1	23406	hgsc.bcm.edu	37	16	84651452	84651452	+	Silent	SNP	G	G	C	rs144159131	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	16	22	0	0.457143	0	G|0.999;C|0.001	0.001	strong	.	COTL1	17	.	NM_021149	exon1	c.C69G	p.A23A	GATGACGGCCGAG	.	PASS	Atlas-SNP
BCL6B	255877	hgsc.bcm.edu	37	17	6930927	6930927	+	Missense_Mutation	SNP	G	G	A	rs201522060	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	44	65	0	0.511628	0	.	.	weak	.	BCL6B	85	.	NM_181844	exon9	c.G1429A	p.G477R	ATTCTCGGGGGGC	.	PASS	Atlas-SNP
PACS2	23241	hgsc.bcm.edu	37	14	105843179	105843179	+	Silent	SNP	C	C	G	rs4074004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	150	0	1	0	C|0.880;G|0.120	0.120	strong	.	PACS2	75	.	NM_001100913	exon9	c.C876G	p.T292T	TGACACCCTGGAC	.	PASS	Atlas-SNP
C9orf172	389813	hgsc.bcm.edu	37	9	139740900	139740900	+	Silent	SNP	C	C	T	rs147735504	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	16	41	0	0.421053	0	C|0.994;T|0.006	0.006	strong	.	C9orf172	23	.	NM_001080482	exon1	c.C2034T	p.N678N	GTTCAACGCCTGC	.	PASS	Atlas-SNP
WDSUB1	151525	hgsc.bcm.edu	37	2	160104988	160104988	+	Missense_Mutation	SNP	T	T	C	rs74475652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	44	101	0	0.483516	0	T|0.958;C|0.042	0.042	strong	.	WDSUB1	39	.	NM_152528	exon10	c.A1168G	p.I390V	CTTCAATTTTCCT	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549589	32549589	+	Missense_Mutation	SNP	A	A	C	rs2308760	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	46	132	0	0.267442	0	.	.	weak	.	HLA-DRB1	41	.	NM_002124	exon3	c.T397G	p.S133A	TCTTTGAAGGATA	.	PASS	Atlas-SNP
BMP3	651	hgsc.bcm.edu	37	4	81952658	81952658	+	Missense_Mutation	SNP	C	C	G	rs61729824	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	78	0	0.456311	0	C|0.988;T|0.012	.	alt	.	BMP3	59	.	NM_001201	exon1	c.C220G	p.R74G	GCGGCCCGGACAC	.	PASS	Atlas-SNP
TMEM127	55654	hgsc.bcm.edu	37	2	96919642	96919642	+	Silent	SNP	C	C	T	rs3852673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	86	157	0	0.518072	0	C|0.874;T|0.126	0.126	strong	TMEM127,NS,carcinoma,-1,2	TMEM127	13	2	NM_001193304	exon4	c.G621A	p.A207A	CTCCAGCGCCTGC	.	PASS	Atlas-SNP
SCAF11	9169	hgsc.bcm.edu	37	12	46321417	46321417	+	Silent	SNP	G	G	A	rs11574971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	45	76	0	0.5	0	G|0.894;A|0.106	0.106	strong	.	SCAF11	145	.	NM_004719	exon11	c.C2067T	p.T689T	ATGTTCGGTCAGC	.	PASS	Atlas-SNP
ALDH18A1	5832	hgsc.bcm.edu	37	10	97371146	97371146	+	Silent	SNP	G	G	A	rs1804934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	98	189	0	0.453704	0	G|0.971;A|0.029	0.029	strong	.	ALDH18A1	63	.	NM_002860	exon16	c.C1977T	p.S659S	CACTTCGGAGGGG	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50720430	50720430	+	Silent	SNP	G	G	C	rs56110807	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	23	48	0	0.560976	0	G|0.953;C|0.047	0.047	strong	.	PLXNB2	172	.	NM_012401	exon20	c.C3198G	p.A1066A	GTTGTAGGCCTCT	.	PASS	Atlas-SNP
TNFSF12	8742	hgsc.bcm.edu	37	17	7460514	7460514	+	Silent	SNP	G	G	A	rs143039184	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	45	87	0	0.535714	0	G|0.999;A|0.001	0.001	strong	.	TNFSF12	20	.	NM_003809	exon7	c.G597A	p.A199A	CACTGCGGCGAGT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133899438	133899438	+	Silent	SNP	C	C	T	rs61742713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	77	141	0	0.516779	0	C|0.974;T|0.026	0.026	strong	.	TG	416	.	NM_003235	exon9	c.C1821T	p.T607T	CCAGACCTGTGAG	.	PASS	Atlas-SNP
KLHL4	56062	hgsc.bcm.edu	37	X	86877348	86877348	+	Silent	SNP	G	G	T	rs2273050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	348	162	373	1	0.465517	0.00268097	G|0.807;T|0.193	0.193	strong	.	KLHL4	263	.	NM_019117	exon5	c.G1062T	p.G354G	GGTGGGGCATGAT	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	46	121	0	0.414414	0	C|0.756;T|0.244	0.244	strong	.	PITRM1	109	.	NM_001242307	exon27	c.G3042A	p.K1014K	TGTGCTCTTCCCA	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	37	4	25806279	25806279	+	Missense_Mutation	SNP	T	T	C	rs16877591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	120	237	0	0.506329	0	T|0.933;C|0.067	0.067	strong	.	SEL1L3	62	.	NM_015187	exon10	c.A1660G	p.I554V	AGCTAATTTGGTG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37158363	37158363	+	Missense_Mutation	SNP	G	G	A	rs16903518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	92	157	0	0.502732	0	G|0.970;A|0.030	0.030	strong	.	C5orf42	422	.	NM_023073	exon39	c.C7775T	p.P2592L	GACCAAGGTTTCT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46860088	46860088	+	Silent	SNP	G	G	C	rs3747251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	108	113	0	0.990826	0	G|0.840;C|0.160	0.160	strong	CELSR1,NS,carcinoma,0,1	CELSR1	242	1	NM_014246	exon2	c.C3699G	p.A1233A	CAGCACGGCGGCC	.	PASS	Atlas-SNP
UCP3	7352	hgsc.bcm.edu	37	11	73717247	73717247	+	Missense_Mutation	SNP	C	C	T	rs2229707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	32	67	0	0.421053	0	C|0.964;T|0.036	0.036	strong	.	UCP3	31	.	NM_003356	exon3	c.G304A	p.V102I	GCTTGACGGAGTC	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	37	100	0	0.393617	0	C|0.678;A|0.322	0.322	strong	.	YTHDC2	118	.	NM_022828	exon5	c.C793A	p.R265R	GAGAGACGGGAAA	.	PASS	Atlas-SNP
BMP10	27302	hgsc.bcm.edu	37	2	69093288	69093288	+	Missense_Mutation	SNP	G	G	T	rs2231345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	349	168	346	0	0.481375	0	G|0.979;T|0.021	0.021	strong	.	BMP10	70	.	NM_014482	exon2	c.C750A	p.N250K	CAAAGGGTTATGC	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802806	57802806	+	Silent	SNP	C	C	T	rs2041109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	40	87	0	0.519481	0	C|0.799;T|0.201	0.201	strong	.	ZNF460	59	.	NM_006635	exon3	c.C897T	p.N299N	GCATAACAAGAGC	.	PASS	Atlas-SNP
ABHD12B	145447	hgsc.bcm.edu	37	14	51370852	51370852	+	Missense_Mutation	SNP	C	C	G	rs34800262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	127	238	0	0.540426	0	C|0.912;G|0.088	0.088	strong	ABHD12B_ENST00000337334,right_upper_lobe,carcinoma,-1,2	ABHD12B	53	2	NM_001206673	exon12	c.C1003G	p.P335A	ATCTTTCCTCCTG	.	PASS	Atlas-SNP
GPR97	222487	hgsc.bcm.edu	37	16	57717889	57717889	+	Silent	SNP	C	C	T	rs73554921	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	85	164	0	0.480226	0	C|0.954;T|0.046	0.046	strong	.	GPR97	74	.	NM_170776	exon9	c.C927T	p.H309H	GATCCACGTGGCC	.	PASS	Atlas-SNP
C2orf61	285051	hgsc.bcm.edu	37	2	47380145	47380145	+	Missense_Mutation	SNP	T	T	C	rs17036300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	54	0	0.471429	0	T|0.866;C|0.134	0.134	strong	.	C2orf61	31	.	NM_173649	exon2	c.A92G	p.Q31R	GTCTTTTGGGCTG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2156153	2156153	+	Missense_Mutation	SNP	C	C	G	rs28369051	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	296	138	223	0	0.466216	0	C|0.972;G|0.028	0.028	strong	.	PKD1	184	.	NM_000296	exon19	c.G7642C	p.E2548Q	CCACCTCGAAGTG	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66625470	66625470	+	Silent	SNP	G	G	A	rs3759785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	14	36	0	0.5	0	G|0.973;A|0.027	0.027	strong	.	DIS3L	175	.	NM_001143688	exon17	c.G2985A	p.E995E	GAGTGAGTTAGTG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33711077	33711077	+	Silent	SNP	C	C	T	rs58130645	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	62	99	0	0.488189	0	C|0.986;T|0.014	0.014	strong	.	URB1	176	.	NM_014825	exon26	c.G4449A	p.S1483S	AAACAGCGAGTGC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7040197	7040197	+	Missense_Mutation	SNP	T	T	C	rs62619829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	52	71	0	0.490566	0	T|0.986;C|0.014	0.014	strong	.	LAMA1	458	.	NM_005559	exon10	c.A1300G	p.T434A	CTCCTGTATAACC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179416556	179416556	+	Silent	SNP	A	A	C	rs11897366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	61	116	0	0.465649	0	A|0.880;C|0.120	0.120	strong	.	TTN	18412	.	NM_001267550	exon335	c.T91071G	p.T30357T	GAATCCAGTAACT	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	Missense_Mutation	SNP	C	C	A	rs9266825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	138	142	1	1	0.00704225	C|0.666;A|0.334	0.334	strong	.	MICA	21	.	NM_000247	exon7	c.C1118A	p.A373D	TGTCAGCTCTTGG	.	PASS	Atlas-SNP
IWS1	55677	hgsc.bcm.edu	37	2	128261099	128261099	+	Missense_Mutation	SNP	C	C	T	rs34785867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	184	176	0	0.994595	0	C|0.977;T|0.023	0.023	strong	.	IWS1	61	.	NM_017969	exon4	c.G1273A	p.V425I	CTGATACAGCATC	.	PASS	Atlas-SNP
G6PC2	57818	hgsc.bcm.edu	37	2	169764546	169764546	+	Missense_Mutation	SNP	C	C	G	rs2232328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	26	61	0	0.433333	0	C|0.776;G|0.224	0.224	strong	G6PC2,NS,carcinoma,0,1	G6PC2	44	1	NM_021176	exon5	c.C1025G	p.S342C	CCTACTCTGTTCA	.	PASS	Atlas-SNP
PCDHA1	56147	hgsc.bcm.edu	37	5	140167175	140167175	+	Missense_Mutation	SNP	T	T	C	rs61743801	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	81	159	0	0.487952	0	T|0.983;C|0.017	0.017	strong	.	PCDHA1	387	.	NM_031411	exon1	c.T1300C	p.S434P	TCGCCTTCGCTGT	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536138	1536138	+	Silent	SNP	T	T	C	rs114122805	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	41	66	0	0.532468	0	T|0.980;C|0.020	0.020	strong	.	PTX4	46	.	NM_001013658	exon3	c.A1224G	p.G408G	GTCGAATCCGCCC	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241830969	241830969	+	Silent	SNP	G	G	A	rs10171067	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	46	91	0	0.505495	0	G|0.490;A|0.510	0.510	strong	.	C2orf54	14	.	NM_001085437	exon2	c.C726T	p.S242S	CTGGGCGCTGGCC	.	PASS	Atlas-SNP
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	70	141	0	0.496454	0	G|0.396;N|0.000	0.396	strong	.	SWT1	88	.	NM_017673	exon5	c.A442G	p.I148V	CATGGAATTAAAA	.	PASS	Atlas-SNP
KCNN1	3780	hgsc.bcm.edu	37	19	18084775	18084775	+	Silent	SNP	G	G	A	rs75754669	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	5	4	1	0	0.8	0	G|0.990;A|0.010	0.010	strong	.	KCNN1	74	.	NM_002248	exon3	c.G78A	p.P26P	CCCTCCGGACCCT	.	PASS	Atlas-SNP
FCGR2B	2213	hgsc.bcm.edu	37	1	161645058	161645058	+	Missense_Mutation	SNP	T	T	G	rs148534844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	141	324	0	0.425982	0	T|0.992;G|0.008	0.008	strong	.	FCGR2B	33	.	NM_004001	exon6	c.T772G	p.Y258D	CCAGGATACCCTG	.	PASS	Atlas-SNP
PLCXD3	345557	hgsc.bcm.edu	37	5	41382536	41382536	+	Silent	SNP	C	C	T	rs16871312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	36	32	0	1	0	C|0.907;T|0.093	0.093	strong	.	PLCXD3	86	.	NM_001005473	exon2	c.G204A	p.V68V	TTTGGCCACAGTT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179474668	179474668	+	Missense_Mutation	SNP	G	G	A	rs16866412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	79	147	0	0.446328	0	G|0.932;A|0.068	0.068	strong	.	TTN	18412	.	NM_001267550	exon272	c.C51482T	p.A17161V	GCCTCCGCTGTAG	.	PASS	Atlas-SNP
RALGPS2	55103	hgsc.bcm.edu	37	1	178745947	178745947	+	Silent	SNP	T	T	G	rs6665037	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	65	85	0	0.546219	0	T|0.908;G|0.092	0.092	strong	.	RALGPS2	69	.	NM_152663	exon2	c.T48G	p.T16T	AGCTACTGCTTCT	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159647584	159647584	+	Silent	SNP	G	G	A	rs12110595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	17	85	0	0.34	0	G|0.929;A|0.071	0.071	strong	.	FNDC1	250	.	NM_032532	exon9	c.G1152A	p.A384A	GGATGCGCTACCA	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66542006	66542006	+	Missense_Mutation	SNP	G	G	T	rs745894	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	16	50	0	0.380952	0	G|0.804;T|0.196	0.196	strong	.	CCDC102B	92	.	NM_001093729	exon7	c.G1037T	p.C346F	TGATTTGTGAGTT	.	PASS	Atlas-SNP
EME1	146956	hgsc.bcm.edu	37	17	48453219	48453219	+	Missense_Mutation	SNP	G	G	A	rs114836030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	64	0	0.448718	0	G|0.994;A|0.006	0.006	strong	.	EME1	39	.	NM_152463	exon2	c.G650A	p.R217K	AGCAGAGACAAGC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28424100	28424100	+	Silent	SNP	C	C	T	rs9806328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	37	76	0	0.402174	0	C|0.864;T|0.136	0.136	strong	.	HERC2	501	.	NM_004667	exon59	c.G9096A	p.T3032T	GGGCACCGTCCCG	.	PASS	Atlas-SNP
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316841	39316841	+	Missense_Mutation	SNP	A	A	T	rs444509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	147	171	0	1	0	A|0.912;T|0.088	0.088	strong	.	KRTAP4-4	21	.	NM_032524	exon1	c.T103A	p.C35S	GGCAGCAGGTGGT	.	PASS	Atlas-SNP
FAM183A	440585	hgsc.bcm.edu	37	1	43621973	43621973	+	Missense_Mutation	SNP	C	C	T	rs59274667	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	60	99	0	0.5	0	C|0.996;T|0.004	0.004	strong	.	FAM183A	28	.	NM_001101376	exon4	c.C394T	p.H132Y	GATGATCACCACA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8196643	8196643	+	Silent	SNP	G	G	A	rs61744943	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	81	157	0	0.457627	0	G|0.823;A|0.177	0.177	strong	.	FBN3	300	.	NM_032447	exon14	c.C1785T	p.R595R	CTGGCAGCGGAAG	.	PASS	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	37	7	31691582	31691582	+	Missense_Mutation	SNP	G	G	A	rs80081783	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	77	168	0	0.503268	0	G|0.995;A|0.005	0.005	strong	LOC223075,right_lower_lobe,carcinoma,-1,2	CCDC129	127	2	NM_001257968	exon13	c.G2819A	p.R940H	CGTTACGTGAGGC	.	PASS	Atlas-SNP
RIN1	9610	hgsc.bcm.edu	37	11	66102088	66102088	+	Silent	SNP	G	G	A	rs3814740	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	22	9	0	1	0	G|0.847;A|0.153	0.153	strong	.	RIN1	64	.	NM_004292	exon6	c.C1182T	p.P394P	GGGCTCGGGCCCA	.	PASS	Atlas-SNP
ERI2	112479	hgsc.bcm.edu	37	16	20809240	20809240	+	Missense_Mutation	SNP	G	G	T	rs61746707	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	114	189	0	0.459677	0	G|0.987;T|0.013	0.013	strong	.	ERI2	50	.	NM_001142725	exon9	c.C1882A	p.Q628K	TTTCTTGGTATTT	.	PASS	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95262890	95262890	+	Silent	SNP	T	T	A	rs61865305	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	19	62	0	0.339286	0	T|0.944;A|0.056	0.056	strong	.	CEP55	35	.	NM_018131	exon3	c.T204A	p.A68A	TGAGGCTGAGAAG	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126715436	126715436	+	Missense_Mutation	SNP	C	C	T	rs3781411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	106	176	0	0.524752	0	C|0.882;T|0.118	0.118	strong	.	CTBP2	100	.	NM_022802	exon1	c.G893A	p.R298Q	TCCGCCCGCAGAA	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595018	55595018	+	Silent	SNP	A	A	G	rs61745634	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	49	183	0	0.362963	0	A|0.993;G|0.007	0.007	strong	OR5L2,NS,carcinoma,0,2	OR5L2	135	2	NM_001004739	exon1	c.A324G	p.G108G	ATGTGGAGTCACT	.	PASS	Atlas-SNP
FRMPD4	9758	hgsc.bcm.edu	37	X	12725701	12725701	+	Silent	SNP	C	C	G	rs6641078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	98	202	0	0.466667	0	C|0.852;G|0.148	0.148	strong	.	FRMPD4	214	.	NM_014728	exon13	c.C1401G	p.V467V	CCACGTCAACAGG	.	PASS	Atlas-SNP
C7orf65	401335	hgsc.bcm.edu	37	7	47698737	47698737	+	Missense_Mutation	SNP	A	A	C	rs114109572	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	100	0	0.421687	0	A|0.999;C|0.001	0.001	strong	.	C7orf65	18	.	NM_001123065	exon3	c.A367C	p.T123P	GGTTTCACTGACC	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	113	268	0	0.470833	0	T|0.685;G|0.315	0.315	strong	.	XRCC4	37	.	NM_022406	exon8	c.T927G	p.S309S	GACGTCTAAAAAG	.	PASS	Atlas-SNP
FAM78B	149297	hgsc.bcm.edu	37	1	166039898	166039898	+	Silent	SNP	C	C	G	rs41269662	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	60	67	0	1	0	C|0.820;G|0.180	0.180	strong	.	FAM78B	51	.	NM_001017961	exon2	c.G366C	p.V122V	CAGGGTCACAGTT	.	PASS	Atlas-SNP
APOF	319	hgsc.bcm.edu	37	12	56755300	56755300	+	Silent	SNP	A	A	C	rs11575217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	53	150	0	0.420635	0	A|0.945;C|0.055	0.055	strong	.	APOF	13	.	NM_001638	exon2	c.T690G	p.A230A	CATCCCAGCCATG	.	PASS	Atlas-SNP
LAIR2	3904	hgsc.bcm.edu	37	19	55019371	55019371	+	Missense_Mutation	SNP	C	C	G	rs61737870	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	57	110	0	0.428571	0	C|0.897;G|0.103	0.103	strong	.	LAIR2	30	.	NM_002288	exon3	c.C336G	p.H112Q	TGAGCACAGTGAC	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60776209	60776209	+	Missense_Mutation	SNP	C	C	T	rs11230563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	89	0	1	0	C|0.622;T|0.378	0.378	strong	.	CD6	122	.	NM_006725	exon4	c.C673T	p.R225W	ATCCACCGGGACC	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	114111156	114111156	+	Missense_Mutation	SNP	C	C	T	rs73701331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	63	109	0	0.504	0	C|0.990;T|0.010	0.010	strong	.	CSMD3	2325	.	NM_052900	exon5	c.G746A	p.S249N	ATGCCACTGGATC	.	PASS	Atlas-SNP
CASC1	55259	hgsc.bcm.edu	37	12	25267613	25267613	+	Missense_Mutation	SNP	T	T	C	rs34164267	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	39	67	0	0.557143	0	T|0.970;C|0.030	0.030	strong	.	CASC1	146	.	NM_001082972	exon13	c.A1762G	p.T588A	TCTCAGTAAATAC	.	PASS	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170136808	170136808	+	Silent	SNP	G	G	T	rs61745740	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	45	96	0	0.424528	0	G|0.999;T|0.001	0.001	strong	.	METTL11B	18	.	NM_001136107	exon4	c.G762T	p.L254L	TGGGCTGGTGGTG	.	PASS	Atlas-SNP
FCRL2	79368	hgsc.bcm.edu	37	1	157736673	157736673	+	Silent	SNP	C	C	T	rs34445670	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	336	150	325	0	0.446429	0	C|0.983;T|0.017	0.017	strong	.	FCRL2	104	.	NM_030764	exon7	c.G1251A	p.L417L	ATACAACAGCAAA	.	PASS	Atlas-SNP
PHC2	1912	hgsc.bcm.edu	37	1	33820520	33820520	+	Silent	SNP	G	G	A	rs79627057	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	46	90	0	0.418182	0	G|0.981;A|0.019	0.019	strong	.	PHC2	78	.	NM_198040	exon7	c.C1311T	p.P437P	GCCCTCGGGATGT	.	PASS	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282685	59282685	+	Silent	SNP	A	A	G	rs76175424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	87	159	0	0.514793	0	A|0.966;G|0.034	0.034	strong	.	OR4D9	47	.	NM_001004711	exon1	c.A300G	p.Q100Q	CACTCAAATGTTC	.	PASS	Atlas-SNP
CATSPER3	347732	hgsc.bcm.edu	37	5	134343799	134343799	+	Silent	SNP	A	A	G	rs177252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	113	222	0	0.439689	0	A|0.562;G|0.438	0.438	strong	.	CATSPER3	38	.	NM_178019	exon4	c.A645G	p.A215A	GGCTGCAGCTTTT	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673015	7673015	+	Silent	SNP	G	G	A	rs5864	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	20	87	0	0.3125	0	G|0.325;A|0.675	0.675	strong	PPFIBP2,NS,carcinoma,+2,1	PPFIBP2	87	1	NM_003621	exon23	c.G2376A	p.E792E	ACAGGAGAAGCGA	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151674270	151674270	+	Missense_Mutation	SNP	G	G	A	rs34713284	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	35	60	0	0.416667	0	G|0.924;A|0.076	0.076	strong	.	AKAP12	170	.	NM_005100	exon4	c.G4744A	p.V1582M	GCTCACGTGATAA	.	PASS	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73625286	73625286	+	Silent	SNP	G	G	A	rs820190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	57	112	0	0.478992	0	G|0.746;A|0.254	0.254	strong	.	RECQL5	77	.	NM_004259	exon16	c.C2217T	p.S739S	AAGGGAGCTGCCC	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	95	141	0	0.484694	0	C|0.737;A|0.262	0.262	strong	.	TMEM132B	207	.	NM_052907	exon2	c.C150A	p.S50S	GGAGTCCTTTTTC	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147788709	147788709	+	Missense_Mutation	SNP	C	C	T	rs10013280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	142	252	2	0.518248	0.00793651	C|0.648;T|0.352	0.352	strong	TTC29,NS,carcinoma,0,1	TTC29	63	1	NM_031956	exon8	c.G826A	p.A276T	AAGAGGCTTCCGC	.	scavenged	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220404726	220404726	+	Silent	SNP	G	G	A	rs1043832	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	146	1	1	0.00684932	G|0.620;C|0.000;A|0.380	0.380	strong	.	CHPF	56	.	NM_024536	exon4	c.C1707T	p.H569H	TGCCACGTGGGCC	.	PASS	Atlas-SNP
ARID2	196528	hgsc.bcm.edu	37	12	46245077	46245077	+	Silent	SNP	G	G	A	rs7296694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	58	116	0	0.483333	0	G|0.905;A|0.095	0.095	strong	.	ARID2	311	.	NM_152641	exon15	c.G3171A	p.S1057S	TGAGTCGAGTCTG	.	PASS	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	37	19	50358133	50358133	+	Silent	SNP	T	T	G	rs75478119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	148	0	1	0	T|0.654;G|0.346	0.346	strong	PTOV1,NS,carcinoma,+1,1	PTOV1	41	1	NM_017432	exon4	c.T438G	p.P146P	GATCCCTCAGCAG	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	715990	715990	+	Missense_Mutation	SNP	G	G	A	rs7190775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	32	31	0	0.666667	0	G|0.423;A|0.577	0.577	strong	.	WDR90	107	.	NM_145294	exon36	c.G4475A	p.R1492H	GTGGCCGCCCTGA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158626382	158626382	+	Missense_Mutation	SNP	G	G	A	rs34706737	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	30	83	0	0.416667	0	G|0.976;A|0.024	0.024	strong	.	SPTA1	720	.	NM_003126	exon20	c.C2870T	p.A957V	CGCAGAGCTTTCA	.	PASS	Atlas-SNP
KLHL24	54800	hgsc.bcm.edu	37	3	183368891	183368891	+	Silent	SNP	C	C	T	rs2293031	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	88	147	0	0.56051	0	C|0.626;T|0.374	0.374	strong	.	KLHL24	56	.	NM_017644	exon3	c.C747T	p.H249H	GTTACACGAGCTC	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201282334	201282334	+	Missense_Mutation	SNP	G	G	A	rs34626929	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	126	223	0	0.557522	0	G|0.974;A|0.026	0.026	strong	.	PKP1	127	.	NM_001005337	exon3	c.G347A	p.R116H	ACAGGCGCTTCAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264823	1264823	+	Missense_Mutation	SNP	T	T	C	rs4963031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	490	489	518	1	0.997959	0.0019305	T|0.297;C|0.703	0.703	strong	MUC5B,brain,glioma,0,2	MUC5B	473	2	NM_002458	exon31	c.T6713C	p.L2238P	ACACCCTAGCAGC	.	PASS	Atlas-SNP
ZNF780A	284323	hgsc.bcm.edu	37	19	40581677	40581677	+	Silent	SNP	G	G	A	rs337795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	89	0	1	0	G|0.928;A|0.072	0.072	strong	.	ZNF780A	156	.	NM_001142577	exon6	c.C675T	p.N225N	ACATTCGTTACAT	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122437536	122437536	+	Missense_Mutation	SNP	C	C	T	rs61732767	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	51	164	0	0.369565	0	C|0.990;T|0.010	0.010	strong	.	PARP14	242	.	NM_017554	exon14	c.C4538T	p.A1513V	TTGAGGCGATGAT	.	PASS	Atlas-SNP
RBPJL	11317	hgsc.bcm.edu	37	20	43938284	43938284	+	Missense_Mutation	SNP	G	G	A	rs35032855	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	39	119	0	0.419355	0	G|0.988;A|0.012	0.012	strong	.	RBPJL	67	.	NM_014276	exon3	c.G209A	p.R70Q	CTGTGCGGATCCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144942097	144942097	+	Silent	SNP	G	G	A	rs73375119	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	132	247	1	0.507692	0.00404858	G|0.984;A|0.016	0.016	strong	EPPK1,NS,NS,-1,1	EPPK1	199	1	NM_031308	exon1	c.C5325T	p.H1775H	CAACACGTGTCTC	.	PASS	Atlas-SNP
CASC5	57082	hgsc.bcm.edu	37	15	40916272	40916272	+	Silent	SNP	G	G	A	rs34758606	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	55	75	0	0.561224	0	G|0.991;A|0.009	0.009	strong	.	CASC5	269	.	NM_170589	exon11	c.G3888A	p.A1296A	AAAAGCGCAAGTT	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053849	95053849	+	Silent	SNP	T	T	C	rs6113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	38	81	0	0.426966	0	C|0.249;N|0.000	0.249	strong	.	SERPINA5	69	.	NM_000624	exon3	c.T150C	p.F50F	TACCTTTGACCTC	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512120	169512120	+	Silent	SNP	G	G	A	rs6016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	75	161	0	0.477707	0	G|0.758;A|0.242	0.242	strong	.	F5	301	.	NM_000130	exon13	c.C2208T	p.I736I	TGACCTGATTCCT	.	PASS	Atlas-SNP
CELA3A	10136	hgsc.bcm.edu	37	1	22328207	22328207	+	Missense_Mutation	SNP	G	G	A	rs11541414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	135	270	0	0.511364	0	G|0.950;A|0.050	0.050	strong	.	CELA3A	35	.	NM_005747	exon1	c.G40A	p.V14I	GTGGCCGTTGGTA	.	PASS	Atlas-SNP
C19orf35	374872	hgsc.bcm.edu	37	19	2278755	2278755	+	Missense_Mutation	SNP	C	C	T	rs73518414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	34	43	0	0.539683	0	C|0.681;T|0.319	0.319	strong	.	C19orf35	18	.	NM_198532	exon3	c.G440A	p.R147H	ATGGTACGGAGGC	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139390958	139390958	+	Silent	SNP	T	T	C	rs11574911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	11	26	0	0.354839	0	T|0.968;C|0.032	0.032	strong	NOTCH1,NS,lymphoid_neoplasm,0,1	NOTCH1	1980	1	NM_017617	exon34	c.A7233G	p.P2411P	TGGTGGTGGCGGC	.	PASS	Atlas-SNP
DSC2	1824	hgsc.bcm.edu	37	18	28681903	28681903	+	Missense_Mutation	SNP	T	T	C	rs868333	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	5	25	0	0.5	0	T|0.923;C|0.077	0.077	strong	.	DSC2	168	.	NM_024422	exon1	c.A32G	p.N11S	GCTCCGTTCCAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509322	195509322	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	11	127	0	0.0621469	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9129T	p.V3043V	GTCGGTGACAGGA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537249	88537249	+	Silent	SNP	T	T	C	rs371359066		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	41	227	11	0.158915	0.0484582	.	.	weak	DSPP,NS,carcinoma,0,5	DSPP	174	5	NM_014208	exon5	c.T3435C	p.S1145S	CAGCAGTGACAGC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511396	195511396	+	Missense_Mutation	SNP	G	G	A	rs201453005	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	63	381	1	0.45	0.00262467	G|0.991;A|0.008	0.008	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7055T	p.P2352L	TGAAGAGGGGTGG	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844265	52844265	+	Missense_Mutation	SNP	T	T	C	rs652423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	383	181	303	0	0.472585	0	T|0.604;C|0.396	0.396	strong	.	KRT6B	90	.	NM_005555	exon2	c.A680G	p.N227S	ACGATGTTGTCCA	.	PASS	Atlas-SNP
TMPRSS4	56649	hgsc.bcm.edu	37	11	117978578	117978578	+	Missense_Mutation	SNP	G	G	A	rs1894176	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	35	57	0	0.686275	0	G|0.955;A|0.045	0.045	strong	TMPRSS4,NS,carcinoma,-1,1	TMPRSS4	46	1	NM_019894	exon6	c.G530A	p.R177Q	GCATGCGGAACTC	.	PASS	Atlas-SNP
C1orf53	388722	hgsc.bcm.edu	37	1	197872001	197872001	+	Silent	SNP	G	G	A	rs73083807	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	7	20	0	0.466667	0	G|0.972;A|0.028	0.028	strong	.	C1orf53	18	.	NM_001024594	exon1	c.G222A	p.A74A	AACCGCGGCGGAG	.	PASS	Atlas-SNP
FOXP4	116113	hgsc.bcm.edu	37	6	41533579	41533579	+	Silent	SNP	C	C	A	rs2104506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	115	185	2	0.552885	0.0108108	C|0.647;A|0.353	0.353	strong	FOXP4_ENST00000373060,NS,carcinoma,0,2	FOXP4	83	2	NM_001012427	exon2	c.C81A	p.A27A	GCAAGCCGATGGC	.	scavenged	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803947	34803947	+	Silent	SNP	C	C	T	rs4259246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	35	75	0	0.426829	0	C|0.564;T|0.436	0.436	strong	.	UHRF1BP1	102	.	NM_017754	exon8	c.C855T	p.A285A	ACCAGCCCCCAGT	.	PASS	Atlas-SNP
AHR	196	hgsc.bcm.edu	37	7	17379157	17379157	+	Missense_Mutation	SNP	G	G	A	rs4986826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	27	53	0	0.627907	0	G|0.974;A|0.026	0.026	strong	.	AHR	89	.	NM_001621	exon10	c.G1708A	p.V570I	GGTGAGGTTGACT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228404864	228404864	+	Missense_Mutation	SNP	G	G	A	rs141921462	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	57	94	0	0.626374	0	G|0.996;A|0.004	0.004	strong	.	OBSCN	2142	.	NM_001271223	exon8	c.G2528A	p.R843H	GTGAGCGCTTCTT	.	PASS	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	37	16	20476974	20476974	+	Missense_Mutation	SNP	C	C	T	rs13332099	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	521	179	502	0	0.34357	0	C|0.993;T|0.007	0.007	strong	ACSM2A,NS,carcinoma,-2,1	ACSM2A	120	1	NM_001010845	exon4	c.C313T	p.R105C	CTGCAGCGTGGGG	.	PASS	Atlas-SNP
DKK3	27122	hgsc.bcm.edu	37	11	12023868	12023868	+	Silent	SNP	A	A	G	rs79628149	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	164	362	1	0.454294	0.00276243	A|0.991;G|0.009	0.009	strong	.	DKK3	35	.	NM_001018057	exon2	c.T330C	p.H110H	GTGCACATGGATG	.	PASS	Atlas-SNP
LYPD1	116372	hgsc.bcm.edu	37	2	133403647	133403647	+	Missense_Mutation	SNP	T	T	C	rs139508764	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	85	180	0	0.537975	0	T|0.998;C|0.002	0.002	strong	.	LYPD1	11	.	NM_144586	exon3	c.A397G	p.K133E	CTAATTTGAGGAA	.	PASS	Atlas-SNP
VLDLR	7436	hgsc.bcm.edu	37	9	2643175	2643175	+	Missense_Mutation	SNP	G	G	C	rs34080096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	22	40	0	0.578947	0	G|0.996;C|0.004	0.004	strong	.	VLDLR	68	.	NM_003383	exon5	c.G464C	p.S155T	CATGTAGTCCCGA	.	PASS	Atlas-SNP
WDR36	134430	hgsc.bcm.edu	37	5	110432841	110432841	+	Silent	SNP	T	T	C	rs17132775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	165	0	1	0	T|0.951;C|0.049	0.049	strong	.	WDR36	111	.	NM_139281	exon3	c.T423C	p.Y141Y	TGCTTATGGAAAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105420927	105420927	+	Silent	SNP	A	A	G	rs879210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	74	0	1	0	A|0.677;G|0.323	0.323	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.T861C	p.P287P	GTCCCTAGGTTCG	.	PASS	Atlas-SNP
GUCA1A	2978	hgsc.bcm.edu	37	6	42141360	42141360	+	Silent	SNP	C	C	T	rs116114043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	19	54	0	0.527778	0	C|0.995;T|0.005	0.005	strong	.	GUCA1A	18	.	NM_000409	exon3	c.C9T	p.N3N	GGGCAACGTGATG	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30702525	30702525	+	Missense_Mutation	SNP	A	A	C	rs323344	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	169	159	1	1	0.00628931	A|0.701;C|0.299	0.299	strong	.	TEX15	350	.	NM_031271	exon1	c.T4009G	p.L1337V	CTGATAACTGAGG	.	PASS	Atlas-SNP
CAP2	10486	hgsc.bcm.edu	37	6	17426846	17426846	+	Silent	SNP	T	T	C	rs59744718	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	117	0	1	0	T|0.967;C|0.033	0.033	strong	.	CAP2	61	.	NM_006366	exon3	c.T147C	p.F49F	AGCCTTTGACAAG	.	PASS	Atlas-SNP
FBXO42	54455	hgsc.bcm.edu	37	1	16577908	16577908	+	Missense_Mutation	SNP	G	G	C	rs12069239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	185	183	0	1	0	G|0.654;C|0.346	0.346	strong	.	FBXO42	53	.	NM_018994	exon10	c.C1411G	p.P471A	CTTCAGGAGCAGA	.	PASS	Atlas-SNP
WFDC3	140686	hgsc.bcm.edu	37	20	44417593	44417593	+	Missense_Mutation	SNP	C	C	A	rs73122754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	70	176	0	0.510949	0	C|0.952;A|0.048	0.048	strong	.	WFDC3	18	.	NM_080614	exon3	c.G188T	p.R63L	CAGATCCGACCAC	.	PASS	Atlas-SNP
SLC35B2	347734	hgsc.bcm.edu	37	6	44223292	44223292	+	Silent	SNP	C	C	T	rs35112470	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	72	114	0	0.571429	0	C|0.977;T|0.023	0.023	strong	.	SLC35B2	40	.	NM_178148	exon4	c.G450A	p.T150T	CGAGTCCGTAAAG	.	PASS	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078488	2078488	+	Silent	SNP	T	T	C	rs2074894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	21	63	0	0.456522	0	T|0.597;C|0.403	0.403	strong	MOBKL2A,rectum,carcinoma,0,1	.	.	1	NM_130807	exon3	c.A72G	p.P24P	GGTGCCTGGCTCA	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241979550	241979550	+	Silent	SNP	T	T	C	rs7571117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	57	88	0	0.548077	0	T|0.554;C|0.446	0.446	strong	.	SNED1	76	.	NM_001080437	exon7	c.T1104C	p.N368N	GGAGAATGGCTCT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170088351	170088351	+	Silent	SNP	G	G	A	rs2302694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	111	191	0	0.620112	0	G|0.806;A|0.194	0.194	strong	.	LRP2	751	.	NM_004525	exon31	c.C5100T	p.S1700S	ATTCACGGCTGCA	.	PASS	Atlas-SNP
SYCP2	10388	hgsc.bcm.edu	37	20	58476774	58476774	+	Silent	SNP	G	G	A	rs6027186	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	50	117	0	0.510204	0	G|0.900;A|0.100	0.100	strong	SYCP2,caecum,carcinoma,0,1	SYCP2	204	1	NM_014258	exon15	c.C1125T	p.D375D	TGATGCGTCAAAA	.	PASS	Atlas-SNP
LRRC3B	116135	hgsc.bcm.edu	37	3	26751526	26751526	+	Silent	SNP	C	C	T	rs141944883		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	3	116	0	0.0218978	0	C|1.000;T|0.000	0.000	weak	LRRC3B,NS,NS,0,1	LRRC3B	51	1	NM_052953	exon2	c.C363T	p.S121S	CTTGTCCGACAAT	.	scavenged	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957311	111957311	+	Missense_Mutation	SNP	G	G	C	rs10067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	78	183	0	0.430939	0	G|0.785;C|0.214	0.214	strong	OVGP1_ENST00000369728,NS,carcinoma,-1,3	OVGP1	177	3	NM_002557	exon11	c.C1812G	p.H604Q	CCTGGGGTGAGTG	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	70934974	70934974	+	Missense_Mutation	SNP	T	T	C	rs75533009		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	46	93	0	0.254144	0	.	.	weak	.	HYDIN	788	.	NM_001270974	exon53	c.A8981G	p.E2994G	CCGTACTCAGCCT	.	PASS	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95542476	95542476	+	Missense_Mutation	SNP	C	C	T	rs1052809	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	9	59	2	0.152542	0.0338983	C|0.667;T|0.333	0.333	strong	TEKT4,NS,carcinoma,0,1	TEKT4	72	1	NM_144705	exon6	c.C1270T	p.R424C	CGTACTCGCTACC	.	scavenged	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581811	99581811	+	Missense_Mutation	SNP	C	C	T	rs4645656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	67	85	1	0.626168	0.0117647	C|0.769;T|0.231	0.231	strong	ZNF782,rectum,carcinoma,-1,2	ZNF782	64	2	NM_001001662	exon6	c.G494A	p.R165H	ACATTACGCTCAT	.	scavenged	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1686410	1686410	+	Missense_Mutation	SNP	T	T	C	rs9902398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	46	105	0	0.446602	0	T|0.220;C|0.780	0.780	strong	.	SMYD4	50	.	NM_052928	exon10	c.A2180G	p.Y727C	ACCACGTAGAGAC	.	PASS	Atlas-SNP
ULBP1	80329	hgsc.bcm.edu	37	6	150285209	150285209	+	Silent	SNP	G	G	C	rs61742437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	74	150	0	0.490066	0	G|0.819;C|0.181	0.181	strong	.	ULBP1	25	.	NM_025218	exon1	c.G24C	p.A8A	CCCCGCGTTCCTT	.	PASS	Atlas-SNP
KLK4	9622	hgsc.bcm.edu	37	19	51412668	51412668	+	Missense_Mutation	SNP	A	A	C	rs1654551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	52	107	0	0.396947	0	A|0.875;C|0.125	0.125	strong	KLK4,colon,carcinoma,+2,2	KLK4	46	2	NM_004917	exon2	c.T64G	p.S22A	CGAGCGATCCTGA	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862937	5862937	+	Missense_Mutation	SNP	C	C	A	rs4495918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	79	157	0	0.509677	0	C|0.611;A|0.389	0.389	strong	.	OR52E6	70	.	NM_001005167	exon1	c.G191T	p.C64F	GCCAGGCAGTAGT	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117104368	117104368	+	Silent	SNP	G	G	A	rs73548990	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	34	79	0	0.68	0	G|0.978;A|0.022	0.022	strong	.	AKNA	119	.	NM_030767	exon20	c.C3795T	p.P1265P	ATCAGCGGGAGGC	.	PASS	Atlas-SNP
RPUSD1	113000	hgsc.bcm.edu	37	16	836111	836111	+	Missense_Mutation	SNP	G	G	T	rs112366818	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	71	59	0	0.986111	0	G|0.962;T|0.038	0.038	strong	.	RPUSD1	19	.	NM_058192	exon6	c.C778A	p.P260T	GGTCAGGGTCGGG	.	PASS	Atlas-SNP
MIER2	54531	hgsc.bcm.edu	37	19	307282	307282	+	Missense_Mutation	SNP	T	T	C	rs35042658	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	85	133	0	0.52795	0	T|0.946;C|0.054	0.054	strong	.	MIER2	51	.	NM_017550	exon13	c.A1453G	p.S485G	CATGGCTGGAGAT	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2166538	2166538	+	Missense_Mutation	SNP	G	G	A	rs149022148	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	45	104	0	0.529412	0	G|0.961;A|0.039	0.039	strong	PKD1,caecum,carcinoma,0,1	PKD1	184	1	NM_000296	exon8	c.C1714T	p.P572S	CCACGGGCTCGTG	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156882996	156882996	+	Silent	SNP	G	G	C	rs822441	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	135	131	0	0.978261	0	G|0.714;C|0.285	0.285	strong	PEAR1,NS,carcinoma,+2,1	PEAR1	118	1	NM_001080471	exon19	c.G2433C	p.P811P	CCCTCCGAGCTAC	.	PASS	Atlas-SNP
LRRC36	55282	hgsc.bcm.edu	37	16	67397580	67397580	+	Missense_Mutation	SNP	G	G	C	rs9922085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	40	159	0	0.363636	0	G|0.813;C|0.187	0.187	strong	.	LRRC36	68	.	NM_018296	exon6	c.G665C	p.R222P	GTACACGTGATCA	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91622249	91622249	+	Missense_Mutation	SNP	C	C	A	rs138567837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	33	87	0	0.445946	0	C|1.000;A|0.000	0.000	strong	.	AKAP9	788	.	NM_005751	exon5	c.C456A	p.D152E	ACAAGACAGTCCG	.	PASS	Atlas-SNP
BIN2	51411	hgsc.bcm.edu	37	12	51696500	51696500	+	Silent	SNP	G	G	A	rs7975715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	66	136	0	0.455172	0	G|0.868;A|0.132	0.132	strong	.	BIN2	58	.	NM_016293	exon4	c.C282T	p.D94D	ATGACCGTCCCAC	.	PASS	Atlas-SNP
DOK6	220164	hgsc.bcm.edu	37	18	67365668	67365668	+	Silent	SNP	A	A	G	rs4426448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	124	112	0	1	0	A|0.522;G|0.478	0.478	strong	.	DOK6	56	.	NM_152721	exon5	c.A438G	p.T146T	GCCTACACCAAAC	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125316033	125316033	+	Silent	SNP	T	T	C	rs1341042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	80	195	0	0.338983	0	T|0.470;C|0.530	0.530	strong	.	OR1N2	51	.	NM_001004457	exon1	c.T585C	p.Y195Y	TTTCTATTGTGAT	.	PASS	Atlas-SNP
LIPH	200879	hgsc.bcm.edu	37	3	185229464	185229464	+	Silent	SNP	T	T	C	rs61730237	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	34	57	0	0.492754	0	T|0.597;C|0.403	0.403	strong	.	LIPH	56	.	NM_139248	exon9	c.A1116G	p.K372K	GTGATATTTCTGA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129907544	129907544	+	Missense_Mutation	SNP	G	G	C	rs2240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	375	156	336	0	0.416	0	G|0.776;C|0.224	0.224	strong	.	MKI67	363	.	NM_002417	exon13	c.C2560G	p.L854V	TCTCCAGAGAAGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	352	33	163	0	0.09375	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.T3335C	p.L1112P	CCAGGCTGGTGGT	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	94	0	0.52	0	C|0.742;G|0.258	0.258	strong	.	FRMD4B	90	.	NM_015123	exon6	c.G519C	p.E173D	TTCGCTCTCTACT	.	PASS	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	41	142	0	0.359649	0	G|0.955;A|0.045	0.045	strong	.	PPARGC1A	129	.	NM_013261	exon8	c.C1425T	p.D475D	TTCGTCGTCAAAA	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119421963	119421963	+	Silent	SNP	C	C	T	rs7612861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	55	94	0	0.45082	0	C|0.824;T|0.176	0.176	strong	C3orf15,NS,carcinoma,0,1	.	.	1	NM_033364	exon1	c.C18T	p.T6T	AGTAACCATCGAG	.	PASS	Atlas-SNP
SULF2	55959	hgsc.bcm.edu	37	20	46292910	46292910	+	Missense_Mutation	SNP	C	C	T	rs10048853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	57	92	0	0.537736	0	C|0.983;T|0.017	0.017	strong	.	SULF2	131	.	NM_001161841	exon15	c.G2021A	p.R674H	TTGAGGCGGCCTT	.	PASS	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	183967500	183967500	+	Silent	SNP	A	A	C	rs2233461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	34	51	0	0.586207	0	A|0.943;C|0.057	0.057	strong	.	ECE2	303	.	NM_014693	exon1	c.A18C	p.A6A	AGGGGCAGGTAGG	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61448933	61448933	+	Silent	SNP	C	C	A	rs2273078	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	19	30	0	0.422222	0	C|0.816;A|0.184	0.184	strong	.	COL9A3	70	.	NM_001853	exon2	c.C93A	p.P31P	ACTCCCCGGCCCC	.	PASS	Atlas-SNP
PBLD	64081	hgsc.bcm.edu	37	10	70044031	70044031	+	Missense_Mutation	SNP	T	T	C	rs4142048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	103	0	1	0	T|0.753;C|0.247	0.247	strong	.	PBLD	53	.	NM_022129	exon10	c.A770G	p.H257R	CCTCGGTGGGAAC	.	PASS	Atlas-SNP
OR10Q1	219960	hgsc.bcm.edu	37	11	57996084	57996084	+	Silent	SNP	G	G	A	rs61902844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	44	60	0	0.54321	0	G|0.667;A|0.333	0.333	strong	OR10Q1,NS,carcinoma,-2,1	OR10Q1	79	1	NM_001004471	exon1	c.C264T	p.N88N	CAAAATGTTGGAA	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71236216	71236216	+	Silent	SNP	C	C	T	rs7740873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	85	202	0	0.5	0	C|0.734;T|0.266	0.266	strong	.	FAM135A	181	.	NM_001162529	exon13	c.C3429T	p.N1143N	TATAAACATGCCT	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11133681	11133681	+	Silent	SNP	C	C	T	rs61740118	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	44	99	0	0.453608	0	C|0.989;T|0.011	0.011	strong	.	CLEC16A	101	.	NM_015226	exon13	c.C1608T	p.N536N	CTACAACCACCCG	.	PASS	Atlas-SNP
KIAA1468	57614	hgsc.bcm.edu	37	18	59895550	59895550	+	Silent	SNP	C	C	T	rs151143967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	66	147	0	0.464789	0	C|0.978;T|0.022	0.022	strong	.	KIAA1468	93	.	NM_020854	exon8	c.C1167T	p.F389F	GGACTTCCTCAAA	.	PASS	Atlas-SNP
LRRC43	254050	hgsc.bcm.edu	37	12	122674807	122674807	+	Missense_Mutation	SNP	T	T	C	rs77473460	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	82	186	0	0.465909	0	T|0.977;C|0.023	0.023	strong	.	LRRC43	105	.	NM_001098519	exon5	c.T793C	p.Y265H	GTGCCCTACTACC	.	PASS	Atlas-SNP
PRDM14	63978	hgsc.bcm.edu	37	8	70978690	70978690	+	Silent	SNP	C	C	T	rs3750227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	77	170	0	0.4375	0	C|0.874;T|0.126	0.126	strong	.	PRDM14	102	.	NM_024504	exon5	c.G963A	p.T321T	GTTCCCCGTACCT	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15852363	15852363	+	Missense_Mutation	SNP	G	G	A	rs11670007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	138	280	0	0.448052	0	G|0.700;A|0.300	0.300	strong	OR10H3,caecum,carcinoma,+1,2	OR10H3	53	2	NM_013938	exon1	c.G161A	p.R54H	TTGAACGCAGACT	.	PASS	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1547477	1547477	+	Silent	SNP	T	T	C	rs2745108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	28	42	0	1	0	T|0.754;C|0.246	0.246	strong	.	TELO2	44	.	NM_016111	exon5	c.T798C	p.A266A	GGAGGCTGTGCTG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9070079	9070079	+	Silent	SNP	C	C	G	rs1559170	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	83	209	0	0.448649	0	C|0.805;G|0.195	0.195	strong	.	MUC16	4315	.	NM_024690	exon3	c.G17367C	p.T5789T	CTCAGACGTCCTG	.	PASS	Atlas-SNP
TMEM120B	144404	hgsc.bcm.edu	37	12	122186317	122186317	+	Missense_Mutation	SNP	G	G	A	rs28655666	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	90	184	0	0.445545	0	G|0.502;A|0.498	0.498	strong	TMEM120B_ENST00000449592,brain,glioma,0,2	TMEM120B	43	2	NM_001080825	exon3	c.G274A	p.D92N	TTCTTCGACATGG	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7413149	7413149	+	Silent	SNP	T	T	C	rs61744841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	59	0	0.522388	0	T|0.927;C|0.073	0.073	strong	COL28A1,NS,carcinoma,-1,1	COL28A1	113	1	NM_001037763	exon32	c.A2388G	p.P796P	CTCTAGTGGAGTC	.	PASS	Atlas-SNP
NCLN	56926	hgsc.bcm.edu	37	19	3186085	3186085	+	Silent	SNP	G	G	T	rs11551095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	45	47	0	0.505618	0	G|0.450;T|0.550	0.550	strong	NCLN,NS,carcinoma,0,1	NCLN	27	1	NM_020170	exon1	c.G57T	p.P19P	TCTGCCGCTCGGC	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102751076	102751076	+	Missense_Mutation	SNP	G	G	A	rs10516487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	96	0	0.489583	0	G|0.748;A|0.252	0.252	strong	.	BANK1	95	.	NM_017935	exon2	c.G182A	p.R61H	TATATCGCTTGGA	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113668453	113668453	+	Silent	SNP	A	A	G	rs11992014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	132	95	0	1	0	A|0.971;G|0.029	0.029	strong	CSMD3_ENST00000343508,NS,carcinoma,-2,2	CSMD3	2325	2	NM_198123	exon18	c.T2934C	p.S978S	AAAATTACTGCTA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133980214	133980214	+	Silent	SNP	A	A	G	rs16904799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	38	59	0	0.535211	0	A|0.949;G|0.051	0.051	strong	.	TG	416	.	NM_003235	exon31	c.A5862G	p.K1954K	GAAGAAAGGTGAG	.	PASS	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	71	0	1	0	A|0.559;G|0.441	0.441	strong	.	GPR123	118	.	NM_001083909	exon7	c.A834G	p.S278S	GGTGTCACAGGGC	.	PASS	Atlas-SNP
PPP2R2C	5522	hgsc.bcm.edu	37	4	6374263	6374263	+	Silent	SNP	G	G	A	rs35410672	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	60	134	0	0.405405	0	G|0.973;A|0.027	0.027	strong	.	PPP2R2C	63	.	NM_181876	exon5	c.C612T	p.T204T	CCTGTCGGTGATG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20443872	20443872	+	Silent	SNP	C	C	G	rs78523266		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	190	174	0	0.989583	0	.	.	weak	OR4K15,NS,carcinoma,+1,1	OR4K15	82	1	NM_001005486	exon1	c.C195G	p.G65G	GTTGGGCAACTTT	.	scavenged	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	60	99	0	0.550459	0	C|0.739;T|0.261	0.261	strong	TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon19	c.C6498T	p.Y2166Y	GGCCTACCAGGAA	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79936579	79936579	+	Missense_Mutation	SNP	G	G	A	rs73467962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	75	99	0	0.6	0	G|0.987;A|0.013	0.013	strong	.	VPS13A	735	.	NM_001018038	exon44	c.G5747A	p.S1916N	GTTTAAGTATGGA	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74709975	74709975	+	Silent	SNP	G	G	A	rs2075589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	13	25	0	0.52	0	G|0.799;A|0.201	0.201	strong	.	SEMA7A	58	.	NM_003612	exon5	c.C507T	p.Y169Y	GGGGGCGTAGCCT	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	37	16	4748825	4748825	+	Silent	SNP	C	C	T	rs841214	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	96	0	0.493151	0	C|0.602;T|0.398	0.398	strong	ANKS3,NS,carcinoma,0,1	ANKS3	44	1	NM_133450	exon13	c.G1527A	p.Q509Q	GAGCTCCTGCATC	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97052754	97052754	+	Silent	SNP	C	C	T	rs2064947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	75	0	0.486842	0	C|0.849;T|0.151	0.151	strong	.	FHL5	73	.	NM_020482	exon4	c.C288T	p.N96N	TTCTAACGAGTGC	.	PASS	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	37	5	35694454	35694454	+	Missense_Mutation	SNP	A	A	G	rs12332369	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	89	166	0	0.494444	0	A|0.973;G|0.027	0.027	strong	.	SPEF2	324	.	NM_024867	exon13	c.A1964G	p.E655G	AAGGTGAAACAAT	.	PASS	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21384578	21384578	+	Missense_Mutation	SNP	C	C	T	rs2270384	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	113	228	0	0.530516	0	C|0.775;T|0.225	0.225	strong	.	SLC7A4	50	.	NM_004173	exon3	c.G1045A	p.A349T	CATCGGCGGCCAT	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158533219	158533219	+	Missense_Mutation	SNP	A	A	C	rs114956415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	96	0	0.476744	0	A|0.987;C|0.013	0.013	strong	.	OR6P1	47	.	NM_001160325	exon1	c.T176G	p.M59R	AAGTACATGGGAC	.	PASS	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	37	2	29356567	29356567	+	Silent	SNP	G	G	C	rs17749904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	44	83	0	0.444444	0	G|0.838;C|0.162	0.162	strong	.	CLIP4	69	.	NM_024692	exon5	c.G414C	p.L138L	TGACCTGGGAGCA	.	PASS	Atlas-SNP
GALNT12	79695	hgsc.bcm.edu	37	9	101594219	101594219	+	Silent	SNP	A	A	G	rs16917929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	56	98	0	0.629214	0	A|0.954;G|0.046	0.046	strong	.	GALNT12	37	.	NM_024642	exon4	c.A897G	p.Q299Q	GATGCAATCCCCC	.	PASS	Atlas-SNP
HIST3H3	8290	hgsc.bcm.edu	37	1	228612994	228612994	+	Silent	SNP	T	T	C	rs61741017	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	64	160	0	0.447552	0	T|0.984;C|0.016	0.016	strong	.	HIST3H3	20	.	NM_003493	exon1	c.A33G	p.S11S	ACCCGTTGACTTG	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14911	14911	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	40	45	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.C165T	p.Y55Y	GCACTACTCACCA	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234411	45234411	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	5	74	0	0.106383	0	.	.	none	CDC27_ENST00000531206,caecum,carcinoma,0,2	CDC27	337	2	NM_001114091	exon7	c.C710A	p.S237X	ACAGCTGAATCAA	.	scavenged	Atlas-SNP
ST6GAL1	6480	hgsc.bcm.edu	37	3	186793423	186793423	+	Silent	SNP	C	C	T	rs7629263	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	87	166	0	0.453125	0	C|0.922;T|0.078	0.078	strong	.	ST6GAL1	36	.	NM_003032	exon7	c.C1053T	p.D351D	GACTGACGTGTGC	.	PASS	Atlas-SNP
D2HGDH	728294	hgsc.bcm.edu	37	2	242674803	242674803	+	Missense_Mutation	SNP	G	G	A	rs77940364	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	21	29	0	0.466667	0	G|0.785;A|0.215	0.215	strong	.	D2HGDH	39	.	NM_152783	exon2	c.G164A	p.R55Q	CCGTGCGGCGCTT	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	73	142	0	0.421965	0	A|0.883;C|0.117	0.117	strong	BST1,colon,carcinoma,0,3	BST1	30	3	NM_004334	exon9	c.A943C	p.R315R	GCTTCCAGGACTC	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52497872	52497872	+	Missense_Mutation	SNP	C	C	T	rs16951186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	52	91	0	0.472727	0	C|0.938;T|0.062	0.062	strong	.	TOX3	121	.	NM_001080430	exon3	c.G382A	p.V128M	GAAGCACGCCATC	.	PASS	Atlas-SNP
GALNT2	2590	hgsc.bcm.edu	37	1	230391058	230391058	+	Silent	SNP	G	G	A	rs75919037	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	69	133	0	0.6	0	G|0.996;A|0.004	0.004	strong	GALNT2,ear,carcinoma,+1,1	GALNT2	83	1	NM_004481	exon11	c.G1104A	p.T368T	CTACACGTTCCCG	.	PASS	Atlas-SNP
DVL2	1856	hgsc.bcm.edu	37	17	7133609	7133609	+	Silent	SNP	G	G	A	rs2074216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	37	108	0	0.430233	0	G|0.674;A|0.326	0.326	strong	.	DVL2	49	.	NM_004422	exon3	c.C405T	p.S135S	CTGGAAGGATGGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415608	105415608	+	Missense_Mutation	SNP	G	G	C	rs11850848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	253	227	1	1	0.00440529	G|0.698;C|0.302	0.302	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C6180G	p.H2060Q	GGGCACGTGGCCC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17084057	17084057	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1363	118	1115	0	0.0865737	0	.	.	none	.	.	.	.	NM_001271733	exon14	c.G1864A	p.E622K	ACATCTCGCTCTC	.	PASS	Atlas-SNP
COMMD10	51397	hgsc.bcm.edu	37	5	115469773	115469773	+	Silent	SNP	C	C	T	rs1129496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	45	80	0	0.494505	0	C|0.523;T|0.477	0.477	strong	COMMD10,NS,carcinoma,0,1	COMMD10	18	1	NM_016144	exon5	c.C408T	p.T136T	AGAGACCGTTGGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678407	100678407	+	Missense_Mutation	SNP	G	G	A	rs4729649	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	26	104	0	0.168831	0	G|0.948;A|0.052	0.052	strong	MUC17,caecum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.G3710A	p.S1237N	AGGCTAGCACCCT	.	PASS	Atlas-SNP
IFNA7	3444	hgsc.bcm.edu	37	9	21201703	21201703	+	Silent	SNP	T	T	C	rs76644201	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	368	177	378	0	0.480978	0	T|0.976;C|0.024	0.024	strong	.	IFNA7	24	.	NM_021057	exon1	c.A462G	p.L154L	CTCCATTAGATAA	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39234723	39234723	+	Missense_Mutation	SNP	C	C	T	rs112433506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	30	65	0	0.47619	0	C|0.998;T|0.002	0.002	strong	.	CAPN12	43	.	NM_144691	exon1	c.G83A	p.R28Q	TGGCCCCGAAAAA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677415	100677415	+	Silent	SNP	T	T	C	rs57597607	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	37	112	0	0.218935	0	T|0.933;C|0.067	0.067	strong	.	MUC17	804	.	NM_001040105	exon3	c.T2718C	p.P906P	GTCTCCTACAACT	.	PASS	Atlas-SNP
CERS4	79603	hgsc.bcm.edu	37	19	8321946	8321946	+	Silent	SNP	T	T	C	rs36247	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	146	146	1	1	0.00684932	T|0.623;C|0.376	0.376	strong	.	.	.	.	NM_024552	exon9	c.T726C	p.S242S	TTCCTCTGACTAC	.	PASS	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	37	3	36887863	36887863	+	Silent	SNP	G	G	A	rs142584752	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	92	175	0	0.410714	0	G|0.998;A|0.002	0.002	strong	.	TRANK1	398	.	NM_014831	exon16	c.C4935T	p.T1645T	GATGGCGGTGTAC	.	PASS	Atlas-SNP
DNASE2B	58511	hgsc.bcm.edu	37	1	84878228	84878228	+	Silent	SNP	C	C	T	rs7511984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	22	55	0	0.338462	0	C|0.841;T|0.159	0.159	strong	.	DNASE2B	40	.	NM_021233	exon5	c.C744T	p.D248D	TCTTGACGGTATG	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104186995	104186995	+	Silent	SNP	G	G	A	rs61748068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	100	233	0	0.446429	0	G|0.908;A|0.092	0.092	strong	.	NT5DC3	113	.	NM_001031701	exon9	c.C966T	p.F322F	CACATCGAACAGG	.	PASS	Atlas-SNP
LY6G6F	259215	hgsc.bcm.edu	37	6	31675501	31675501	+	Missense_Mutation	SNP	G	G	A	rs9267547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	113	191	0	0.588542	0	G|0.854;A|0.146	0.146	strong	LY6G6F,NS,lymphoid_neoplasm,0,1	LY6G6F	23	1	NM_001003693	exon2	c.G319A	p.A107T	TGGTGCGCTGTGC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489708	32489708	+	Missense_Mutation	SNP	C	C	A	rs41556512	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	20	23	0	0.540541	0	.	.	weak	.	HLA-DRB5	31	.	NM_002125	exon2	c.G344T	p.G115V	CTCTCACCAACCC	.	PASS	Atlas-SNP
KCNV2	169522	hgsc.bcm.edu	37	9	2729686	2729686	+	Missense_Mutation	SNP	C	C	G	rs12352254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	67	110	0	0.51938	0	C|0.857;G|0.143	0.143	strong	.	KCNV2	72	.	NM_133497	exon2	c.C1597G	p.L533V	TGTTTGCTTGGAA	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	12540	12540	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	18	18	8	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.A204G	p.W68W	ACACTGAGCCACA	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31249861	31249861	+	Missense_Mutation	SNP	C	C	G	rs2075322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	77	220	0	0.44	0	C|0.436;G|0.564	0.564	strong	.	DDX11	188	.	NM_030653	exon17	c.C1699G	p.Q567E	CACATCCAAGGCT	.	PASS	Atlas-SNP
PADI6	353238	hgsc.bcm.edu	37	1	17727847	17727847	+	Silent	SNP	T	T	C	rs183565903	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	52	128	0	0.429752	0	T|1.000;C|0.000	0.000	strong	.	PADI6	51	.	NM_207421	exon17	c.T1998C	p.C666C	TGACTGTTACCTG	.	PASS	Atlas-SNP
C3orf58	205428	hgsc.bcm.edu	37	3	143691756	143691756	+	Silent	SNP	T	T	C	rs139703156	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	33	48	0	0.540984	0	T|0.999;C|0.001	0.001	strong	.	C3orf58	36	.	NM_173552	exon1	c.T582C	p.L194L	CCTGCTTCGCAAC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	124	215	0	0.48249	0	G|0.828;A|0.172	0.172	strong	.	OBSCN	2142	.	NM_001271223	exon64	c.G16867A	p.G5623S	CAGCCCGGTGGGC	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171176912	171176912	+	Missense_Mutation	SNP	T	T	G	rs2020865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	77	143	0	0.538462	0	T|0.887;G|0.113	0.113	strong	.	FMO2	66	.	NM_001460	exon8	c.T1239G	p.N413K	AAGGAATGAAAAA	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32137852	32137852	+	Silent	SNP	C	C	G	rs3759297	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	71	0	0.478873	0	C|0.840;G|0.160	0.160	strong	C12orf35,NS,lymphoid_neoplasm,+1,1	.	.	1	NM_018169	exon4	c.C3963G	p.T1321T	GGAAACCCGACAG	.	PASS	Atlas-SNP
XCL1	6375	hgsc.bcm.edu	37	1	168549325	168549325	+	Missense_Mutation	SNP	A	A	G	rs61546281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	68	292	0	0.4	0	A|0.981;G|0.019	0.019	strong	.	XCL1	16	.	NM_002995	exon2	c.A86G	p.K29R	CAGATAAGAGGAC	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	60	118	0	0.495868	0	C|0.907;T|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon11	c.G1268A	p.R423Q	GAAGGCCGGTGCA	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118598362	118598362	+	Missense_Mutation	SNP	A	A	G	rs138706127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	38	64	1	0.633333	0.015625	A|0.993;G|0.007	0.007	strong	SPAG17,NS,haematopoietic_neoplasm,0,1	SPAG17	263	1	NM_206996	exon19	c.T2716C	p.S906P	TTTTAGATTCTTT	.	scavenged	Atlas-SNP
PLXNB1	5364	hgsc.bcm.edu	37	3	48454018	48454018	+	Silent	SNP	C	C	T	rs34555887	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	74	131	0	0.521127	0	C|0.985;T|0.015	0.015	strong	.	PLXNB1	150	.	NM_001130082	exon26	c.G4866A	p.T1622T	CTCCAGCGTGTGG	.	PASS	Atlas-SNP
TRIM71	131405	hgsc.bcm.edu	37	3	32933036	32933036	+	Silent	SNP	G	G	A	rs13096271	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	41	68	0	0.5	0	G|0.873;A|0.127	0.127	strong	TRIM71,NS,meningioma,+1,1	TRIM71	73	1	NM_001039111	exon4	c.G2340A	p.S780S	CCAGTCGGCACGC	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101719004	101719004	+	Missense_Mutation	SNP	G	G	A	rs62513924	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	42	102	0	0.304348	0	.	.	strong	.	PABPC1	76	.	NM_002568	exon11	c.C1477T	p.R493C	CAGGACGTGGACC	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41628014	41628014	+	Missense_Mutation	SNP	G	G	C	rs75405062	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	14	120	0	0.205882	0	G|0.250;C|0.750	0.750	weak	CYP2F1,NS,carcinoma,+2,1	CYP2F1	60	1	NM_000774	exon6	c.G798C	p.Q266H	CATCCAGTGCTTC	.	scavenged	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443442	5443442	+	Silent	SNP	G	G	C	rs2736590	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	208	196	0	0.995215	0	G|0.587;C|0.413	0.413	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.G12C	p.V4V	CCAGGTGACTAAC	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64216854	64216854	+	Missense_Mutation	SNP	A	A	G	rs52797880	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	34	96	0	0.333333	0	A|0.927;G|0.073	0.073	strong	.	APOH	45	.	NM_000042	exon5	c.T422C	p.I141T	GGGCAGATGATGG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	45	76	0	0.535714	0	G|0.844;A|0.156	0.156	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C1851T	p.C617C	TCCAGAGCACGTT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73676189	73676189	+	Silent	SNP	C	C	T	rs77517267	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	79	141	0	0.503185	0	C|0.976;T|0.024	0.024	strong	ALMS1,NS,carcinoma,+2,1	ALMS1	384	1	NM_015120	exon8	c.C2532T	p.D844D	AGCTGACGGAAAG	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58386314	58386314	+	Silent	SNP	G	G	A	rs111313171	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	779	332	744	1	0.426187	0.00134409	G|0.941;A|0.059	0.059	strong	.	ZNF814	93	.	NM_001144989	exon3	c.C444T	p.Y148Y	CCCTCTGTAGGGT	.	PASS	Atlas-SNP
SEC61A2	55176	hgsc.bcm.edu	37	10	12200092	12200092	+	Silent	SNP	A	A	G	rs61731911	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	82	141	0	0.577465	0	A|0.974;G|0.026	0.026	strong	.	SEC61A2	48	.	NM_001142627	exon9	c.A963G	p.L321L	TTTACTAGGACAG	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924955	70924955	+	Missense_Mutation	SNP	A	A	C	rs3829456		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	32	87	0	0.432432	0	.	.	weak	ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A739C	p.K247Q	ATGTATAAGCAGT	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11865462	11865462	+	Missense_Mutation	SNP	G	G	A	rs1990236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	67	0	0.986667	0	G|0.834;A|0.166	0.166	strong	.	DNAH9	695	.	NM_001372	exon68	c.G13122A	p.M4374I	CCAGATGGCCCTG	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73786188	73786188	+	Missense_Mutation	SNP	A	A	G	rs34071195	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	70	131	0	0.48951	0	A|0.991;G|0.009	0.009	strong	.	ALMS1	384	.	NM_015120	exon15	c.A10300G	p.K3434E	ACACAGAAAGAGG	.	PASS	Atlas-SNP
ZSCAN31	64288	hgsc.bcm.edu	37	6	28294550	28294550	+	Missense_Mutation	SNP	T	T	C	rs853684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	128	1	1	0.0078125	T|0.428;C|0.572	0.572	strong	.	.	.	.	NM_030899	exon4	c.A614G	p.K205R	TGGAGTTTGCTAT	.	PASS	Atlas-SNP
SORBS2	8470	hgsc.bcm.edu	37	4	186545346	186545346	+	Missense_Mutation	SNP	A	A	T	rs61736043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	121	249	1	0.478261	0.00401606	A|0.977;T|0.023	0.023	strong	.	SORBS2	300	.	NM_001270771	exon16	c.T1525A	p.L509I	CACATAACAGGGA	.	PASS	Atlas-SNP
TLR5	7100	hgsc.bcm.edu	37	1	223285042	223285042	+	Silent	SNP	G	G	A	rs5744169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	63	136	0	0.440559	0	G|0.976;A|0.024	0.024	strong	.	TLR5	86	.	NM_003268	exon6	c.C1332T	p.L444L	CCGTAGGAGAAAG	.	PASS	Atlas-SNP
ZNFX1	57169	hgsc.bcm.edu	37	20	47865784	47865784	+	Missense_Mutation	SNP	C	C	T	rs6512577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	106	192	0	0.471111	0	C|0.824;T|0.176	0.176	strong	.	ZNFX1	194	.	NM_021035	exon14	c.G3777A	p.M1259I	CCGGAGCATGGGG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47933494	47933494	+	Missense_Mutation	SNP	C	C	T	rs17131915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	16	46	0	0.432432	0	C|0.974;T|0.026	0.026	strong	.	PKD1L1	328	.	NM_138295	exon15	c.G2434A	p.D812N	CAGGGTCGTCAGG	.	PASS	Atlas-SNP
KIAA0196	9897	hgsc.bcm.edu	37	8	126087351	126087351	+	Silent	SNP	T	T	G	rs79464415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	39	116	0	0.549296	0	T|0.994;G|0.006	0.006	strong	.	KIAA0196	90	.	NM_014846	exon8	c.A867C	p.V289V	ACTAATTACCTGA	.	PASS	Atlas-SNP
P2RX2	22953	hgsc.bcm.edu	37	12	133196596	133196596	+	Silent	SNP	T	T	C	rs7964634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	60	56	0	1	0	T|0.323;C|0.677	0.677	strong	P2RX2,NS,carcinoma,0,1	P2RX2	49	1	NM_170683	exon5	c.T468C	p.T156T	GAGGACTGGGCGC	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72340965	72340965	+	Silent	SNP	G	G	A	rs34914485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	80	127	0	0.512821	0	G|0.965;A|0.035	0.035	strong	.	KIF19	102	.	NM_153209	exon7	c.G648A	p.T216T	CCAGACGTCCTCC	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5372863	5372863	+	Silent	SNP	T	T	A	rs10837882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	304	290	0	0.993464	0	T|0.871;A|0.129	0.129	strong	.	OR51B6	53	.	NM_001004750	exon1	c.T126A	p.T42T	TGGCACTCTTCTC	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106190862	106190862	+	Silent	SNP	T	T	C	rs3733609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	84	163	1	0.459016	0.00613497	T|0.866;C|0.134	0.134	strong	TET2,NS,haematopoietic_neoplasm,+2,8	TET2	1762	8	NM_001127208	exon9	c.T4140C	p.H1380H	TGCTCATGCCCAC	.	scavenged	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117657991	117657991	+	Silent	SNP	G	G	T	rs2293044	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	21	52	0	0.375	0	G|0.966;T|0.034	0.034	strong	.	NOS1	240	.	NM_001204218	exon28	c.C4161A	p.V1387V	CCCACAGACGTAT	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140589738	140589738	+	Missense_Mutation	SNP	C	C	T	rs2910327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	92	205	0	0.476684	0	C|0.860;T|0.140	0.140	strong	.	PCDHB12	179	.	NM_018932	exon1	c.C1259T	p.T420I	ACATCACCATCAC	.	PASS	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95537622	95537622	+	Missense_Mutation	SNP	A	A	G	rs11164112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	13	9	0	1	0	A|0.602;G|0.398	0.398	strong	.	TEKT4	72	.	NM_144705	exon1	c.A298G	p.S100G	ACGCACAGCTGGA	.	PASS	Atlas-SNP
KDM1A	23028	hgsc.bcm.edu	37	1	23409674	23409674	+	Silent	SNP	G	G	A	rs137940710	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	140	318	1	0.501792	0.00314465	G|0.999;A|0.001	0.001	strong	.	KDM1A	49	.	NM_001009999	exon21	c.G2448A	p.P816P	ATAGCCGATTCCA	.	PASS	Atlas-SNP
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346594	39346594	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	8	81	0	0.0720721	0	.	.	none	KRTAP9-1_ENST00000398470,colon,carcinoma,+2,2	KRTAP9-1	34	2	NM_001190460	exon1	c.C456T	p.T152T	GCCCACCTGCTGT	.	scavenged	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117846580	117846580	+	Missense_Mutation	SNP	T	T	C	rs1061494	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	95	0	1	0	T|0.531;C|0.469	0.469	strong	TNC,NS,carcinoma,0,1	TNC	282	1	NM_002160	exon4	c.A2039G	p.Q680R	AGCTCCTGGATGA	.	PASS	Atlas-SNP
PRKACG	5568	hgsc.bcm.edu	37	9	71628207	71628207	+	Missense_Mutation	SNP	G	G	C	rs3730386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	90	0	1	0	G|0.707;C|0.293	0.293	strong	.	PRKACG	65	.	NM_002732	exon1	c.C802G	p.H268D	GCAGATGCTTGAG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263634	78263634	+	Silent	SNP	A	A	G	rs141921176	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	40	102	0	0.493827	0	A|0.995;G|0.005	0.005	strong	.	RNF213	766	.	NM_001256071	exon6	c.A1110G	p.A370A	GAAGGCAAGGTAG	.	PASS	Atlas-SNP
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	355	207	274	1	0.583099	0.00364964	A|0.598;G|0.402	0.402	strong	.	KRTAP3-3	11	.	NM_033185	exon1	c.T66C	p.S22S	TTTGTCAGAGGAG	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101529594	101529594	+	Silent	SNP	G	G	A	rs2412000	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	55	137	0	0.443548	0	G|0.871;A|0.129	0.129	strong	.	LRRK1	310	.	NM_024652	exon6	c.G753A	p.P251P	TTATCCGGGAAAA	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765164	66765164	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	4	64	0	0.0588235	0	.	.	none	.	AR	249	.	NM_000044	exon1	c.A176T	p.Q59L	TGCAGCAGCAGCA	.	PASS	Atlas-SNP
UNC5D	137970	hgsc.bcm.edu	37	8	35583815	35583815	+	Silent	SNP	G	G	C	rs6996645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	104	0	0.508475	0	G|0.839;C|0.161	0.161	strong	.	UNC5D	393	.	NM_080872	exon10	c.G1449C	p.V483V	CAAAGTGAAAGTC	.	PASS	Atlas-SNP
PTPN2	5771	hgsc.bcm.edu	37	18	12817348	12817348	+	Missense_Mutation	SNP	G	G	T	rs78174797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	109	254	0	0.43254	0	G|0.981;T|0.019	0.019	strong	.	PTPN2	37	.	NM_001207013	exon7	c.C581A	p.T194K	GATATTGTTCTGG	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133749077	133749077	+	Silent	SNP	C	C	T	rs139944066	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	52	94	0	0.440678	0	C|0.997;T|0.003	0.003	strong	.	EXOC4	118	.	NM_021807	exon18	c.C2721T	p.D907D	AGCTGACGAGCTC	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74493432	74493432	+	Missense_Mutation	SNP	A	A	C	rs10455097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	77	59	0	1	0	A|0.454;C|0.546	0.546	strong	.	CD109	170	.	NM_133493	exon19	c.A2108C	p.Y703S	TCAGTTACAGGAT	.	PASS	Atlas-SNP
ATN1	1822	hgsc.bcm.edu	37	12	7045939	7045939	+	Missense_Mutation	SNP	T	T	G	rs146578563	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	8	118	0	0.0879121	0	C|0.001;G|0.000;T|0.999	0.000	strong	ATN1,colon,carcinoma,0,1	ATN1	95	1	NM_001007026	exon5	c.T1509G	p.H503Q	GCAGCATCACGGA	.	PASS	Atlas-SNP
MBD6	114785	hgsc.bcm.edu	37	12	57920368	57920368	+	Silent	SNP	T	T	C	rs34551572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	65	140	0	0.445205	0	T|0.893;C|0.107	0.107	strong	.	MBD6	99	.	NM_052897	exon7	c.T1440C	p.A480A	ACCAGCTGCCTCC	.	PASS	Atlas-SNP
CYP3A43	64816	hgsc.bcm.edu	37	7	99463556	99463556	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	12	113	0	0.16	0	.	.	none	.	CYP3A43	52	.	NM_022820	exon13	c.A1447T	p.I483F	CTACCAATTCTTC	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52986187	52986187	+	Missense_Mutation	SNP	T	T	C	rs12833456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	57	101	0	0.57	0	C|0.351;N|0.000	0.351	strong	.	KRT72	70	.	NM_001146225	exon4	c.A791G	p.Y264C	CCTTCATAAAGGC	.	PASS	Atlas-SNP
POLD1	5424	hgsc.bcm.edu	37	19	50916772	50916772	+	Silent	SNP	T	T	C	rs1274607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	25	54	0	0.446429	0	T|0.877;C|0.123	0.123	strong	.	POLD1	174	.	NM_002691	exon18	c.T2244C	p.S748S	CACCAGTGCCAAG	.	PASS	Atlas-SNP
DHRS2	10202	hgsc.bcm.edu	37	14	24114483	24114483	+	Missense_Mutation	SNP	T	T	C	rs7156794	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	41	64	0	0.554054	0	T|0.941;C|0.059	0.059	strong	.	DHRS2	78	.	NM_182908	exon9	c.T875C	p.V292A	GCTGCGTAGCTGT	.	PASS	Atlas-SNP
SCN1B	6324	hgsc.bcm.edu	37	19	35524824	35524824	+	Missense_Mutation	SNP	T	T	C	rs55742440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	55	67	0	0.625	0	T|0.619;C|0.381	0.381	strong	.	SCN1B	32	.	NM_199037	exon3	c.T629C	p.L210P	TGTTTCTCTCCAG	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24207438	24207438	+	Missense_Mutation	SNP	G	G	A	rs7829965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	72	145	0	0.470588	0	G|0.931;A|0.069	0.069	strong	.	ADAM28	100	.	NM_014265	exon19	c.G2052A	p.M684I	TGCTATGGTAATC	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56702323	56702323	+	Missense_Mutation	SNP	C	C	T	rs4801296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	300	286	0	0.993378	0	C|0.531;T|0.469	0.469	strong	.	ZSCAN5B	160	.	NM_001080456	exon3	c.G622A	p.V208I	CTGTTACGTCAAT	.	PASS	Atlas-SNP
RBM42	79171	hgsc.bcm.edu	37	19	36124822	36124822	+	Silent	SNP	C	C	A	rs147020112	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	18	26	0	0.45	0	C|0.990;A|0.010	0.010	strong	.	RBM42	40	.	NM_024321	exon7	c.C918A	p.R306R	CGTCCGCGGCCTC	.	PASS	Atlas-SNP
SLC35A5	55032	hgsc.bcm.edu	37	3	112292765	112292765	+	Silent	SNP	C	C	T	rs61732187	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	183	168	0	1	0	C|0.976;T|0.024	0.024	strong	.	SLC35A5	40	.	NM_017945	exon5	c.C390T	p.S130S	TTTTAGCATTATA	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132626425	132626425	+	Missense_Mutation	SNP	G	G	A	rs60927391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	75	153	0	0.451807	0	G|0.765;A|0.235	0.235	strong	.	DDX51	33	.	NM_175066	exon6	c.C965T	p.A322V	TCCTTGGCCAGAG	.	PASS	Atlas-SNP
LONRF3	79836	hgsc.bcm.edu	37	X	118148229	118148229	+	Silent	SNP	A	A	G	rs2278954	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	132	1	1	0.00757576	0|0.014;G|0.475	0.475	strong	.	LONRF3	138	.	NM_001031855	exon10	c.A2034G	p.A678A	GCAAGCATCATTG	.	PASS	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140247103	140247103	+	Missense_Mutation	SNP	C	C	T	rs115998217	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	29	47	0	0.371795	0	C|0.960;T|0.040	0.040	strong	.	EXD3	86	.	NM_017820	exon11	c.G1006A	p.V336M	GTTCCACAGCCAC	.	PASS	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	37	8	121256150	121256150	+	Silent	SNP	T	T	C	rs2305603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	44	88	0	0.444444	0	T|0.882;C|0.118	0.118	strong	.	COL14A1	292	.	NM_021110	exon20	c.T2382C	p.L794L	CCTCCTTCTGAAG	.	PASS	Atlas-SNP
FKBP11	51303	hgsc.bcm.edu	37	12	49315821	49315821	+	Silent	SNP	T	T	C	rs148302547	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	29	75	0	0.483333	0	T|0.999;C|0.001	0.001	strong	FKBP11,colon,carcinoma,-1,1	FKBP11	12	1	NM_016594	exon6	c.A552G	p.K184K	GGAGACTTTGGGT	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101727716	101727716	+	Missense_Mutation	SNP	C	C	T	rs201157005	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	5	79	1	0.0434783	0.0126582	C|0.940;T|0.060	0.060	strong	PABPC1,NS,carcinoma,-1,1	PABPC1	76	1	NM_002568	exon4	c.G617A	p.R206H	TTAAGGCGCTCAT	.	scavenged	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	40	75	0	0.487805	0	C|0.958;T|0.042	0.042	strong	.	TNFRSF10C	30	.	NM_003841	exon1	c.C20T	p.T7I	CCAAGACCCTAAA	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66102257	66102257	+	Silent	SNP	G	G	A	rs1805096	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	52	101	0	0.553191	0	G|0.516;A|0.484	0.484	strong	.	LEPR	284	.	NM_002303	exon20	c.G3057A	p.P1019P	TTCTCCGTTGAAG	.	PASS	Atlas-SNP
TMC3	342125	hgsc.bcm.edu	37	15	81625028	81625028	+	Missense_Mutation	SNP	C	C	T	rs8031046	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	93	158	0	0.553571	0	C|0.811;T|0.189	0.189	strong	.	TMC3	112	.	NM_001080532	exon22	c.G3035A	p.R1012K	GGCTTTCTGGGCA	.	PASS	Atlas-SNP
FGD2	221472	hgsc.bcm.edu	37	6	36995222	36995222	+	Silent	SNP	G	G	A	rs2274587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	94	136	0	0.552941	0	G|0.824;A|0.175	0.175	strong	.	FGD2	65	.	NM_173558	exon15	c.G1623A	p.T541T	AGCCACGCCTGAC	.	PASS	Atlas-SNP
CDK16	5127	hgsc.bcm.edu	37	X	47084037	47084037	+	Silent	SNP	A	A	G	rs5952422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	47	154	0	0.391667	0	A|0.873;0|0.013	.	strong	.	CDK16	59	.	NM_001170460	exon4	c.A579G	p.S193S	CCTATCACTACCA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159672542	159672542	+	Silent	SNP	C	C	T	rs550443	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	83	0	0.486842	0	C|0.789;T|0.211	0.211	strong	.	FNDC1	250	.	NM_032532	exon17	c.C5043T	p.A1681A	CAAAGCCACCCCA	.	PASS	Atlas-SNP
C1QTNF9	338872	hgsc.bcm.edu	37	13	24890157	24890157	+	Missense_Mutation	SNP	C	C	T	rs1974332	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	113	211	0	0.45749	0	C|0.782;T|0.218	0.218	strong	.	C1QTNF9	22	.	NM_178540	exon2	c.C16T	p.L6F	TGGTGGCTTCTGC	.	PASS	Atlas-SNP
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69100200	69100200	+	Silent	SNP	A	A	G	rs4431295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	83	0	0.518519	0	A|0.970;G|0.030	0.030	strong	.	TMPRSS11B	66	.	NM_182502	exon5	c.T450C	p.P150P	GGAAGCAGGAACT	.	PASS	Atlas-SNP
CMKLR1	1240	hgsc.bcm.edu	37	12	108686008	108686008	+	Silent	SNP	C	C	G	rs1057401	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	38	70	0	0.452381	0	C|0.627;G|0.373	0.373	strong	CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	NM_001142344	exon3	c.G732C	p.V244V	TTTGCACACGATG	.	PASS	Atlas-SNP
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Missense_Mutation	SNP	G	G	A	rs79338777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	31	83	0	0.356322	0	G|0.937;A|0.063	0.063	strong	.	ETFB	46	.	NM_001014763	exon1	c.C155T	p.P52L	GGCAGGGGCAGGT	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	37	83	0	0.445783	0	T|0.902;C|0.098	0.098	strong	.	C5orf20	16	.	NM_130848	exon1	c.A356G	p.K119R	CCTGTCTTCCTTC	.	PASS	Atlas-SNP
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	137	0	0.508065	0	T|0.706;C|0.294	0.294	strong	.	PMP2	21	.	NM_002677	exon2	c.A186G	p.E62E	GGAGATTTCTGTA	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90274756	90274756	+	Silent	SNP	C	C	T	rs35502270	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	72	131	0	0.489796	0	C|0.973;T|0.027	0.027	strong	.	WDR93	63	.	NM_020212	exon12	c.C1293T	p.C431C	GGCCTGCGAGGAT	.	PASS	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169566313	169566313	+	Missense_Mutation	SNP	C	C	T	rs6127	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	190	199	0	1	0	C|0.306;T|0.694	0.694	strong	.	SELP	132	.	NM_003005	exon11	c.G1807A	p.D603N	CGTTGTCACAAGA	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6977844	6977844	+	Missense_Mutation	SNP	A	A	G	rs671871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	54	0	0.490196	0	A|0.717;G|0.283	0.283	strong	.	LAMA1	458	.	NM_005559	exon44	c.T6227C	p.I2076T	GCTTGAATTTCCA	.	PASS	Atlas-SNP
REEP6	92840	hgsc.bcm.edu	37	19	1495327	1495327	+	Silent	SNP	C	C	T	rs79574672	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	85	169	0	0.467033	0	C|0.974;T|0.026	0.026	strong	REEP6_ENST00000395484,NS,carcinoma,-2,1	REEP6	21	1	NM_138393	exon2	c.C150T	p.F50F	GCTGTTCGGCTAC	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14135394	14135394	+	Missense_Mutation	SNP	G	G	A	rs2230193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	48	104	0	0.45283	0	G|0.982;A|0.018	0.018	strong	.	CD83	23	.	NM_004233	exon5	c.G545A	p.R182Q	TGGAACGAGCTTT	.	PASS	Atlas-SNP
CPEB3	22849	hgsc.bcm.edu	37	10	93999850	93999850	+	Silent	SNP	A	A	G	rs3824734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	13	27	0	0.393939	0	A|0.307;G|0.693	0.693	strong	.	CPEB3	43	.	NM_014912	exon2	c.T258C	p.P86P	CTGAGGAGGCTGA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176051	8176051	+	Silent	SNP	G	G	A	rs114220337	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	27	44	0	0.613636	0	G|0.980;A|0.020	0.020	strong	SgK223,caecum,carcinoma,0,2	.	.	2	NM_001080826	exon5	c.C3834T	p.Y1278Y	CTGCCGGTAGTCT	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101718968	101718968	+	Missense_Mutation	SNP	C	C	T	rs62513922	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	73	144	0	0.341121	0	.	.	weak	.	PABPC1	76	.	NM_002568	exon11	c.G1513A	p.V505I	TGCGGACAGCAGG	.	PASS	Atlas-SNP
EPB41L4B	54566	hgsc.bcm.edu	37	9	112017883	112017883	+	Silent	SNP	A	A	G	rs73529389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	34	107	0	0.293103	0	A|0.997;G|0.003	0.003	strong	.	EPB41L4B	111	.	NM_019114	exon11	c.T1077C	p.V359V	GTGCTCAACTGCA	.	PASS	Atlas-SNP
COL1A2	1278	hgsc.bcm.edu	37	7	94057007	94057007	+	Silent	SNP	C	C	T	rs34691365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	67	106	0	0.507576	0	C|0.995;T|0.005	0.005	strong	.	COL1A2	240	.	NM_000089	exon49	c.C3336T	p.Y1112Y	TGGTTACGATGGA	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38776491	38776491	+	Missense_Mutation	SNP	T	T	G	rs11096957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	78	108	0	1	0	T|0.541;G|0.459	0.459	strong	.	TLR10	87	.	NM_001017388	exon2	c.A721C	p.N241H	TAGCATTTTCTAA	.	PASS	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62295149	62295149	+	Missense_Mutation	SNP	T	T	G	rs61524789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	274	131	210	0	0.478102	0	T|0.965;G|0.035	0.035	strong	.	AHNAK	532	.	NM_001620	exon5	c.A6740C	p.K2247T	GGCATTTTCATCT	.	PASS	Atlas-SNP
FKBPL	63943	hgsc.bcm.edu	37	6	32096528	32096528	+	Silent	SNP	G	G	A	rs61747172	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	83	144	0	0.51875	0	G|0.998;A|0.002	0.002	strong	.	FKBPL	25	.	NM_022110	exon2	c.C1030T	p.L344L	TGCGCAGACCCTG	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327856	43327856	+	Silent	SNP	A	A	G	rs3746906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	113	0	0.456311	0	A|0.367;G|0.633	0.633	strong	.	C2CD2	47	.	NM_015500	exon9	c.T1056C	p.F352F	CTTCTTAAATAAG	.	PASS	Atlas-SNP
ST3GAL1	6482	hgsc.bcm.edu	37	8	134478178	134478178	+	Silent	SNP	A	A	G	rs112787936	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	82	146	0	0.5125	0	A|0.984;G|0.016	0.016	strong	.	ST3GAL1	39	.	NM_173344	exon6	c.T462C	p.S154S	ATAAGAAGACTCC	.	PASS	Atlas-SNP
NUP188	23511	hgsc.bcm.edu	37	9	131755891	131755891	+	Silent	SNP	C	C	T	rs17485583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	140	234	0	0.642202	0	C|0.962;T|0.038	0.038	strong	.	NUP188	140	.	NM_015354	exon27	c.C2935T	p.L979L	CCACCCCTGCTGC	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239010690	239010690	+	Silent	SNP	C	C	A	rs34878344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	46	103	0	0.621622	0	C|0.882;A|0.118	0.118	strong	.	ESPNL	63	.	NM_194312	exon2	c.C403A	p.R135R	GAGACCCGGGAGG	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1537874	1537874	+	Missense_Mutation	SNP	G	G	A	rs7202502	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	37	86	0	0.373737	0	G|0.894;A|0.106	0.106	strong	PTX4,colon,carcinoma,0,1	PTX4	46	1	NM_001013658	exon2	c.C224T	p.A75V	TCTTCCGCCAGGC	.	PASS	Atlas-SNP
GRIK1	2897	hgsc.bcm.edu	37	21	31062070	31062070	+	Silent	SNP	T	T	G	rs363538	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	280	294	1	1	0.00340136	T|0.690;G|0.310	0.310	strong	.	GRIK1	293	.	NM_175611	exon3	c.A522C	p.T174T	CACCACTGTCACT	.	PASS	Atlas-SNP
CDYL2	124359	hgsc.bcm.edu	37	16	80642076	80642076	+	Silent	SNP	C	C	T	rs117351184	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	59	117	0	0.453846	0	C|0.990;T|0.010	0.010	strong	.	CDYL2	66	.	NM_152342	exon6	c.G1275A	p.R425R	CAGCCCCCTGCTG	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39521517	39521517	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	23	191	0	0.0905512	0	.	.	none	KRT33B,caecum,carcinoma,0,1	KRT33B	46	1	NM_002279	exon5	c.G786A	p.S262S	CTGCTCCGAGCTG	.	scavenged	Atlas-SNP
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	80	0	1	0	A|0.580;G|0.420	0.420	strong	.	PROP1	28	.	NM_006261	exon1	c.T27C	p.A9A	CTTCTCAGCCTGG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170034473	170034473	+	Silent	SNP	G	G	A	rs139363553	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	116	346	1	0.432836	0.00289017	G|0.999;A|0.001	0.001	strong	.	LRP2	751	.	NM_004525	exon53	c.C10233T	p.F3411F	AATAGCGAAAGGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551949	32551949	+	Missense_Mutation	SNP	C	C	G	rs16822805	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	11	31	4	1	0.129032	G|0.114;C|0.886	0.114	strong	HLA-DRB1,brain,glioma,+1,2	HLA-DRB1	41	2	NM_002124	exon2	c.G307C	p.A103P	CCACCGCGGCCCG	.	scavenged	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94505604	94505604	+	Missense_Mutation	SNP	A	A	C	rs61750126	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	39	92	0	0.438202	0	A|0.968;C|0.032	0.032	strong	.	ABCA4	275	.	NM_000350	exon24	c.T3602G	p.L1201R	CCATCCAGGACTT	.	PASS	Atlas-SNP
HABP4	22927	hgsc.bcm.edu	37	9	99250463	99250463	+	Silent	SNP	C	C	T	rs7030316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	21	81	0	0.238636	0	C|0.771;T|0.229	0.229	strong	.	HABP4	25	.	NM_014282	exon7	c.C1092T	p.L364L	TAACCTCCCTCGT	.	PASS	Atlas-SNP
MZT2A	653784	hgsc.bcm.edu	37	2	132241704	132241704	+	Missense_Mutation	SNP	C	C	T	rs11553182	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	286	142	271	1	0.496504	0.00369004	C|0.872;T|0.128	0.128	strong	.	MZT2A	6	.	NM_001085365	exon3	c.G407A	p.R136H	GGCTGGCGTGGCA	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48653144	48653144	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	44	56	0	0.564103	0	.	.	none	.	CACNA1G	659	.	NM_001256360	exon8	c.C1381T	p.R461W	GGTGTGCGGGTTG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901726	129901726	+	Missense_Mutation	SNP	C	C	T	rs10082533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	103	289	1	0.443966	0.00346021	C|0.784;T|0.216	0.216	strong	.	MKI67	363	.	NM_002417	exon13	c.G8378A	p.S2793N	TGGGCACTTTCCC	.	PASS	Atlas-SNP
DLK2	65989	hgsc.bcm.edu	37	6	43418733	43418733	+	Silent	SNP	G	G	A	rs1214749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	118	0	1	0	G|0.662;A|0.338	0.338	strong	.	DLK2	22	.	NM_023932	exon6	c.C696T	p.H232H	GAAGTCGTGGACA	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234398065	234398065	+	Missense_Mutation	SNP	G	G	A	rs34026756	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	102	218	1	0.51	0.00458716	G|0.985;A|0.015	0.015	strong	USP40_ENST00000450966,NS,carcinoma,+1,2	USP40	174	2	NM_018218	exon26	c.C3110T	p.T1037M	TCCACCGTCCAGG	.	PASS	Atlas-SNP
PIGB	9488	hgsc.bcm.edu	37	15	55647617	55647617	+	Missense_Mutation	SNP	A	A	C	rs2444042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	47	94	0	0.456311	0	A|0.977;C|0.023	0.023	strong	.	PIGB	36	.	NM_004855	exon12	c.A1652C	p.K551T	ACATGAAGATGAA	.	PASS	Atlas-SNP
ASB15	142685	hgsc.bcm.edu	37	7	123267200	123267200	+	Missense_Mutation	SNP	C	C	T	rs73718440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	315	149	277	0	0.473016	0	C|0.993;T|0.007	0.007	strong	.	ASB15	94	.	NM_080928	exon7	c.C734T	p.S245L	GGGCGTCGGTGCT	.	PASS	Atlas-SNP
DUOX1	53905	hgsc.bcm.edu	37	15	45442896	45442896	+	Missense_Mutation	SNP	T	T	C	rs16939743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	19	32	0	0.422222	0	T|0.927;C|0.073	0.073	strong	DUOX1,caecum,carcinoma,0,2	DUOX1	125	2	NM_017434	exon23	c.T2885C	p.I962T	ATATGATCTGGTG	.	PASS	Atlas-SNP
TYW3	127253	hgsc.bcm.edu	37	1	75214441	75214441	+	Missense_Mutation	SNP	A	A	G	rs1133891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	136	277	0	0.480565	0	A|0.763;G|0.237	0.237	strong	.	TYW3	36	.	NM_138467	exon4	c.A361G	p.M121V	CATTCCATGGCAA	.	PASS	Atlas-SNP
SEMA3C	10512	hgsc.bcm.edu	37	7	80387766	80387766	+	Silent	SNP	C	C	T	rs1058425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	112	0	1	0	C|0.633;T|0.367	0.367	strong	.	SEMA3C	106	.	NM_006379	exon15	c.G1524A	p.Q508Q	AGATACCTGGGAA	.	PASS	Atlas-SNP
UBASH3B	84959	hgsc.bcm.edu	37	11	122678778	122678778	+	Missense_Mutation	SNP	A	A	G	rs35343548	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	49	176	0	0.376923	0	A|0.992;G|0.008	0.008	strong	.	UBASH3B	73	.	NM_032873	exon13	c.A1706G	p.N569S	CAGGAAATAACAT	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002394	36002394	+	Silent	SNP	G	G	A	rs146822312	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	30	92	0	0.337079	0	G|0.933;A|0.067	0.067	strong	.	DMKN	116	.	NM_001126058	exon5	c.C837T	p.G279G	GCTGCCGCCACTG	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134055275	134055275	+	Missense_Mutation	SNP	C	C	T	rs61744119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	74	114	0	0.552239	0	C|0.995;T|0.005	0.005	strong	.	NCAPD3	141	.	NM_015261	exon17	c.G2192A	p.R731K	TCCAGCCTGGGTG	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	764	15	238	2	0.0196335	0.00840336	.	.	weak	PRB1,NS,carcinoma,0,2	PRB1	33	2	NM_199353	exon4	c.A350G	p.K117R	TGAGGTTTGTTGC	.	scavenged	Atlas-SNP
CYBB	1536	hgsc.bcm.edu	37	X	37663234	37663234	+	Silent	SNP	G	G	A	rs2228117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	367	190	324	1	0.517711	0.00308642	0|0.006;A|0.061	0.061	strong	.	CYBB	62	.	NM_000397	exon9	c.G1002A	p.K334K	GTCCAAGCTGGAG	.	PASS	Atlas-SNP
MICALL2	79778	hgsc.bcm.edu	37	7	1488317	1488317	+	Silent	SNP	G	G	A	rs78897087	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	123	0	1	0	G|0.968;A|0.032	0.032	strong	.	MICALL2	63	.	NM_182924	exon3	c.C273T	p.D91D	CAGCCGGTCAGGC	.	PASS	Atlas-SNP
SSX3	10214	hgsc.bcm.edu	37	X	48213485	48213485	+	Missense_Mutation	SNP	T	T	C	rs150370741	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	760	357	713	0	0.469737	0	T|0.940;C|0.060	0.060	strong	.	SSX3	64	.	NM_021014	exon4	c.A229G	p.T77A	AGTCTGTGACCCG	.	PASS	Atlas-SNP
SPAG4	6676	hgsc.bcm.edu	37	20	34205080	34205080	+	Silent	SNP	C	C	T	rs116016997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	35	65	0	0.421687	0	C|0.982;T|0.018	0.018	strong	.	SPAG4	36	.	NM_003116	exon2	c.C327T	p.V109V	AGTAGTCTCTGAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284497	152284497	+	Silent	SNP	A	A	G	rs144437056	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	640	161	455	1	0.251563	0.0021978	A|0.972;G|0.028	0.028	strong	.	FLG	900	.	NM_002016	exon3	c.T2865C	p.H955H	TTCTGAATGTCCC	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12859004	12859004	+	Missense_Mutation	SNP	A	A	C	rs3732678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	114	109	0	0.991304	0	A|0.402;C|0.597;G|0.000	0.597	strong	.	CAND2	138	.	NM_001162499	exon10	c.A2573C	p.H858P	CAGGCCACCAGCG	.	PASS	Atlas-SNP
C7orf31	136895	hgsc.bcm.edu	37	7	25182405	25182405	+	Missense_Mutation	SNP	G	G	T	rs11984293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	49	153	0	0.347518	0	G|0.777;T|0.223	0.223	strong	.	C7orf31	53	.	NM_138811	exon8	c.C713A	p.P238Q	AATACTGGCTTAT	.	PASS	Atlas-SNP
WDR38	401551	hgsc.bcm.edu	37	9	127616537	127616537	+	Missense_Mutation	SNP	A	A	G	rs12375547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	79	137	0	0.738318	0	A|0.541;G|0.459	0.459	strong	.	WDR38	21	.	NM_001276376	exon2	c.A29G	p.K10R	CTCAGAAGATGGC	.	PASS	Atlas-SNP
CLCN6	1185	hgsc.bcm.edu	37	1	11876692	11876692	+	Silent	SNP	G	G	A	rs57044879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	111	158	0	0.578125	0	G|0.971;A|0.029	0.029	strong	.	CLCN6	77	.	NM_001286	exon4	c.G234A	p.A78A	TGAGGCGGTGAAG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42866296	42866296	+	Silent	SNP	T	T	C	rs3787950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	64	122	0	0.576577	0	C|0.135;N|0.001	0.135	strong	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	NM_001135099	exon3	c.A336G	p.T112T	GCACACTGTCCCG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92624276	92624276	+	Silent	SNP	G	G	A	rs371790138		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	24	60	0	0.5	0	.	.	weak	.	FAT3	1822	.	NM_001008781	exon25	c.G13671A	p.V4557V	TCAAGTGTAGACA	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74037369	74037369	+	Silent	SNP	C	C	T	rs35565659	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	110	279	0	0.445344	0	C|0.976;T|0.024	0.024	strong	.	GFM2	38	.	NM_032380	exon11	c.G915A	p.L305L	TGGTAACAAATCA	.	PASS	Atlas-SNP
TBATA	219793	hgsc.bcm.edu	37	10	72536936	72536936	+	Silent	SNP	A	A	G	rs2254433	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	24	49	1	0.461538	0.0204082	A|0.710;G|0.290	0.290	strong	C10orf27,NS,carcinoma,-2,1	.	.	1	NM_152710	exon7	c.T663C	p.A221A	GAGGAAAGCCTGG	.	scavenged	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71740073	71740073	+	Missense_Mutation	SNP	A	A	T	rs116305374	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	42	108	0	0.411765	0	A|0.999;T|0.001	0.001	strong	.	ZNF366	108	.	NM_152625	exon5	c.T1745A	p.L582Q	CTCCTCAGGACAC	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	63822357	63822357	+	Missense_Mutation	SNP	T	T	C	rs62065084	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	395	176	348	0	0.44557	0	T|0.765;C|0.235	0.235	strong	.	CEP112	192	.	NM_001037325	exon1	c.A61G	p.I21V	TCTCTATCAGTCT	.	PASS	Atlas-SNP
C17orf85	55421	hgsc.bcm.edu	37	17	3749411	3749411	+	Missense_Mutation	SNP	T	T	G	rs12449334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	26	55	0	0.472727	0	T|0.949;G|0.051	0.051	strong	.	C17orf85	66	.	NM_001114118	exon1	c.A107C	p.E36A	TCCGGCTCGCCAC	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12856087	12856087	+	Missense_Mutation	SNP	C	C	T	rs141070565	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	835	136	699	0	0.162874	0	C|0.968;T|0.032	0.032	strong	PRAMEF1,trunk,malignant_melanoma,0,4	PRAMEF1	78	4	NM_023013	exon4	c.C1367T	p.P456L	CCACCCCCTGCCC	.	scavenged	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27277051	27277051	+	Missense_Mutation	SNP	C	C	T	rs41269255	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	49	98	0	0.457944	0	C|0.891;T|0.109	0.109	strong	POM121L2,colon,carcinoma,0,1	POM121L2	61	1	NM_033482	exon1	c.G2899A	p.A967T	TGGGGGCCATAGT	.	PASS	Atlas-SNP
FCRL5	83416	hgsc.bcm.edu	37	1	157514091	157514091	+	Missense_Mutation	SNP	C	C	T	rs12036228	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	75	166	0	0.480769	0	C|0.772;T|0.228	0.228	strong	.	FCRL5	177	.	NM_031281	exon5	c.G805A	p.V269I	ATATGACGCTGTA	.	PASS	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	50	94	0	0.485437	0	A|0.936;C|0.064	0.064	strong	.	MCM8	125	.	NM_032485	exon4	c.A303C	p.K101N	TGAAAAATTTTTC	.	PASS	Atlas-SNP
ECM1	1893	hgsc.bcm.edu	37	1	150484016	150484016	+	Silent	SNP	G	G	A	rs78194273	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	54	88	0	0.545455	0	G|0.984;A|0.016	0.016	strong	.	ECM1	96	.	NM_001202858	exon7	c.G873A	p.E291E	GGGGGAGGCTCGG	.	PASS	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	37	3	58139172	58139172	+	Silent	SNP	G	G	A	rs60599272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	73	127	0	0.51773	0	G|0.971;A|0.029	0.029	strong	.	FLNB	430	.	NM_001164317	exon40	c.G6531A	p.V2177V	GATTGTGCCCATG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170038097	170038097	+	Missense_Mutation	SNP	C	C	T	rs137983840	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	82	197	0	0.448087	0	C|0.999;T|0.001	0.001	strong	LRP2,NS,carcinoma,0,1	LRP2	751	1	NM_004525	exon52	c.G10030A	p.A3344T	TGTATGCGCGGTG	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14131854	14131854	+	Missense_Mutation	SNP	A	A	G	rs35118414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	61	151	0	0.442029	0	A|0.956;G|0.044	0.044	strong	.	CD83	23	.	NM_004233	exon3	c.A257G	p.N86S	CCCCCAATGAAAG	.	PASS	Atlas-SNP
RAET1L	154064	hgsc.bcm.edu	37	6	150342232	150342232	+	Missense_Mutation	SNP	G	G	A	rs61730071	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	391	199	361	0	0.508951	0	G|0.611;A|0.389	0.389	strong	.	RAET1L	21	.	NM_130900	exon3	c.C440T	p.T147I	AGGAAGGTCTGTC	.	PASS	Atlas-SNP
CDT1	81620	hgsc.bcm.edu	37	16	88871908	88871908	+	Silent	SNP	A	A	G	rs1834065	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	80	82	0	0.987654	0	A|0.864;G|0.136	0.136	strong	.	CDT1	30	.	NM_030928	exon4	c.A549G	p.G183G	GCCGGGACTCGTG	.	PASS	Atlas-SNP
TCEB3	6924	hgsc.bcm.edu	37	1	24077554	24077554	+	Silent	SNP	T	T	C	rs35397069	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	68	148	0	0.427673	0	T|0.913;C|0.087	0.087	strong	.	TCEB3	61	.	NM_003198	exon4	c.T537C	p.D179D	GAGAGATGAGAGA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82836912	82836912	+	Missense_Mutation	SNP	G	G	A	rs61733389	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	51	92	0	0.586207	0	G|0.967;A|0.033	0.033	strong	.	VCAN	498	.	NM_004385	exon8	c.G8090A	p.R2697H	TTCCTCGTAAGTC	.	PASS	Atlas-SNP
C12orf43	64897	hgsc.bcm.edu	37	12	121442833	121442833	+	Missense_Mutation	SNP	C	C	T	rs34543757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	57	84	0	0.57	0	C|0.990;G|0.000;T|0.009	0.009	strong	.	C12orf43	30	.	NM_022895	exon5	c.G425A	p.R142H	TTTCGGCGGGGTT	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	70	127	0	0.443038	0	T|0.655;C|0.345	0.345	strong	SLC6A11,NS,adenoma,0,1	SLC6A11	87	1	NM_014229	exon5	c.T645C	p.S215S	CATCTCTGACGGG	.	PASS	Atlas-SNP
PRSS27	83886	hgsc.bcm.edu	37	16	2762637	2762637	+	Missense_Mutation	SNP	A	A	G	rs61734617	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	82	164	0	0.479532	0	A|0.948;G|0.052	0.052	strong	.	PRSS27	20	.	NM_031948	exon6	c.T857C	p.L286S	CCGCCCAACCTCG	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43023482	43023482	+	Missense_Mutation	SNP	T	T	C	rs12917189	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	217	183	0	0.995413	0	C|0.419;N|0.000	0.419	strong	.	CDAN1	70	.	NM_138477	exon12	c.A1787G	p.Q596R	AGCTCCTGGATCT	.	PASS	Atlas-SNP
NF1	4763	hgsc.bcm.edu	37	17	29553485	29553485	+	Silent	SNP	G	G	A	rs2285892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	25	80	0	0.396825	0	G|0.568;A|0.432	0.432	strong	.	NF1	1586	.	NM_000267	exon18	c.G2034A	p.P678P	CCCCCCGATTTGC	.	PASS	Atlas-SNP
CECR6	27439	hgsc.bcm.edu	37	22	17600977	17600977	+	Silent	SNP	G	G	A	rs5994165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	22	36	0	0.52381	0	G|0.559;A|0.441	0.441	strong	.	CECR6	11	.	NM_031890	exon1	c.C1041T	p.F347F	GGTGCCGAAGGGC	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274161	39274161	+	Missense_Mutation	SNP	T	T	C	rs78125590		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	52	143	6	0.403101	0.041958	T|0.500;C|0.500	0.500	weak	KRTAP4-11,NS,carcinoma,0,3	KRTAP4-11	94	3	NM_033059	exon1	c.A407G	p.H136R	CTGGGGTGGCAGC	.	scavenged	Atlas-SNP
SLC4A2	6522	hgsc.bcm.edu	37	7	150768849	150768849	+	Silent	SNP	C	C	T	rs11542749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	81	104	0	0.50625	0	C|0.927;T|0.073	0.073	strong	.	SLC4A2	98	.	NM_003040	exon15	c.C2265T	p.C755C	CTTCTGCCTGCTG	.	PASS	Atlas-SNP
ZNF645	158506	hgsc.bcm.edu	37	X	22291606	22291606	+	Missense_Mutation	SNP	C	C	A	rs5951426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	135	218	0	0.496324	0	C|0.602;0|0.023	.	strong	.	ZNF645	67	.	NM_152577	exon1	c.C498A	p.D166E	CTCTGACATCCCT	.	PASS	Atlas-SNP
CGNL1	84952	hgsc.bcm.edu	37	15	57839587	57839587	+	Missense_Mutation	SNP	A	A	G	rs16977594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	48	96	0	0.470588	0	A|0.914;G|0.086	0.086	strong	CGNL1,NS,carcinoma,0,1	CGNL1	125	1	NM_032866	exon19	c.A3808G	p.M1270V	GATGACATGGATG	.	PASS	Atlas-SNP
LIPE	3991	hgsc.bcm.edu	37	19	42931004	42931004	+	Missense_Mutation	SNP	A	A	G	rs16975750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	434	193	434	1	0.4447	0.00230415	A|0.915;G|0.085	0.085	strong	.	LIPE	83	.	NM_005357	exon1	c.T298C	p.Y100H	GGATGTAAGGTGA	.	PASS	Atlas-SNP
ZNF71	58491	hgsc.bcm.edu	37	19	57132879	57132879	+	Missense_Mutation	SNP	G	G	A	rs79950845	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	43	72	0	0.558442	0	G|0.976;A|0.024	0.024	strong	.	ZNF71	69	.	NM_021216	exon3	c.G224A	p.C75Y	CCGCATGTCATGA	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112648222	112648222	+	Missense_Mutation	SNP	T	T	C	rs75530703		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	419	407	388	0	0.97136	0	.	.	weak	.	CD200R1	91	.	NM_138806	exon4	c.A335G	p.K112R	TCTTTCTTGTAGG	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13105	13105	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	7	6	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.A769G	p.I257V	GCAGGAATCTTCT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	rs200657736	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	875	120	500	1	0.137143	0.002	G|0.999;C|0.001	0.001	weak	LILRA6,NS,carcinoma,0,2	LILRA6	75	2	NM_024318	exon4	c.C451G	p.H151D	AATGGTGATATCC	.	scavenged	Atlas-SNP
RAET1G	353091	hgsc.bcm.edu	37	6	150239330	150239330	+	Silent	SNP	C	C	T	rs17079029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	422	214	467	0	0.507109	0	C|0.785;T|0.215	0.215	strong	.	RAET1G	31	.	NM_001001788	exon4	c.G822A	p.R274R	GACTCTCCTCAGC	.	PASS	Atlas-SNP
DKK4	27121	hgsc.bcm.edu	37	8	42231786	42231786	+	Silent	SNP	G	G	A	rs2073664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	168	143	0	0.988235	0	G|0.739;A|0.261	0.261	strong	.	DKK4	28	.	NM_014420	exon4	c.C507T	p.V169V	CAAAAGGACTGGC	.	PASS	Atlas-SNP
CPB1	1360	hgsc.bcm.edu	37	3	148545789	148545789	+	Silent	SNP	C	C	T	rs80013498	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	71	111	0	0.486301	0	C|0.986;T|0.014	0.014	strong	.	CPB1	74	.	NM_001871	exon2	c.C72T	p.G24G	ATTCAGCGAGAAG	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36340753	36340753	+	Missense_Mutation	SNP	G	G	A	rs9654132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	46	105	0	0.438095	0	G|0.809;A|0.191	0.191	strong	DTHD1_ENST00000456874,NS,carcinoma,0,5	DTHD1	63	5	NM_001170700	exon8	c.G1985A	p.R662H	TCAACCGTCCACA	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	57	154	0	0.401408	0	T|0.754;A|0.246	0.246	strong	APLF,colon,carcinoma,0,1	APLF	69	1	NM_173545	exon6	c.T670A	p.S224T	GATAAATCCCAGC	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10769873	10769873	+	Silent	SNP	G	G	A	rs115325161	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	56	86	0	0.554455	0	G|0.995;A|0.005	0.005	strong	.	TEKT5	66	.	NM_144674	exon5	c.C1029T	p.N343N	GCGGGCGTTGAAG	.	PASS	Atlas-SNP
MYBPH	4608	hgsc.bcm.edu	37	1	203143725	203143725	+	Missense_Mutation	SNP	G	G	C	rs2642531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	487	243	416	0	0.498973	0	G|0.736;C|0.264	0.264	strong	.	MYBPH	41	.	NM_004997	exon3	c.C341G	p.A114G	TCCGAGGCTGAGG	.	PASS	Atlas-SNP
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	rs62638680	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	101	82	0	0.990196	0	G|0.968;A|0.032	0.032	strong	.	ZKSCAN4	42	.	NM_019110	exon1	c.C64T	p.L22F	TCAGGAGCCCCGT	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47927650	47927650	+	Missense_Mutation	SNP	G	G	A	rs79105203	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	54	125	1	0.55102	0.008	G|0.945;A|0.055	0.055	strong	PKD1L1,colon,carcinoma,0,1	PKD1L1	328	1	NM_138295	exon17	c.C2774T	p.P925L	AGATTCGGTATTT	.	scavenged	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448590	4448590	+	Silent	SNP	C	C	T	rs9911631	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	50	95	0	0.561798	0	C|0.931;T|0.069	0.069	strong	.	MYBBP1A	69	.	NM_014520	exon16	c.G2124A	p.T708T	ATCGTCCGTCACC	.	PASS	Atlas-SNP
RRAGC	64121	hgsc.bcm.edu	37	1	39325136	39325136	+	Silent	SNP	C	C	T	rs112925356	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	53	0	0.517857	0	C|0.978;T|0.022	0.022	strong	.	RRAGC	28	.	NM_001271851	exon1	c.G183A	p.K61K	CCTCGGCTTGGAG	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66416511	66416511	+	Silent	SNP	C	C	T	rs35268505	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	125	238	0	0.520833	0	C|0.981;T|0.019	0.019	strong	.	ARSG	55	.	NM_001267727	exon12	c.C1485T	p.N495N	TGCCAACGACAAC	.	PASS	Atlas-SNP
ACTN4	81	hgsc.bcm.edu	37	19	39212226	39212226	+	Missense_Mutation	SNP	C	C	T	rs140271107	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	43	68	0	0.477778	0	C|1.000;T|0.000	0.000	strong	.	ACTN4	69	.	NM_004924	exon12	c.C1340T	p.S447L	CACTATCGGACAT	.	PASS	Atlas-SNP
TMEM19	55266	hgsc.bcm.edu	37	12	72094627	72094627	+	Missense_Mutation	SNP	C	C	G	rs74104122	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	95	157	0	0.505319	0	C|0.976;G|0.024	0.024	strong	.	TMEM19	35	.	NM_018279	exon6	c.C863G	p.T288S	AAAGCACTGGCAT	.	PASS	Atlas-SNP
TMC2	117532	hgsc.bcm.edu	37	20	2582839	2582839	+	Missense_Mutation	SNP	T	T	A	rs140733869	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	137	226	0	0.559184	0	T|0.997;A|0.003	0.003	strong	.	TMC2	121	.	NM_080751	exon11	c.T1305A	p.F435L	CAACTTTCTCATC	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464487	39464487	+	Missense_Mutation	SNP	G	G	C	rs2074285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	120	125	0	1	0	G|0.614;C|0.386	0.386	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C1019G	p.P340R	ACAGAAGGACAGC	.	PASS	Atlas-SNP
ZNF665	79788	hgsc.bcm.edu	37	19	53668549	53668549	+	Silent	SNP	T	T	G	rs10409924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	98	96	0	0.989899	0	T|0.774;G|0.226	0.226	strong	.	ZNF665	136	.	NM_024733	exon4	c.A1194C	p.G398G	CTTTTCTCCGGTA	.	PASS	Atlas-SNP
TRPV6	55503	hgsc.bcm.edu	37	7	142573332	142573332	+	Silent	SNP	C	C	T	rs4987664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	28	47	0	0.571429	0	C|0.971;T|0.029	0.029	strong	.	TRPV6	108	.	NM_018646	exon8	c.G1011A	p.L337L	GTACAGCAGATAT	.	PASS	Atlas-SNP
OR1D2	4991	hgsc.bcm.edu	37	17	2995572	2995572	+	Missense_Mutation	SNP	G	G	A	rs4300683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	69	159	0	0.43949	0	G|0.842;A|0.158	0.158	strong	.	OR1D2	39	.	NM_002548	exon1	c.C719T	p.T240I	GCACAGGTGGAGA	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81211548	81211548	+	Silent	SNP	G	G	A	rs9934605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	29	43	0	0.58	0	G|0.813;A|0.187	0.187	strong	.	PKD1L2	361	.	NM_001076780	exon14	c.C2301T	p.I767I	AGTGCTGATCACA	.	PASS	Atlas-SNP
TAS2R9	50835	hgsc.bcm.edu	37	12	10962115	10962115	+	Missense_Mutation	SNP	A	A	G	rs3741845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	38	102	0	0.44186	0	G|0.526;N|0.001	0.526	strong	.	TAS2R9	39	.	NM_023917	exon1	c.T560C	p.V187A	ACCATCACCCCCA	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16255644	16255644	+	Missense_Mutation	SNP	C	C	T	rs848208	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	36	84	0	0.455696	0	C|0.896;T|0.104	0.104	strong	.	SPEN	374	.	NM_015001	exon11	c.C2909T	p.A970V	AGCCTGCAGATGG	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	67	105	0	0.5	0	T|0.567;C|0.433	0.433	strong	ZNF407,NS,carcinoma,0,1	ZNF407	231	1	NM_001146190	exon1	c.T4507C	p.L1503L	TTATTTTTACATA	.	PASS	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	37	22	44586519	44586519	+	Missense_Mutation	SNP	C	C	A	rs3842780	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	32	71	0	0.385542	0	C|0.985;A|0.015	0.015	strong	PARVG,NS,carcinoma,0,1	PARVG	41	1	NM_001137606	exon7	c.C477A	p.N159K	AACCAACGTCCAG	.	PASS	Atlas-SNP
ACOX2	8309	hgsc.bcm.edu	37	3	58512237	58512237	+	Silent	SNP	A	A	G	rs1127745	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	68	169	0	0.409639	0	A|0.718;G|0.282	0.282	strong	.	ACOX2	53	.	NM_003500	exon10	c.T1302C	p.C434C	GTAGGTACAGGAG	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5795412	5795412	+	Silent	SNP	C	C	T	rs11737221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	90	187	2	0.42654	0.0106952	C|0.742;T|0.258	0.258	strong	EVC,caecum,carcinoma,0,1	EVC	90	1	NM_153717	exon13	c.C1854T	p.G618G	CCGCGGCGTCTTG	.	scavenged	Atlas-SNP
CKAP2L	150468	hgsc.bcm.edu	37	2	113509891	113509891	+	Missense_Mutation	SNP	T	T	C	rs36046436	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	382	184	396	0	0.481675	0	T|0.983;C|0.017	0.017	strong	.	CKAP2L	54	.	NM_152515	exon5	c.A1555G	p.S519G	TTTTACTGGACAG	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45518396	45518396	+	Silent	SNP	G	G	A	rs115989144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	39	62	0	0.573529	0	G|0.996;A|0.004	0.004	strong	TRAPPC10,colon,carcinoma,+1,1	TRAPPC10	109	1	NM_003274	exon21	c.G3327A	p.S1109S	TTTTTCGACAAAG	.	PASS	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	306	39	197	0	0.127451	0	C|0.946;T|0.054	0.054	strong	.	BOD1	15	.	NM_138369	exon3	c.G406A	p.V136M	CCACCACCTGAGA	.	PASS	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	37	12	7021957	7021957	+	Silent	SNP	G	G	A	rs3759353	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	56	0	0.490909	0	G|0.967;A|0.033	0.033	strong	LRRC23,colon,carcinoma,0,2	LRRC23	46	2	NM_001135217	exon7	c.G822A	p.A274A	GCGAGCGTTGGTG	.	PASS	Atlas-SNP
GRHL3	57822	hgsc.bcm.edu	37	1	24664220	24664220	+	Missense_Mutation	SNP	G	G	A	rs145470039	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	37	93	0	0.468354	0	G|0.997;A|0.003	0.003	strong	GRHL3_ENST00000350501,NS,carcinoma,0,4	GRHL3	69	4	NM_021180	exon6	c.G796A	p.V266I	TACCCCGTCACCC	.	PASS	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	147	239	1	0.462264	0.0041841	C|0.841;T|0.159	0.159	strong	.	SLC39A8	24	.	NM_022154	exon3	c.G411A	p.T137T	AATAATCGTCACT	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38743649	38743649	+	Silent	SNP	A	A	G	rs149534667	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	59	176	0	0.395973	0	A|0.995;G|0.005	0.005	strong	.	DNAH8	1239	.	NM_001206927	exon13	c.A1884G	p.Q628Q	AAAGCAATATGAC	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63721251	63721251	+	Missense_Mutation	SNP	A	A	G	rs12154540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	17	30	0	0.53125	0	A|0.805;G|0.195	0.195	strong	ZNF679,NS,carcinoma,0,1	ZNF679	80	1	NM_153363	exon4	c.A206G	p.E69G	GTCTGGAGCAAAA	.	PASS	Atlas-SNP
PPWD1	23398	hgsc.bcm.edu	37	5	64881936	64881936	+	Silent	SNP	A	A	G	rs27141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	83	140	0	0.549669	0	A|0.396;G|0.604	0.604	strong	.	PPWD1	47	.	NM_015342	exon10	c.A1725G	p.P575P	CAGGCCATACACA	.	PASS	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31963780	31963780	+	Silent	SNP	A	A	G	rs371801898		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	867	299	927	2	0.344867	0.0021575	.	.	weak	.	C4A	15	.	NM_007293	exon26	c.A3279G	p.V1093V	GCAGGTAGGAGGC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151155197	151155197	+	Silent	SNP	T	T	C	rs141741834	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	71	130	0	0.550388	0	T|0.993;C|0.007	0.007	strong	.	IGSF10	279	.	NM_178822	exon6	c.A7152G	p.Q2384Q	ATAACTTTGTGGT	.	PASS	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	37	16	1706480	1706480	+	Silent	SNP	C	C	G	rs80154657	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	9	30	0	0.375	0	C|0.979;G|0.021	0.021	strong	.	CRAMP1L	60	.	NM_020825	exon9	c.C1722G	p.P574P	TGTCCCCGAGCAG	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386300	7386300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	5	146	0	0.0285714	0	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,-1,1	.	.	1	NM_001102614	exon2	c.G997A	p.E333K	GAGAGGGAAGGGA	.	scavenged	Atlas-SNP
SLC5A10	125206	hgsc.bcm.edu	37	17	18918396	18918396	+	Silent	SNP	G	G	C	rs2074279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	348	172	247	1	0.494253	0.00404858	G|0.872;C|0.128	0.128	strong	.	SLC5A10	55	.	NM_152351	exon11	c.G1173C	p.A391A	GCTGGCGGCGCTC	.	PASS	Atlas-SNP
OR5I1	10798	hgsc.bcm.edu	37	11	55703728	55703728	+	Missense_Mutation	SNP	A	A	G	rs4367963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	69	118	0	0.5	0	A|0.901;G|0.099	0.099	strong	OR5I1,caecum,carcinoma,+1,2	OR5I1	110	2	NM_006637	exon1	c.T149C	p.L50S	CTGATCAACAGCA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557477	32557477	+	Silent	SNP	G	G	A	rs150644773	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	268	24	390	0	0.0895522	0	G|0.868;A|0.132	0.132	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.C43T	p.L15L	CTGTCAGCGCTGT	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3180316	3180316	+	Silent	SNP	T	T	C	rs11414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	97	106	0	1	0	T|0.393;G|0.000;C|0.607	0.607	strong	PITRM1,NS,carcinoma,0,1	PITRM1	109	1	NM_001242307	exon27	c.A3024G	p.R1008R	GAGGTATCTGAGA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	392	180	323	4	0.459184	0.0123839	T|0.824;G|0.176	0.176	strong	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon2	c.T200G	p.V67G	CTCTGGTATCGCT	.	scavenged	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	368030	368030	+	Silent	SNP	T	T	C	rs10972587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	144	0	0.45614	0	T|0.862;C|0.138	0.138	strong	.	DOCK8	401	.	NM_203447	exon15	c.T1692C	p.Y564Y	TCTCTATGTCTAC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9070186	9070186	+	Missense_Mutation	SNP	C	C	T	rs1559171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	132	273	0	0.468085	0	C|0.987;T|0.013	0.013	strong	.	MUC16	4315	.	NM_024690	exon3	c.G17260A	p.A5754T	CCATGGCGAAGGT	.	PASS	Atlas-SNP
C10orf113	387638	hgsc.bcm.edu	37	10	21414892	21414892	+	Missense_Mutation	SNP	C	C	G	rs625223	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	62	156	0	0.488189	0	C|0.539;G|0.461	0.461	strong	.	C10orf113	32	.	NM_001010896	exon2	c.G328C	p.D110H	CTGGATCTGGTTC	.	PASS	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1827565	1827565	+	Missense_Mutation	SNP	A	A	G	rs10415018	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	38	91	0	0.339286	0	A|0.781;G|0.219	0.219	strong	REXO1,NS,carcinoma,0,1	REXO1	55	1	NM_020695	exon2	c.T1223C	p.V408A	TTCTCCACAGGCC	.	PASS	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	37	11	88027393	88027393	+	Silent	SNP	A	A	C	rs17594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	79	188	0	0.411458	0	A|0.942;C|0.058	0.058	strong	.	CTSC	46	.	NM_001814	exon7	c.T1173G	p.T391T	TAGACCAGTGTGG	.	PASS	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	37	15	94858808	94858808	+	Silent	SNP	G	G	A	rs146431277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	105	191	0	0.517241	0	G|0.998;A|0.002	0.002	strong	MCTP2,NS,adenoma,0,1	MCTP2	122	1	NM_001159643	exon3	c.G579A	p.A193A	TTTTGCGTACCTC	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43680147	43680147	+	Missense_Mutation	SNP	C	C	T	rs72623883		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	29	59	0	0.278846	0	.	.	weak	PSG5,NS,carcinoma,0,1	PSG5	58	1	NM_002781	exon3	c.G584A	p.R195Q	ATGGGTCGCTTTA	.	PASS	Atlas-SNP
ADCK2	90956	hgsc.bcm.edu	37	7	140374482	140374482	+	Silent	SNP	G	G	C	rs142577491	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	71	113	0	0.572581	0	G|0.999;C|0.001	0.001	strong	.	ADCK2	37	.	NM_052853	exon2	c.G1005C	p.L335L	AGTCCTGGGAGTT	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	147	0	1	0	A|0.686;G|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T690C	p.S230S	CTGATCACTGACC	.	PASS	Atlas-SNP
RGPD8	727851	hgsc.bcm.edu	37	2	113147666	113147666	+	Missense_Mutation	SNP	C	C	A	rs71227755		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1597	126	1391	2	0.0788979	0.00143781	C|0.500;A|0.500	0.500	weak	RGPD8_ENST00000302558,NS,carcinoma,-1,2	RGPD8	81	2	NM_001164463	exon20	c.G2856T	p.R952S	CCGGCCCCTAATA	.	scavenged	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169504743	169504743	+	Silent	SNP	T	T	C	rs1045168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	125	0	1	0	A|0.000;C|0.311;T|0.689	0.311	strong	DOCK2,NS,carcinoma,0,3	DOCK2	389	3	NM_004946	exon48	c.T4896C	p.R1632R	GGGCCGTCCCAGG	.	PASS	Atlas-SNP
ZNF488	118738	hgsc.bcm.edu	37	10	48370595	48370595	+	Silent	SNP	G	G	A	rs11204210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	29	73	0	0.333333	0	G|0.644;A|0.356	0.356	strong	ZNF488,NS,carcinoma,0,2	ZNF488	38	2	NM_153034	exon2	c.G63A	p.G21G	AGCTGGGAAGGGA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	46	154	0	0.300654	0	T|0.684;G|0.316	0.316	strong	SVEP1,NS,carcinoma,0,2	SVEP1	326	2	NM_153366	exon26	c.A4330C	p.M1444L	GGAGCATGCCATC	.	PASS	Atlas-SNP
ZBTB40	9923	hgsc.bcm.edu	37	1	22835677	22835677	+	Missense_Mutation	SNP	A	A	G	rs209729	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	171	163	1	0.994186	0.00613497	G|0.812;N|0.000	0.812	strong	.	ZBTB40	87	.	NM_001083621	exon10	c.A1784G	p.Y595C	TTGAGTACAAGCT	.	PASS	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	19	44	0	0.431818	0	G|0.905;A|0.095	0.095	strong	.	CDC14A	65	.	NM_033313	exon11	c.G990A	p.S330S	AGCATCGTTGTGG	.	PASS	Atlas-SNP
C22orf43	51233	hgsc.bcm.edu	37	22	23974200	23974200	+	Missense_Mutation	SNP	A	A	G	rs3827318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	95	195	0	0.454545	0	A|0.842;G|0.156	0.156	strong	.	C22orf43	18	.	NM_016449	exon1	c.T11C	p.I4T	GTCAGTATATTCC	.	PASS	Atlas-SNP
C15orf43	145645	hgsc.bcm.edu	37	15	45250685	45250685	+	Missense_Mutation	SNP	T	T	G	rs147135555	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	63	98	0	0.477273	0	T|0.997;G|0.003	0.003	strong	.	C15orf43	19	.	NM_152448	exon3	c.T261G	p.I87M	TTTCATTCTTCCT	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113286405	113286405	+	Silent	SNP	C	C	T	rs2292511	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	77	112	0	0.587786	0	C|0.717;T|0.283	0.283	strong	SIDT1,NS,carcinoma,0,1	SIDT1	99	1	NM_017699	exon3	c.C363T	p.N121N	CTACAACTATCAA	.	PASS	Atlas-SNP
DUPD1	338599	hgsc.bcm.edu	37	10	76797660	76797660	+	Silent	SNP	C	C	T	rs1868624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	69	0	0.453333	0	C|0.959;T|0.041	0.041	strong	.	DUPD1	30	.	NM_001003892	exon3	c.G597A	p.Q199Q	CACCAGCTGCTTG	.	PASS	Atlas-SNP
AMPD3	272	hgsc.bcm.edu	37	11	10526179	10526179	+	Silent	SNP	C	C	T	rs375685508		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	43	98	0	0.358333	0	.	.	weak	.	AMPD3	68	.	NM_000480	exon14	c.C2127T	p.S709S	GAACAGCGTGCTG	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121207083	121207083	+	Missense_Mutation	SNP	C	C	A	rs3218639	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	24	78	0	0.421053	0	C|0.993;A|0.007	0.007	strong	.	POLQ	273	.	NM_199420	exon16	c.G4695T	p.Q1565H	AACCATCTGAACA	.	PASS	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	37	14	94754804	94754804	+	Missense_Mutation	SNP	C	C	T	rs2232708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	66	148	0	0.461538	0	C|0.961;T|0.039	0.039	strong	.	SERPINA10	83	.	NM_001100607	exon3	c.G811A	p.G271S	CTGCACCGTACAT	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	99049593	99049593	+	Missense_Mutation	SNP	A	A	G	rs17558193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	92	204	0	0.474227	0	A|0.611;G|0.389	0.389	strong	.	.	.	.	NM_174952	exon3	c.T373C	p.Y125H	GTTTGTAGTATGC	.	PASS	Atlas-SNP
HAS1	3036	hgsc.bcm.edu	37	19	52222552	52222552	+	Silent	SNP	G	G	A	rs11084112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	17	25	0	0.548387	0	G|0.658;A|0.342	0.342	strong	HAS1,NS,lymphoid_neoplasm,0,1	HAS1	61	1	NM_001523	exon2	c.C609T	p.R203R	GCACCTGCGAGTC	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71631109	71631109	+	Missense_Mutation	SNP	A	A	G	rs3732235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	138	0	1	0	A|0.891;G|0.109	0.109	strong	.	ZNF638	179	.	NM_014497	exon17	c.A2939G	p.N980S	CTGAAAACATGAA	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88780603	88780603	+	Silent	SNP	C	C	G	rs73262673	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	41	145	0	0.44086	0	C|0.960;G|0.040	0.040	strong	.	CTU2	66	.	NM_001012759	exon10	c.C1065G	p.T355T	GCAGACCCAGTTC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305626	48305626	+	Silent	SNP	T	T	C	rs62130757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	87	0	0.480519	0	T|0.887;C|0.113	0.113	strong	.	TPRX1	46	.	NM_198479	exon2	c.A642G	p.P214P	TGAGATTGGGCCT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218683154	218683154	+	Missense_Mutation	SNP	A	A	G	rs2571445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	66	0	1	0	A|0.321;G|0.679	0.679	strong	.	TNS1	251	.	NM_022648	exon24	c.T3589C	p.W1197R	CCCGCCAGCCGAA	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106815286	106815286	+	Silent	SNP	T	T	C	rs1442320	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	53	117	0	0.441667	0	T|0.939;C|0.061	0.061	strong	.	ZFPM2	219	.	NM_012082	exon8	c.T2976C	p.Y992Y	TGATTATATTTCT	.	PASS	Atlas-SNP
PGR	5241	hgsc.bcm.edu	37	11	100909991	100909991	+	Silent	SNP	T	T	C	rs500760	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	92	85	0	1	0	T|0.704;C|0.296	0.296	strong	.	PGR	115	.	NM_000926	exon8	c.A2658G	p.Q886Q	ATGAAGTTGTTTG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39263646	39263646	+	Missense_Mutation	SNP	G	G	A	rs58363253	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	58	97	0	0.456693	0	G|0.949;A|0.051	0.051	strong	.	FREM2	385	.	NM_207361	exon1	c.G2165A	p.R722K	CACTGAGGAAGAA	.	PASS	Atlas-SNP
TMEM106B	54664	hgsc.bcm.edu	37	7	12269417	12269417	+	Missense_Mutation	SNP	C	C	G	rs3173615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	271	325	0	1	0	C|0.481;G|0.519	0.519	strong	TMEM106B,NS,adenoma,0,1	TMEM106B	34	1	NM_001134232	exon5	c.C554G	p.T185S	ACATAACCATTAT	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68729992	68729992	+	Missense_Mutation	SNP	A	A	G	rs11902811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	69	139	0	0.485915	0	A|0.831;G|0.169	0.169	strong	.	APLF	69	.	NM_173545	exon3	c.A298G	p.I100V	TTCCGCATTCTCT	.	PASS	Atlas-SNP
ZNF205	7755	hgsc.bcm.edu	37	16	3169321	3169321	+	Silent	SNP	C	C	T	rs59049520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	52	88	0	0.626506	0	C|0.944;T|0.056	0.056	strong	.	ZNF205	42	.	NM_003456	exon7	c.C660T	p.P220P	GAAGCCCTTCAGA	.	PASS	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19565338	19565338	+	Missense_Mutation	SNP	C	C	T	rs709682	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	38	98	1	0.413043	0.0102041	C|0.816;T|0.184	0.184	strong	KIAA0090,NS,carcinoma,0,1	.	.	1	NM_001271428	exon10	c.G1040A	p.S347N	TCAGAACTGCTAC	.	scavenged	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	37	20	50310559	50310559	+	Silent	SNP	G	G	A	rs2031344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	82	218	0	0.43617	0	G|0.985;A|0.015	0.015	strong	.	ATP9A	135	.	NM_006045	exon7	c.C630T	p.L210L	CGTGGGGAGCCTC	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104080217	104080217	+	Missense_Mutation	SNP	A	A	C	rs75568479	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	107	174	0	0.52451	0	A|0.985;C|0.015	0.015	strong	.	CENPE	253	.	NM_001813	exon22	c.T2551G	p.S851A	CTTTAGAGAGATT	.	PASS	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48806977	48806977	+	Silent	SNP	G	G	A	rs2242463	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	158	147	0	0.9875	0	G|0.817;A|0.183	0.183	strong	.	CCDC114	100	.	NM_144577	exon8	c.C807T	p.D269D	CAGGGCGTCCTCG	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7385661	7385661	+	Missense_Mutation	SNP	A	A	G	rs192630658	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	119	214	1	0.540909	0.0046729	A|0.977;G|0.023	0.023	strong	.	.	.	.	NM_001102614	exon2	c.A358G	p.S120G	GCCTACAGTGCGG	.	PASS	Atlas-SNP
RGP1	9827	hgsc.bcm.edu	37	9	35749845	35749845	+	Silent	SNP	G	G	C	rs2236288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	68	125	0	0.548387	0	G|0.688;C|0.312	0.312	strong	.	RGP1	60	.	NM_001080496	exon2	c.G93C	p.P31P	CCTTCCGCCCACG	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	37	2	198266834	198266834	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	70	173	0	0.327103	0	.	.	none	SF3B1,NS,haematopoietic_neoplasm,0,263	SF3B1	1038	263	NM_012433	exon15	c.A2098G	p.K700E	GAACTTTCTGCTG	.	PASS	Atlas-SNP
RASGEF1A	221002	hgsc.bcm.edu	37	10	43696279	43696279	+	Silent	SNP	A	A	G	rs41301585	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	52	85	0	0.490566	0	A|0.937;G|0.063	0.063	strong	RASGEF1A,NS,carcinoma,0,1	RASGEF1A	66	1	NM_145313	exon5	c.T517C	p.L173L	CAGCCAAGGACAG	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	37	9	15744683	15744683	+	Missense_Mutation	SNP	G	G	A	rs34816651	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	31	56	0	0.563636	0	G|0.951;A|0.049	0.049	strong	.	.	.	.	NM_173550	exon17	c.G2462A	p.C821Y	AATCATGTGCCTC	.	PASS	Atlas-SNP
FTHL17	53940	hgsc.bcm.edu	37	X	31089873	31089873	+	Missense_Mutation	SNP	A	A	T	rs73617043	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	87	180	0	0.467742	0	A|0.996;T|0.004	0.004	strong	.	FTHL17	99	.	NM_031894	exon1	c.T198A	p.H66Q	CTGGGCATGCTCC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305674	48305674	+	Silent	SNP	T	T	C	rs78381908	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	49	106	0	0.515789	0	T|0.885;C|0.115	0.115	strong	.	TPRX1	46	.	NM_198479	exon2	c.A594G	p.P198P	TGAGATTGGGCCT	.	PASS	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125854404	125854404	+	Silent	SNP	C	C	T	rs114109734	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	35	75	0	0.443038	0	C|0.996;T|0.004	0.004	strong	.	ALDH1L1	138	.	NM_001270364	exon12	c.G1476A	p.A492A	GTCCCGCGCACTG	.	PASS	Atlas-SNP
PVR	5817	hgsc.bcm.edu	37	19	45161070	45161070	+	Missense_Mutation	SNP	G	G	A	rs35365841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	42	84	0	0.451613	0	G|0.951;A|0.049	0.049	strong	.	PVR	23	.	NM_001135769	exon5	c.G883A	p.A295T	CAGGGCGCCCAGC	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964162	88964162	+	Missense_Mutation	SNP	T	T	G	rs150870900	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	46	83	0	0.45098	0	T|0.996;G|0.004	0.004	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T1866G	p.D622E	TATAGATGAGGAC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124360037	124360037	+	Missense_Mutation	SNP	C	C	T	rs61732737	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	49	88	0	0.475728	0	C|0.976;T|0.024	0.024	strong	.	DNAH10	888	.	NM_207437	exon46	c.C7844T	p.S2615L	ACACCTCGGTAAC	.	PASS	Atlas-SNP
USP13	8975	hgsc.bcm.edu	37	3	179371154	179371154	+	Silent	SNP	C	C	T	rs2276803	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	124	0	1	0	C|0.795;T|0.205	0.205	strong	.	USP13	117	.	NM_003940	exon1	c.C141T	p.N47N	CAAGAACGAGTGC	.	PASS	Atlas-SNP
SLC9A4	389015	hgsc.bcm.edu	37	2	103142761	103142761	+	Missense_Mutation	SNP	A	A	T	rs115217520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	59	123	0	0.450382	0	A|0.997;T|0.003	0.003	strong	.	SLC9A4	115	.	NM_001011552	exon11	c.A1994T	p.N665I	ACGGGAATCCTCA	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39741280	39741280	+	Silent	SNP	A	A	G	rs35849957	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	55	87	0	0.539216	0	A|0.944;G|0.056	0.056	strong	.	KRT14	65	.	NM_000526	exon2	c.T555C	p.N185N	AAGGACATTGGCA	.	PASS	Atlas-SNP
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	71	160	0	0.470199	0	C|0.865;A|0.135	0.135	strong	.	LRRC43	105	.	NM_001098519	exon5	c.C766A	p.Q256K	GTGCTGCAGGGAA	.	PASS	Atlas-SNP
NKX3-2	579	hgsc.bcm.edu	37	4	13545610	13545610	+	Silent	SNP	C	C	T	rs10032202	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	13	24	0	0.5	0	C|0.964;T|0.036	0.036	strong	.	NKX3-2	15	.	NM_001189	exon1	c.G429A	p.A143A	CCGGCCCGCGGCT	.	PASS	Atlas-SNP
RUFY4	285180	hgsc.bcm.edu	37	2	218940259	218940259	+	Silent	SNP	C	C	T	rs7423696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	65	134	0	0.414013	0	C|0.769;T|0.231	0.231	strong	.	RUFY4	59	.	NM_198483	exon9	c.C1044T	p.P348P	GATGCCCAGCCCC	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19518855	19518855	+	Silent	SNP	T	T	C	rs147313932	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	37	76	0	0.474359	0	T|0.999;C|0.001	0.001	strong	.	UBR4	415	.	NM_020765	exon11	c.A1221G	p.Q407Q	CAGCAATTGGAAA	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7887234	7887234	+	Missense_Mutation	SNP	C	C	T	rs35687686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	34	80	0	0.459459	0	C|0.993;T|0.007	0.007	strong	PER3,colon,carcinoma,0,1	PER3	95	1	NM_016831	exon17	c.C2221T	p.R741W	CACAAGCGGAAGA	.	PASS	Atlas-SNP
C17orf105	284067	hgsc.bcm.edu	37	17	41857869	41857869	+	Silent	SNP	C	C	T	rs73987086	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	67	98	0	0.482014	0	C|0.953;T|0.047	0.047	strong	.	C17orf105	3	.	NM_001136483	exon1	c.C39T	p.I13I	TGTTATCGTCTCT	.	PASS	Atlas-SNP
MBP	4155	hgsc.bcm.edu	37	18	74701984	74701984	+	Silent	SNP	G	G	A	rs470797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	66	141	0	0.485294	0	A|0.185;C|0.000;G|0.815;T|0.000	0.185	strong	MBP,colon,carcinoma,0,2	MBP	45	2	NM_001025101	exon5	c.C609T	p.Y203Y	GGAGCCGTAGTGA	.	PASS	Atlas-SNP
VAMP5	10791	hgsc.bcm.edu	37	2	85818886	85818886	+	Silent	SNP	C	C	T	rs14976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	135	176	0	0.544355	0	C|0.797;T|0.203	0.203	strong	.	VAMP5	13	.	NM_006634	exon2	c.C42T	p.N14N	GGCGAACGAGGTG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592312	1592312	+	Missense_Mutation	SNP	T	T	C	rs72484087	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	40	114	0	0.285714	0	T|0.465;C|0.535	0.535	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.A124G	p.I42V	CTGATATGGACTT	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11583245	11583245	+	Silent	SNP	G	G	A	rs8070788	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	37	82	0	0.4625	0	G|0.988;A|0.012	0.012	strong	.	DNAH9	695	.	NM_001372	exon18	c.G3525A	p.L1175L	TGAATTGCTGAAG	.	PASS	Atlas-SNP
CSPG5	10675	hgsc.bcm.edu	37	3	47619025	47619025	+	Missense_Mutation	SNP	G	G	C	rs35863063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	60	0	0.45614	0	G|0.981;C|0.019	0.019	strong	.	CSPG5	46	.	NM_006574	exon2	c.C491G	p.A164G	TCAGAAGCTGGGC	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151874498	151874498	+	Silent	SNP	C	C	T	rs10252263	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	60	161	0	0.361446	0	C|0.865;T|0.135	0.135	strong	.	MLL3	1564	.	NM_170606	exon38	c.G8040A	p.Q2680Q	AGAAGGCTGGGTG	.	PASS	Atlas-SNP
ZNF488	118738	hgsc.bcm.edu	37	10	48370747	48370747	+	Missense_Mutation	SNP	C	C	T	rs35618062	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	41	44	0	0.554054	0	C|0.890;T|0.110	0.110	strong	.	ZNF488	38	.	NM_153034	exon2	c.C215T	p.A72V	GCAGTGCGGAGCT	.	PASS	Atlas-SNP
C10orf118	55088	hgsc.bcm.edu	37	10	115910928	115910928	+	Missense_Mutation	SNP	G	G	T	rs7095762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	64	183	0	0.365714	0	G|0.758;T|0.242	0.242	strong	.	C10orf118	70	.	NM_018017	exon4	c.C811A	p.Q271K	TTAGTTGATCTCT	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	73000131	73000131	+	Silent	SNP	G	G	A	rs35073557	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	37	69	0	0.544118	0	G|0.981;A|0.019	0.019	strong	.	TSHZ1	104	.	NM_005786	exon2	c.G2634A	p.P878P	GGGCCCGCAGGAG	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254184	39254184	+	Silent	SNP	T	T	C	rs7217470	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	83	101	1	0.568493	0.00990099	T|0.820;C|0.180	0.180	strong	KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	NM_031960	exon1	c.A153G	p.R51R	CTGGGGTCTGCAG	.	scavenged	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39537616	39537616	+	Silent	SNP	C	C	T	rs28454772	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	67	126	0	0.527559	0	C|0.914;T|0.086	0.086	strong	ADAM18,colon,carcinoma,0,1	ADAM18	169	1	NM_014237	exon16	c.C1692T	p.D564D	AAGTGACGCTCAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9005719	9005719	+	Silent	SNP	A	A	G	rs4804375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	204	216	0	0.995122	0	A|0.267;G|0.733	0.733	strong	.	MUC16	4315	.	NM_024690	exon46	c.T39687C	p.D13229D	TACTCCATCCTTC	.	PASS	Atlas-SNP
NDUFAF7	55471	hgsc.bcm.edu	37	2	37459308	37459308	+	Missense_Mutation	SNP	C	C	G	rs2714473	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	64	123	0	0.481203	0	C|0.931;G|0.069	0.069	strong	.	.	.	.	NM_001083946	exon2	c.C115G	p.P39A	GAAAACCCGGTGA	.	PASS	Atlas-SNP
CYBRD1	79901	hgsc.bcm.edu	37	2	172411273	172411273	+	Missense_Mutation	SNP	G	G	A	rs10455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	207	0	1	0	A|0.688;C|0.004	0.688	strong	.	CYBRD1	16	.	NM_024843	exon4	c.G797A	p.S266N	TAAACAGTGAAGT	.	PASS	Atlas-SNP
ERC2	26059	hgsc.bcm.edu	37	3	56026204	56026204	+	Silent	SNP	C	C	T	rs61732592	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	118	217	0	0.510823	0	C|0.988;T|0.012	0.012	strong	ERC2_ENST00000288221,caecum,carcinoma,-1,2	ERC2	221	2	NM_015576	exon11	c.G2136A	p.A712A	GTAAGACGCCTCT	.	PASS	Atlas-SNP
GJB4	127534	hgsc.bcm.edu	37	1	35227466	35227466	+	Missense_Mutation	SNP	A	A	C	rs3738346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	30	58	0	0.508475	0	A|0.915;C|0.085	0.085	strong	.	GJB4	51	.	NM_153212	exon2	c.A611C	p.E204A	TCAGTGAAGTCTT	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23874507	23874507	+	Silent	SNP	G	G	T	rs2277473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	100	177	0	0.531915	0	A|0.000;C|0.007	.	strong	.	MYH6	274	.	NM_002471	exon5	c.C427A	p.R143R	TGCCCCGGTAGGC	.	PASS	Atlas-SNP
FAM193A	8603	hgsc.bcm.edu	37	4	2661342	2661342	+	Missense_Mutation	SNP	A	A	G	rs17164077	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	42	98	0	0.47191	0	A|0.937;G|0.063	0.063	strong	FAM193A,colon,carcinoma,0,1	FAM193A	103	1	NM_001256667	exon8	c.A646G	p.M216V	AGGCACATGTTAT	.	PASS	Atlas-SNP
NOL11	25926	hgsc.bcm.edu	37	17	65735054	65735054	+	Silent	SNP	A	A	G	rs151002760	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	53	103	0	0.452991	0	A|0.997;G|0.003	0.003	strong	.	NOL11	48	.	NM_015462	exon15	c.A1770G	p.A590A	TAATGCAATTCTT	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807938	18807938	+	Missense_Mutation	SNP	C	C	A	rs2992754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	82	82	0	0.987952	0	C|0.770;A|0.230	0.230	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.C463A	p.P155T	CCTGACCCTCCCC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170155460	170155460	+	Missense_Mutation	SNP	C	C	A	rs61735516	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	149	268	0	0.501683	0	C|0.987;A|0.013	0.013	strong	.	C6orf70	63	.	NM_018341	exon3	c.C257A	p.T86N	CTCTGACCAAGGG	.	PASS	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38431436	38431436	+	Silent	SNP	C	C	T	rs1058656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	64	122	0	0.484848	0	C|0.804;T|0.196	0.196	strong	.	AMPH	157	.	NM_001635	exon19	c.G1791A	p.T597T	AGAAGGCGTGGGC	.	PASS	Atlas-SNP
ZSCAN22	342945	hgsc.bcm.edu	37	19	58850341	58850341	+	Silent	SNP	G	G	C	rs59054150	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	75	0	0.471429	0	G|0.905;C|0.095	0.095	strong	.	ZSCAN22	47	.	NM_181846	exon3	c.G1125C	p.T375T	GCACACGGGGGAG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149509079	149509079	+	Missense_Mutation	SNP	T	T	C	rs73727633	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	34	73	0	0.395349	0	T|0.957;C|0.043	0.043	strong	.	.	.	.	NM_198455	exon68	c.T9625C	p.F3209L	CACCGGTTCTGTG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367556	128367556	+	Missense_Mutation	SNP	G	G	A	rs199654311	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	58	100	0	0.537037	0	G|0.999;A|0.001	0.001	strong	.	MYO7B	359	.	NM_001080527	exon24	c.G3157A	p.G1053S	GAGCACGGTGCCC	.	PASS	Atlas-SNP
FBXW8	26259	hgsc.bcm.edu	37	12	117387465	117387465	+	Missense_Mutation	SNP	A	A	G	rs36021180	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	85	163	0	0.555556	0	A|0.983;G|0.017	0.017	strong	.	FBXW8	53	.	NM_153348	exon4	c.A631G	p.T211A	CCTGACACAGTTT	.	PASS	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	183976108	183976108	+	Silent	SNP	T	T	C	rs902415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	81	156	0	0.460227	0	T|0.697;C|0.303	0.303	strong	.	ECE2	303	.	NM_032331	exon3	c.T513C	p.F171F	CCGGTTTATCTCA	.	PASS	Atlas-SNP
PACS2	23241	hgsc.bcm.edu	37	14	105821457	105821457	+	Silent	SNP	G	G	A	rs61738367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	48	105	0	0.494845	0	G|0.986;A|0.014	0.014	strong	.	PACS2	75	.	NM_001100913	exon4	c.G366A	p.K122K	CTACAAGAACAGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515199	195515199	+	Silent	SNP	A	A	C	rs201720234	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	384	45	197	0	0.117188	0	A|0.994;C|0.006	0.006	strong	.	MUC4	1505	.	NM_018406	exon2	c.T3252G	p.G1084G	GGTGTCACCTGTG	.	PASS	Atlas-SNP
TM9SF3	56889	hgsc.bcm.edu	37	10	98282083	98282083	+	Silent	SNP	C	C	T	rs35359279	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	35	80	0	0.368421	0	C|0.990;T|0.010	0.010	strong	.	TM9SF3	45	.	NM_020123	exon15	c.G1707A	p.A569A	ACCAATCGCTCCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124387574	124387574	+	Silent	SNP	G	G	A	rs58411567	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	45	81	0	0.56962	0	G|0.697;A|0.303	0.303	strong	.	DNAH10	888	.	NM_207437	exon56	c.G9375A	p.E3125E	GGCCGAGACGACC	.	PASS	Atlas-SNP
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297262	179297262	+	Silent	SNP	T	T	C	rs407437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	104	0	0.428571	0	T|0.882;C|0.118	0.118	strong	.	TBC1D9B	157	.	NM_198868	exon16	c.A2718G	p.T906T	CATCCCTGTCACG	.	PASS	Atlas-SNP
MIER2	54531	hgsc.bcm.edu	37	19	334474	334474	+	Silent	SNP	T	T	G	rs11084956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	108	105	0	1	0	T|0.793;G|0.207	0.207	strong	.	MIER2	51	.	NM_017550	exon3	c.A169C	p.R57R	CCCCCCTAACACT	.	PASS	Atlas-SNP
ARMC9	80210	hgsc.bcm.edu	37	2	232072912	232072912	+	Silent	SNP	T	T	C	rs11558174	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	109	217	0	0.480176	0	T|0.713;C|0.287	0.287	strong	ARMC9_ENST00000359743,NS,carcinoma,0,2	ARMC9	129	2	NM_025139	exon3	c.T124C	p.L42L	AAACCATTGTGTA	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	13356807	13356807	+	Silent	SNP	C	C	T	rs62637614	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	49	98	0	0.433628	0	C|0.968;T|0.032	0.032	strong	.	DLC1	411	.	NM_182643	exon2	c.G774A	p.L258L	AGTATCCAAGAAC	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72324139	72324139	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	60	127	0	0.444444	0	.	.	none	KIAA1274,NS,carcinoma,-1,1	.	.	1	NM_014431	exon19	c.C2282T	p.A761V	AAGAGGCGCAAGA	.	PASS	Atlas-SNP
ZNF135	7694	hgsc.bcm.edu	37	19	58579464	58579464	+	Missense_Mutation	SNP	A	A	G	rs75381380		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	31	66	0	0.462687	0	.	.	weak	.	ZNF135	159	.	NM_007134	exon4	c.A1684G	p.I562V	CCCCTCATTCAGC	.	PASS	Atlas-SNP
COLEC11	78989	hgsc.bcm.edu	37	2	3691548	3691548	+	Missense_Mutation	SNP	A	A	G	rs7567833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	110	1	1	0.00909091	A|0.765;G|0.235	0.235	strong	.	COLEC11	93	.	NM_001255985	exon8	c.A698G	p.H233R	CTGACCACTCCCC	.	PASS	Atlas-SNP
SYTL4	94121	hgsc.bcm.edu	37	X	99955925	99955925	+	Silent	SNP	T	T	C	rs16983588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	269	318	0	1	0	0|0.004;C|0.166	0.166	strong	.	SYTL4	72	.	NM_001129896	exon6	c.A507G	p.R169R	GATCTTTCTTCCT	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39225549	39225549	+	Silent	SNP	G	G	C	rs36091974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	107	187	0	0.5	0	G|0.973;C|0.027	0.027	strong	.	XIRP1	173	.	NM_194293	exon2	c.C5388G	p.P1796P	GTTCCTGGGTGGC	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139563914	139563914	+	Missense_Mutation	SNP	C	C	G	rs9495391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	127	121	1	0.992188	0.00826446	C|0.511;G|0.489	0.489	strong	TXLNB,caecum,carcinoma,+2,2	TXLNB	96	2	NM_153235	exon10	c.G1804C	p.A602P	AGGACGCCTGATC	.	PASS	Atlas-SNP
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	44	86	0	0.44898	0	A|0.807;G|0.193	0.193	strong	.	ATL1	46	.	NM_015915	exon2	c.A84G	p.P28P	GGAGCCAGTGAAA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129913960	129913960	+	Missense_Mutation	SNP	A	A	T	rs7095325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	19	45	0	0.452381	0	A|0.739;T|0.261	0.261	strong	.	MKI67	363	.	NM_002417	exon7	c.T712A	p.W238R	GCTTCCAAAAGGG	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672703	238672703	+	Missense_Mutation	SNP	C	C	G	rs3739038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	57	139	0	0.416058	0	C|0.687;G|0.312	0.312	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.C2347G	p.H783D	CCAGGGCACTTCA	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	37	14	36153177	36153177	+	Missense_Mutation	SNP	T	T	C	rs2274068	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	175	171	1	1	0.00584795	T|0.603;C|0.397	0.397	strong	.	RALGAPA1	289	.	NM_194301	exon20	c.A2791G	p.T931A	TGTCGGTTCCAAA	.	PASS	Atlas-SNP
LRRC7	57554	hgsc.bcm.edu	37	1	70460304	70460304	+	Missense_Mutation	SNP	A	A	G	rs72676879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	16	47	0	0.4	0	A|0.991;G|0.009	0.009	strong	.	LRRC7	400	.	NM_020794	exon9	c.A878G	p.N293S	TACCCAATACAAT	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	58	63	0	1	0	A|0.528;G|0.472	0.472	strong	LAMA1,NS,carcinoma,0,1	LAMA1	458	1	NM_005559	exon24	c.T3378C	p.G1126G	CTGAGGACCAAAG	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	96058298	96058298	+	Missense_Mutation	SNP	C	C	T	rs3765524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	75	126	0	0.520833	0	C|0.684;T|0.316	0.316	strong	.	PLCE1	543	.	NM_016341	exon24	c.C5330T	p.T1777I	AACTGACCCAGCA	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80935365	80935365	+	Silent	SNP	C	C	T	rs61729275	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	45	58	0	0.511364	0	C|0.977;T|0.023	0.023	strong	.	PTPRQ	119	.	NM_001145026	exon18	c.C2670T	p.Y890Y	GACTTACGAATCC	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152321618	152321618	+	Missense_Mutation	SNP	G	G	A	rs2444258	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	29	84	0	0.298969	0	G|0.918;A|0.082	0.082	strong	.	RIF1	244	.	NM_018151	exon30	c.G5584A	p.V1862I	AAAACTGTTGGCC	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1004740	1004740	+	Missense_Mutation	SNP	T	T	C	rs2240157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	13	21	0	0.65	0	T|0.304;C|0.696	0.696	strong	.	GRIN3B	46	.	NM_138690	exon3	c.T1240C	p.W414R	CAGGTCTGGCCCA	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17295764	17295764	+	Missense_Mutation	SNP	A	A	G	rs56278097	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	123	301	0	0.473077	0	A|0.901;G|0.099	0.099	strong	.	CROCC	185	.	NM_014675	exon32	c.A5230G	p.S1744G	CTCAACAGCACCC	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38799710	38799710	+	Missense_Mutation	SNP	T	T	C	rs4833095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	97	0	1	0	T|0.512;C|0.488	0.488	strong	.	TLR1	70	.	NM_003263	exon4	c.A743G	p.N248S	GTAAGATTTGATA	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155156875	155156875	+	Missense_Mutation	SNP	T	T	G	rs61746101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	48	74	0	0.494845	0	T|0.959;G|0.041	0.041	strong	.	DCHS2	594	.	NM_017639	exon25	c.A7564C	p.N2522H	ACACATTCACAAA	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595401	55595401	+	Missense_Mutation	SNP	A	A	G	rs148148644	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	73	166	0	0.459119	0	A|0.997;G|0.003	0.003	strong	.	OR5L2	135	.	NM_001004739	exon1	c.A707G	p.K236R	GGCACAAAGCTTT	.	PASS	Atlas-SNP
PRLR	5618	hgsc.bcm.edu	37	5	35065551	35065551	+	Silent	SNP	G	G	A	rs368647716		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	3	177	0	0.0140187	0	.	.	weak	PRLR,pharynx,carcinoma,0,1	PRLR	90	1	NM_000949	exon10	c.C1509T	p.S503S	TTTAGCGGAGCCA	.	scavenged	Atlas-SNP
IQSEC2	23096	hgsc.bcm.edu	37	X	53263764	53263764	+	Silent	SNP	C	C	T	rs184087864	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	97	225	0	0.436937	0	C|0.937;T|0.063	0.063	strong	.	IQSEC2	195	.	NM_001111125	exon15	c.G4104A	p.L1368L	CAGGGGCAGTGGG	.	PASS	Atlas-SNP
PARP12	64761	hgsc.bcm.edu	37	7	139724555	139724555	+	Silent	SNP	C	C	G	rs3735352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	68	135	0	0.503704	0	T|0.364;G|0.008;C|0.628	0.008	strong	.	PARP12	59	.	NM_022750	exon12	c.G1911C	p.P637P	GGCCGGCGGACGG	.	PASS	Atlas-SNP
HSH2D	84941	hgsc.bcm.edu	37	19	16265241	16265241	+	Silent	SNP	C	C	T	rs36088948	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	26	36	0	0.577778	0	C|0.927;T|0.073	0.073	strong	.	HSH2D	16	.	NM_032855	exon7	c.C414T	p.L138L	GGATCTCTTCCTC	.	PASS	Atlas-SNP
PPIB	5479	hgsc.bcm.edu	37	15	64455123	64455123	+	Silent	SNP	G	G	T	rs4904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	100	159	0	0.529101	0	G|0.969;T|0.031	0.031	strong	.	PPIB	20	.	NM_000942	exon1	c.C63A	p.S21S	GAAGACGGACCCC	.	PASS	Atlas-SNP
TERF2	7014	hgsc.bcm.edu	37	16	69401085	69401085	+	Missense_Mutation	SNP	G	G	T	rs34014829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	69	0	0.486486	0	G|0.991;T|0.009	0.009	strong	.	TERF2	24	.	NM_005652	exon7	c.C965A	p.P322Q	GTGGTTGGAGGAT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036951	33036951	+	Missense_Mutation	SNP	A	A	G	rs2308930	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	140	0	1	0	A|0.698;G|0.302	0.302	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.T473C	p.L158P	GTGACCAGCTCCC	.	PASS	Atlas-SNP
PARD6G	84552	hgsc.bcm.edu	37	18	77918221	77918221	+	Silent	SNP	C	C	T	rs2280349	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	23	33	0	0.5	0	C|0.871;T|0.129	0.129	strong	.	PARD6G	20	.	NM_032510	exon3	c.G564A	p.E188E	CACCTTCTCCAGC	.	PASS	Atlas-SNP
CFTR	1080	hgsc.bcm.edu	37	7	117199533	117199533	+	Missense_Mutation	SNP	G	G	A	rs213950	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	39	44	0	1	0	G|0.436;A|0.564	0.564	strong	.	CFTR	171	.	NM_000492	exon11	c.G1408A	p.V470M	CTAATGGTGATTA	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24383873	24383873	+	Missense_Mutation	SNP	T	T	C	rs59805085	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	83	147	0	0.525316	0	T|0.975;C|0.025	0.025	strong	.	MYOM3	131	.	NM_152372	exon37	c.A4295G	p.K1432R	AGCTCCTTGGGCT	.	PASS	Atlas-SNP
RTKN2	219790	hgsc.bcm.edu	37	10	63964653	63964653	+	Silent	SNP	C	C	T	rs41274060	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	49	0	1	0	C|0.821;T|0.179	0.179	strong	.	RTKN2	68	.	NM_145307	exon10	c.G1149A	p.K383K	CATCCACTTCTGA	.	PASS	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5943985	5943985	+	Silent	SNP	G	G	A	rs35102646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	23	58	0	0.425926	0	G|0.992;A|0.008	0.008	strong	.	MCM8	125	.	NM_032485	exon8	c.G855A	p.T285T	AGTTACGATGGAC	.	PASS	Atlas-SNP
C6orf201	404220	hgsc.bcm.edu	37	6	4122279	4122279	+	Silent	SNP	A	A	G	rs17137678	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	114	209	0	0.542857	0	A|0.978;G|0.022	0.022	strong	.	C6orf201	17	.	NM_001085401	exon4	c.A381G	p.T127T	ACAAACAGGTACA	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84539619	84539619	+	Missense_Mutation	SNP	C	C	G	rs4144691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	25	36	0	1	0	C|0.164;G|0.836	0.836	strong	.	ADAMTSL3	290	.	NM_207517	exon9	c.C868G	p.L290V	GTCTTTCTCGTAG	.	PASS	Atlas-SNP
USP39	10713	hgsc.bcm.edu	37	2	85852667	85852667	+	Silent	SNP	G	G	A	rs2304564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	66	116	0	0.492537	0	G|0.889;A|0.111	0.111	strong	USP39,NS,carcinoma,0,1	USP39	33	1	NM_001256725	exon5	c.G576A	p.V192V	GTATGTGTTGAAG	.	PASS	Atlas-SNP
IL1R2	7850	hgsc.bcm.edu	37	2	102626187	102626187	+	Silent	SNP	G	G	A	rs2230401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	34	81	0	0.419753	0	G|0.958;A|0.042	0.042	strong	.	IL1R2	58	.	NM_001261419	exon3	c.G231A	p.T77T	TAGGACGGTCCCA	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101748741	101748741	+	Missense_Mutation	SNP	G	G	C	rs10073333	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	85	85	0	0.52795	0	G|0.932;C|0.068	0.068	strong	.	SLCO6A1	153	.	NM_173488	exon9	c.C1579G	p.P527A	AGCAGGGAGAAAA	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	831811	831811	+	Silent	SNP	C	C	T	rs588442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	54	105	0	0.446281	0	C|0.897;T|0.103	0.103	strong	.	AZU1	31	.	NM_001700	exon5	c.C690T	p.T230T	CTTCACCCGAGTG	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	Missense_Mutation	SNP	C	C	T	rs147946451	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	13	11	0	0.168831	0	C|0.753;T|0.247	0.247	strong	ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	NM_001128223	exon3	c.G148A	p.V50M	GCATCACGTCCCT	.	scavenged	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38588602	38588602	+	Missense_Mutation	SNP	T	T	C	rs2799163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	88	272	0	0.407407	0	T|0.588;C|0.412	0.412	strong	ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	NM_147195	exon11	c.A2063G	p.Y688C	GCAGTATAGTTCA	.	PASS	Atlas-SNP
KIAA0020	9933	hgsc.bcm.edu	37	9	2811522	2811522	+	Missense_Mutation	SNP	T	T	A	rs60717199	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	42	107	0	0.411765	0	T|0.980;A|0.020	0.020	strong	.	KIAA0020	56	.	NM_014878	exon15	c.A1474T	p.S492C	GGTAGCTTAACAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416621	105416621	+	Missense_Mutation	SNP	T	T	C	rs11848082	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	109	275	1	0.429134	0.00363636	T|0.977;C|0.023	0.023	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A5167G	p.N1723D	TCACGTTCACTTG	.	PASS	Atlas-SNP
KLHL13	90293	hgsc.bcm.edu	37	X	117053499	117053499	+	Silent	SNP	C	C	T	rs6645994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	270	362	0	1	0	C|0.688;0|0.003	.	strong	.	KLHL13	87	.	NM_001168299	exon5	c.G564A	p.V188V	GAGAAACACTTTA	.	PASS	Atlas-SNP
HELQ	113510	hgsc.bcm.edu	37	4	84361071	84361071	+	Missense_Mutation	SNP	G	G	A	rs6817280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	376	192	335	1	0.510638	0.00298507	G|0.916;A|0.084	0.084	strong	.	HELQ	95	.	NM_133636	exon8	c.C1753T	p.P585S	TACTAGGACAAAA	.	PASS	Atlas-SNP
WNK4	65266	hgsc.bcm.edu	37	17	40939855	40939855	+	Missense_Mutation	SNP	G	G	T	rs55781437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	27	65	0	0.5	0	G|0.929;T|0.071	0.071	strong	WNK4_ENST00000246914,NS,carcinoma,0,2	WNK4	182	2	NM_032387	exon8	c.G1801T	p.A601S	GACCCTGCCCTTC	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129691132	129691132	+	Silent	SNP	C	C	G	rs17057184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	35	77	0	0.416667	0	C|0.919;G|0.081	0.081	strong	.	LAMA2	481	.	NM_000426	exon34	c.C4956G	p.T1652T	GCTGACCAGGGTA	.	PASS	Atlas-SNP
IDH3B	3420	hgsc.bcm.edu	37	20	2639162	2639162	+	Missense_Mutation	SNP	T	T	C	rs8296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	76	111	0	0.535211	0	T|0.938;C|0.062	0.062	strong	.	IDH3B	25	.	NM_174855	exon12	c.A1078G	p.T360A	CAGAGGTTCGAAC	.	PASS	Atlas-SNP
ACADL	33	hgsc.bcm.edu	37	2	211060050	211060050	+	Missense_Mutation	SNP	T	T	G	rs2286963	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	62	119	0	0.53913	0	G|0.250;N|0.000	0.250	strong	.	ACADL	38	.	NM_001608	exon9	c.A997C	p.K333Q	CTAATTTATGTTG	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766474	27766474	+	Missense_Mutation	SNP	G	G	A	rs375048390		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	138	295	1	0.552	0.00338983	.	.	weak	.	DCAF8L2	79	.	NM_001136533	exon1	c.G1462A	p.G488S	GTGAGCGGTAGTG	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56389631	56389631	+	Missense_Mutation	SNP	A	A	G	rs9905604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	91	0	0.515152	0	A|0.901;G|0.099	0.099	strong	.	BZRAP1	287	.	NM_004758	exon17	c.T2551C	p.W851R	CGGCCCACAGGTC	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942695	6942695	+	Missense_Mutation	SNP	C	C	T	rs12806437	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	335	168	301	0	0.501493	0	C|0.859;T|0.141	0.141	strong	OR2D3,NS,carcinoma,0,1	OR2D3	51	1	NM_001004684	exon1	c.C463T	p.R155W	ACACAACGGGTGT	.	PASS	Atlas-SNP
C3orf43	255798	hgsc.bcm.edu	37	3	196235191	196235191	+	Missense_Mutation	SNP	A	A	G	rs73891273	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	37	0	0.407407	0	A|0.971;G|0.029	0.029	strong	C3orf43,NS,carcinoma,+1,1	C3orf43	25	1	NM_001077657	exon3	c.T212C	p.M71T	AATTCCATTGAAG	.	PASS	Atlas-SNP
ZNF224	7767	hgsc.bcm.edu	37	19	44611162	44611162	+	Silent	SNP	G	G	T	rs13346417	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	63	90	0	0.459854	0	G|0.904;T|0.096	0.096	strong	ZNF224,NS,carcinoma,0,1	ZNF224	70	1	NM_013398	exon6	c.G849T	p.T283T	CCATACGGGGGAG	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59789892	59789892	+	Silent	SNP	G	G	T	rs17096074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	63	129	1	0.543103	0.00775194	G|0.945;T|0.055	0.055	strong	DAAM1,NS,carcinoma,+2,1	DAAM1	95	1	NM_001270520	exon6	c.G723T	p.L241L	GGTTCTGCAGGCC	.	scavenged	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219515109	219515109	+	Missense_Mutation	SNP	T	T	G	rs61733648	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	96	175	0	0.502618	0	T|0.990;G|0.010	0.010	strong	.	ZNF142	190	.	NM_001105537	exon5	c.A421C	p.K141Q	GGCCTTTATCCAC	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626790	140626790	+	Silent	SNP	A	A	C	rs3096082	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	130	141	0	1	0	A|0.846;C|0.154	0.154	strong	.	PCDHB15	138	.	NM_018935	exon1	c.A1644C	p.R548R	GGTGCGAGTGCTG	.	PASS	Atlas-SNP
MORN4	118812	hgsc.bcm.edu	37	10	99376092	99376092	+	Silent	SNP	T	T	C	rs3814555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	36	48	0	0.391304	0	T|0.703;C|0.297	0.297	strong	MORN4_ENST00000307450,NS,carcinoma,0,4	MORN4	24	4	NM_001098831	exon5	c.A369G	p.R123R	CTCACGTCGCAGC	.	PASS	Atlas-SNP
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753136	41753136	+	Missense_Mutation	SNP	G	G	A	rs35880970	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	77	89	0	0.974684	0	G|0.982;A|0.018	0.018	strong	.	PRICKLE4	29	.	NM_013397	exon6	c.G440A	p.R147H	AACAGCGCTGCTG	.	PASS	Atlas-SNP
KIF26B	55083	hgsc.bcm.edu	37	1	245775265	245775265	+	Silent	SNP	C	C	T	rs61741293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	43	94	0	0.387387	0	C|0.989;T|0.011	0.011	strong	.	KIF26B	343	.	NM_018012	exon9	c.C2085T	p.S695S	GAAGAGCGGGAAA	.	PASS	Atlas-SNP
DPH1	1801	hgsc.bcm.edu	37	17	1943525	1943525	+	Missense_Mutation	SNP	A	A	G	rs200693145	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	34	55	0	0.666667	0	A|1.000;G|0.000	0.000	strong	.	DPH1	32	.	NM_001383	exon8	c.A778G	p.S260G	CCATATAGCAAAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416784	105416784	+	Silent	SNP	A	A	G	rs59373922	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	79	320	0	0.365741	0	A|0.835;G|0.165	0.165	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T5004C	p.F1668F	CACCCCAAATGAT	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123886822	123886822	+	Missense_Mutation	SNP	C	C	T	rs41528551	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	482	266	501	0	0.551867	0	C|0.907;T|0.093	0.093	strong	OR10G4,rectum,carcinoma,-2,8	OR10G4	77	8	NM_001004462	exon1	c.C541T	p.P181S	GACGCACCGCCCA	.	PASS	Atlas-SNP
DHX40	79665	hgsc.bcm.edu	37	17	57652789	57652789	+	Silent	SNP	C	C	T	rs77178464	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	386	201	392	1	0.520725	0.00255102	C|0.957;T|0.043	0.043	strong	.	DHX40	40	.	NM_024612	exon7	c.C930T	p.L310L	CACCCTCGATGGC	.	PASS	Atlas-SNP
SLC30A4	7782	hgsc.bcm.edu	37	15	45814306	45814306	+	Silent	SNP	A	A	G	rs61756712	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	64	149	0	0.512	0	A|0.912;G|0.088	0.088	strong	.	SLC30A4	25	.	NM_013309	exon2	c.T247C	p.L83L	TGGTCAAAGGTAA	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73199595	73199595	+	Missense_Mutation	SNP	C	C	T	rs7902757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	64	106	0	0.481203	0	C|0.895;T|0.105	0.105	strong	.	CDH23	365	.	NM_052836	exon2	c.C7T	p.R3C	ATGGGGCGCCATG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144942934	144942934	+	Silent	SNP	C	C	T	rs114155737	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	16	33	0	0.64	0	C|0.987;T|0.013	0.013	strong	.	EPPK1	199	.	NM_031308	exon1	c.G4488A	p.A1496A	CAGGGCCGCAGCC	.	PASS	Atlas-SNP
SLC9A4	389015	hgsc.bcm.edu	37	2	103095494	103095494	+	Silent	SNP	C	C	T	rs61731285	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	41	74	0	0.43617	0	C|0.965;T|0.035	0.035	strong	.	SLC9A4	115	.	NM_001011552	exon2	c.C453T	p.F151F	GCCCTTCTTTGAG	.	PASS	Atlas-SNP
FNDC9	408263	hgsc.bcm.edu	37	5	156770209	156770209	+	Silent	SNP	G	G	A	rs10214194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	144	105	1	0.993103	0.00952381	G|0.764;A|0.236	0.236	strong	.	FNDC9	22	.	NM_001001343	exon2	c.C336T	p.S112S	CCAAAGGGAGATC	.	PASS	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92467626	92467626	+	Missense_Mutation	SNP	A	A	G	rs78267346	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	159	275	0	0.535354	0	A|0.988;G|0.012	0.012	strong	.	BRDT	133	.	NM_001242806	exon16	c.A2320G	p.N774D	CTCTCAAATGGCA	.	PASS	Atlas-SNP
CLDN14	23562	hgsc.bcm.edu	37	21	37833361	37833361	+	Silent	SNP	G	G	A	rs61745291	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	419	228	332	0	0.544153	0	G|0.976;A|0.024	0.024	strong	.	CLDN14	25	.	NM_144492	exon3	c.C633T	p.Y211Y	TGGCTGGTAGGCA	.	PASS	Atlas-SNP
CEP250	11190	hgsc.bcm.edu	37	20	34084415	34084415	+	Silent	SNP	G	G	C	rs224376	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	60	0	0.5	0	G|0.991;C|0.009	0.009	strong	.	CEP250	141	.	NM_007186	exon25	c.G3177C	p.L1059L	GACTCTGTCACTG	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167167126	167167126	+	Silent	SNP	A	A	G	rs61750372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	117	216	0	0.534247	0	A|0.931;G|0.069	0.069	strong	.	SERPINI2	85	.	NM_001012303	exon8	c.T1059C	p.G353G	TTCACTACCATCT	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	27	60	0	0.473684	0	C|0.868;T|0.132	0.132	strong	.	BTBD11	122	.	NM_001018072	exon1	c.C163T	p.L55L	CCGCCTCTAGCTG	.	PASS	Atlas-SNP
NSUN3	63899	hgsc.bcm.edu	37	3	93845062	93845062	+	Missense_Mutation	SNP	A	A	G	rs61730354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	82	124	0	0.546667	0	A|0.982;G|0.018	0.018	strong	.	NSUN3	33	.	NM_022072	exon6	c.A751G	p.I251V	TCTGCAATTAAGG	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	38	71	0	0.469136	0	T|0.642;C|0.358	0.358	strong	.	DTHD1	63	.	NM_001170700	exon7	c.T1827C	p.S609S	CTATAGTTGCCCT	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72351024	72351024	+	Missense_Mutation	SNP	T	T	C	rs9891620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	61	116	0	0.508333	0	T|0.855;C|0.145	0.145	strong	.	KIF19	102	.	NM_153209	exon19	c.T2810C	p.L937P	GGCATCTGGGAAA	.	PASS	Atlas-SNP
PRICKLE1	144165	hgsc.bcm.edu	37	12	42862431	42862431	+	Silent	SNP	G	G	A	rs74081707	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	45	90	0	0.555556	0	G|0.967;A|0.033	0.033	strong	.	PRICKLE1	105	.	NM_001144882	exon5	c.C585T	p.D195D	TACCTCGTCACAT	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37244669	37244669	+	Silent	SNP	C	C	T	rs73750958	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	49	157	0	0.360294	0	C|0.980;T|0.020	0.020	strong	.	C5orf42	422	.	NM_023073	exon5	c.G378A	p.G126G	TCTTTTCCCATTT	.	PASS	Atlas-SNP
GTF3C3	9330	hgsc.bcm.edu	37	2	197662526	197662526	+	Missense_Mutation	SNP	T	T	C	rs11559078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	70	190	0	0.448718	0	T|0.737;G|0.020;C|0.079;N|0.000;A|0.164	0.079	strong	GTF3C3,NS,carcinoma,0,1	GTF3C3	96	1	NM_001206774	exon2	c.A209G	p.N70S	CCTTCATTGACAT	.	PASS	Atlas-SNP
PPCS	79717	hgsc.bcm.edu	37	1	42925501	42925501	+	Silent	SNP	A	A	G	rs142078638	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	56	139	0	0.455285	0	A|0.998;G|0.002	0.002	strong	.	PPCS	30	.	NM_024664	exon3	c.A840G	p.L280L	ATTGCTATCAGAG	.	PASS	Atlas-SNP
NSUN5	55695	hgsc.bcm.edu	37	7	72719048	72719048	+	Missense_Mutation	SNP	G	G	A	rs34913552	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	496	155	568	0	0.3125	0	G|0.971;A|0.029	0.029	strong	.	NSUN5	47	.	NM_148956	exon5	c.C547T	p.P183S	TCAAGGGGTCCAG	.	PASS	Atlas-SNP
SLC37A1	54020	hgsc.bcm.edu	37	21	43954850	43954850	+	Missense_Mutation	SNP	G	G	A	rs115669950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	68	101	0	0.576271	0	G|0.984;A|0.016	0.016	strong	.	SLC37A1	48	.	NM_018964	exon5	c.G181A	p.V61I	GCTGACGTCAGGT	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96123981	96123981	+	Silent	SNP	C	C	T	rs3733212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	207	179	0	1	0	C|0.347;T|0.653	0.653	strong	.	UNC5C	141	.	NM_003728	exon12	c.G2037A	p.A679A	GCGCTTCGCAGCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs7030192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	239	65	221	0	0.271967	0	A|0.380;G|0.620	0.380	strong	.	SVEP1	326	.	NM_153366	exon38	c.C8249T	p.A2750V	GAGCCTGCTAGAA	.	PASS	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46719100	46719100	+	Missense_Mutation	SNP	C	C	G	rs6008684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	86	169	0	0.562092	0	C|0.856;G|0.144	0.144	strong	.	GTSE1	100	.	NM_016426	exon8	c.C1446G	p.D482E	CCCGGACAGCTCA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	A	rs2290787	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	85	205	0	0.452128	0	A|0.076;C|0.019;T|0.905	0.076	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon16	c.A1993T	p.T665S	GGGCTGTGCTGGA	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93412587	93412587	+	Missense_Mutation	SNP	C	C	T	rs111783199	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	75	134	0	0.568182	0	C|0.995;T|0.005	0.005	strong	.	KIAA1731	173	.	NM_033395	exon7	c.C634T	p.R212C	GATGCTCGTTTGG	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	66	111	0	0.52381	0	A|0.734;G|0.266	0.266	strong	.	COL12A1	385	.	NM_004370	exon29	c.T5213C	p.I1738T	CTGCCAATCAGGT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134108459	134108459	+	Missense_Mutation	SNP	G	G	C	rs61730222	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	85	159	0	0.469613	0	G|0.978;C|0.022	0.022	strong	TG,colon,carcinoma,0,2	TG	416	2	NM_003235	exon43	c.G7414C	p.V2472L	CTGGCCGTGAGTG	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85436500	85436500	+	Missense_Mutation	SNP	T	T	C	rs580459	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	70	0	1	0	T|0.304;C|0.696	0.696	strong	.	SYTL2	231	.	NM_206927	exon1	c.A1000G	p.M334V	CAGCCATCTGAAT	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7942785	7942785	+	Missense_Mutation	SNP	C	C	G	rs78230493	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	15	29	0	0.681818	0	C|0.966;G|0.034	0.034	strong	.	ALOX15B	66	.	NM_001141	exon2	c.C229G	p.P77A	GTGCTGCCCCTGC	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38038982	38038982	+	Silent	SNP	T	T	C	rs6809649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	46	87	0	0.516854	0	T|0.768;C|0.232	0.232	strong	.	VILL	61	.	NM_015873	exon6	c.T570C	p.A190A	GCTGGCTTTGACC	.	PASS	Atlas-SNP
SMC2	10592	hgsc.bcm.edu	37	9	106896809	106896809	+	Silent	SNP	G	G	A	rs7872034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	81	107	0	0.987805	0	G|0.502;A|0.498	0.498	strong	.	SMC2	127	.	NM_006444	exon23	c.G3222A	p.L1074L	TGCCTTGGGAAAT	.	PASS	Atlas-SNP
TMEM104	54868	hgsc.bcm.edu	37	17	72784931	72784931	+	Silent	SNP	C	C	T	rs62638676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	15	35	0	0.365854	0	C|0.968;T|0.032	0.032	strong	.	TMEM104	49	.	NM_017728	exon4	c.C171T	p.F57F	CAGCTTCGTGACC	.	PASS	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51791559	51791559	+	Missense_Mutation	SNP	A	A	G	rs12102203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	72	141	0	0.489796	0	A|0.527;G|0.472	0.472	strong	DMXL2,NS,carcinoma,0,1	DMXL2	262	1	NM_001174116	exon18	c.T3862C	p.S1288P	CATTAGAACTATC	.	PASS	Atlas-SNP
MSTN	2660	hgsc.bcm.edu	37	2	190925077	190925077	+	Missense_Mutation	SNP	T	T	C	rs1805086	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	77	141	0	0.553957	0	T|0.932;C|0.068	0.068	strong	.	MSTN	46	.	NM_005259	exon2	c.A458G	p.K153R	TGGGCCTTTACTA	.	PASS	Atlas-SNP
LMTK2	22853	hgsc.bcm.edu	37	7	97822990	97822990	+	Silent	SNP	G	G	A	rs56064038	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	25	49	0	0.462963	0	G|0.985;A|0.015	0.015	strong	.	LMTK2	228	.	NM_014916	exon11	c.G3213A	p.P1071P	CAACCCGGTCATT	.	PASS	Atlas-SNP
SLC35F3	148641	hgsc.bcm.edu	37	1	234041422	234041422	+	Silent	SNP	G	G	C	rs57010808	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	101	0	1	0	G|0.531;C|0.469	0.469	strong	.	SLC35F3	81	.	NM_173508	exon2	c.G201C	p.P67P	CGGGCCGGTGGGG	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38144856	38144856	+	Silent	SNP	G	G	A	rs12687163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	88	220	0	0.453608	0	G|0.844;A|0.156	0.156	strong	.	RPGR	175	.	NM_001034853	exon15	c.C3396T	p.N1132N	TGGCCCGTTTTTT	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595106	140595106	+	Missense_Mutation	SNP	C	C	G	rs2910329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	181	0	1	0	C|0.532;G|0.468	0.468	strong	.	PCDHB13	142	.	NM_018933	exon1	c.C1411G	p.R471G	CACATCCGCAGCG	.	PASS	Atlas-SNP
ZP2	7783	hgsc.bcm.edu	37	16	21222672	21222672	+	Missense_Mutation	SNP	C	C	A	rs2075520	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	75	63	0	1	0	C|0.593;A|0.407	0.407	strong	.	ZP2	92	.	NM_003460	exon2	c.G107T	p.G36V	GAGTTCCCTGAAG	.	PASS	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	15	47	0	0.384615	0	C|0.756;G|0.244	0.244	strong	.	CEP55	35	.	NM_018131	exon2	c.C171G	p.H57Q	GAGACACAGACTT	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136595253	136595253	+	Silent	SNP	C	C	T	rs35457000	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	40	128	0	0.353982	0	C|0.985;T|0.015	0.015	strong	.	SARDH	112	.	NM_007101	exon5	c.G747A	p.V249V	CCGCCGCACCCCA	.	PASS	Atlas-SNP
PRR3	80742	hgsc.bcm.edu	37	6	30529816	30529816	+	Silent	SNP	G	G	A	rs3888777	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	96	0	0.45	0	G|0.952;A|0.048	0.048	strong	.	PRR3	5	.	NM_025263	exon3	c.G375A	p.K125K	TCACAAGGAACAG	.	PASS	Atlas-SNP
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346595	39346595	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	9	80	0	0.0818182	0	.	.	none	KRTAP9-1_ENST00000398470,rectum,carcinoma,0,2	KRTAP9-1	34	2	NM_001190460	exon1	c.T457A	p.C153S	CCCACCTGCTGTG	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	159	346	0	0.5	0	T|0.774;C|0.226	0.226	strong	.	SPATA22	49	.	NM_032598	exon9	c.A1014G	p.E338E	TTTTTGTTCAGAA	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56387859	56387859	+	Silent	SNP	T	T	C	rs3803459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	102	247	0	0.401575	0	T|0.799;C|0.201	0.201	strong	.	RFX7	170	.	NM_022841	exon9	c.A2067G	p.K689K	GCCTTGTTTCTGC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	39	37	0	0.696429	0	A|0.724;G|0.276	0.276	strong	.	.	.	.	NM_014811	exon4	c.A616G	p.K206E	TCCAGCAAGGACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513010	195513010	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	508	14	645	5	0.0275591	0.00775194	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C5441T	p.P1814L	GAGGAAGGGCTGG	.	scavenged	Atlas-SNP
OR2Y1	134083	hgsc.bcm.edu	37	5	180166141	180166141	+	Silent	SNP	C	C	T	rs9329115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	31	43	0	0.659574	0	C|0.913;T|0.087	0.087	strong	OR2Y1,NS,carcinoma,0,1	OR2Y1	49	1	NM_001001657	exon1	c.G918A	p.R306R	CCTGCCCCTCCAT	.	PASS	Atlas-SNP
EMCN	51705	hgsc.bcm.edu	37	4	101386643	101386643	+	Missense_Mutation	SNP	C	C	T	rs78403369	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	65	127	0	0.492424	0	C|0.980;T|0.020	0.020	strong	.	EMCN	37	.	NM_001159694	exon4	c.G313A	p.V105I	CTGTTACGTTTGA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129905429	129905429	+	Missense_Mutation	SNP	C	C	T	rs7918199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	369	186	394	0	0.504065	0	C|0.914;T|0.086	0.086	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.G4675A	p.V1559M	TCTGCACTGGAGT	.	PASS	Atlas-SNP
FBN1	2200	hgsc.bcm.edu	37	15	48734008	48734008	+	Missense_Mutation	SNP	C	C	A	rs113577372	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	34	59	0	0.5	0	C|0.998;A|0.002	0.002	strong	.	FBN1	310	.	NM_000138	exon50	c.G6073T	p.A2025S	CCAGGGCACAAAT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487229	32487229	+	Silent	SNP	C	C	T	rs148633289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	91	78	0	0.728	0	C|0.781;T|0.219	0.219	strong	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G570A	p.L190L	TGTTTCCAGCATC	.	scavenged	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62393420	62393420	+	Missense_Mutation	SNP	C	C	T	rs61743112	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	45	84	0	0.5	0	C|0.959;T|0.041	0.041	strong	.	INADL	179	.	NM_176877	exon27	c.C3589T	p.P1197S	GCTCCACCGCCAA	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	37	92	0	0.355769	0	A|0.676;G|0.324	0.324	strong	LRRFIP1_ENST00000392000,colon,carcinoma,+1,3	LRRFIP1	171	3	NM_001137550	exon19	c.A1413G	p.T471T	GATGACAAAAGAA	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108383676	108383676	+	Missense_Mutation	SNP	A	A	G	rs10749920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	125	147	0	1	0	A|0.676;G|0.324	0.324	strong	.	EXPH5	193	.	NM_015065	exon6	c.T2558C	p.L853P	TCAGTCAGTGCAG	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5085806	5085806	+	Silent	SNP	G	G	A	rs114624606	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	47	124	0	0.419643	0	G|0.990;A|0.010	0.010	strong	.	ZNF594	89	.	NM_032530	exon2	c.C1746T	p.D582D	GATGAGGTCTGAG	.	PASS	Atlas-SNP
TMC8	147138	hgsc.bcm.edu	37	17	76127746	76127746	+	Missense_Mutation	SNP	T	T	C	rs145016347	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	26	33	0	0.433333	0	T|0.985;C|0.015	0.015	strong	.	TMC8	44	.	NM_152468	exon2	c.T77C	p.M26T	CAGAGATGGAGCG	.	PASS	Atlas-SNP
DDR2	4921	hgsc.bcm.edu	37	1	162737116	162737116	+	Silent	SNP	C	C	G	rs2298258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	89	189	0	0.447236	0	C|0.718;G|0.282	0.282	strong	DDR2_ENST00000367922,NS,carcinoma,+2,1	DDR2	228	1	NM_001014796	exon12	c.C1260G	p.L420L	CATCCTCTGGAGG	.	PASS	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	119	222	0	0.526549	0	G|0.650;C|0.350	0.350	strong	.	OR2L2	115	.	NM_001004686	exon1	c.G775C	p.V259L	ACCTATGTACGTC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604564	140604564	+	Missense_Mutation	SNP	G	G	C	rs61997246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	135	254	0	0.490909	0	G|0.918;C|0.082	0.082	strong	.	PCDHB14	132	.	NM_018934	exon1	c.G1487C	p.R496P	AGGACCGGCACCT	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84683428	84683428	+	Missense_Mutation	SNP	A	A	G	rs17158450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	63	122	0	0.396226	0	A|0.943;G|0.057	0.057	strong	.	ADAMTSL3	290	.	NM_207517	exon24	c.A4108G	p.T1370A	ATAGCCACCAATG	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	101993024	101993024	+	Missense_Mutation	SNP	C	C	T	rs7922946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	33	105	0	0.428571	0	C|0.993;T|0.007	0.007	strong	.	CWF19L1	39	.	NM_018294	exon14	c.G1577A	p.R526Q	TCTTTCCGGAAGC	.	PASS	Atlas-SNP
SRF	6722	hgsc.bcm.edu	37	6	43146105	43146105	+	Silent	SNP	G	G	T	rs140883192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	28	57	0	0.444444	0	G|0.997;T|0.003	0.003	strong	.	SRF	24	.	NM_003131	exon5	c.G1236T	p.P412P	TAGCCCGCATGCG	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78176193	78176193	+	Silent	SNP	G	G	A	rs35692270	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	70	0	0.448718	0	G|0.992;A|0.008	0.008	strong	.	CARD14	98	.	NM_024110	exon15	c.G2193A	p.A731A	TGCCGCGCACGGC	.	PASS	Atlas-SNP
TRIM49C	642612	hgsc.bcm.edu	37	11	89774236	89774236	+	Missense_Mutation	SNP	C	C	G	rs74584169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	82	49	0	0.5	0	C|0.658;G|0.342	0.342	strong	.	TRIM49C	48	.	NM_001195234	exon8	c.C877G	p.H293D	CTGCATCATGAAG	.	PASS	Atlas-SNP
SPINK2	6691	hgsc.bcm.edu	37	4	57687719	57687719	+	Missense_Mutation	SNP	C	C	T	rs781544	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	12	19	0	0.342857	0	C|0.791;T|0.209	0.209	strong	.	SPINK2	12	.	NM_001271722	exon1	c.G110A	p.G37E	TGACTCCCAAACC	.	PASS	Atlas-SNP
LGALS2	3957	hgsc.bcm.edu	37	22	37966314	37966314	+	Missense_Mutation	SNP	C	C	T	rs2235339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	54	114	0	0.425197	0	C|0.948;T|0.052	0.052	strong	LGALS2,NS,carcinoma,0,1	LGALS2	16	1	NM_006498	exon4	c.G355A	p.V119I	CCCTTACGCTCAG	.	PASS	Atlas-SNP
CXXC11	285093	hgsc.bcm.edu	37	2	242815157	242815157	+	Missense_Mutation	SNP	C	C	T	rs77317868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	76	0	0.493151	0	C|0.973;T|0.027	0.027	strong	.	.	.	.	NM_173821	exon2	c.C1450T	p.R484C	ATAAAGCGCAAGG	.	PASS	Atlas-SNP
ZNF20	7568	hgsc.bcm.edu	37	19	12244624	12244624	+	Missense_Mutation	SNP	G	G	A	rs61743205	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	88	182	0	0.483516	0	G|0.981;A|0.019	0.019	strong	.	ZNF20	86	.	NM_021143	exon4	c.C377T	p.A126V	GTGTCAGCTCTGA	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98779418	98779418	+	Missense_Mutation	SNP	G	G	A	rs77092382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	60	133	0	0.431655	0	G|0.981;A|0.019	0.019	strong	.	VWA3B	138	.	NM_144992	exon8	c.G1093A	p.D365N	AAGCCCGACGTGG	.	PASS	Atlas-SNP
CSNK1G1	53944	hgsc.bcm.edu	37	15	64592522	64592522	+	Silent	SNP	T	T	C	rs7163558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	91	147	0	0.478947	0	T|0.968;C|0.032	0.032	strong	.	CSNK1G1	56	.	NM_022048	exon2	c.A177G	p.R59R	ACCTAATCTGAGC	.	PASS	Atlas-SNP
SEC14L3	266629	hgsc.bcm.edu	37	22	30864545	30864545	+	Missense_Mutation	SNP	T	T	A	rs115380280	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	57	112	0	0.504425	0	T|0.998;A|0.002	0.002	strong	.	SEC14L3	46	.	NM_174975	exon5	c.A373T	p.M125L	CCCTCATCTTGGT	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370605	26370605	+	Silent	SNP	T	T	C	rs9379860	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	84	157	0	0.497041	0	T|0.614;C|0.386	0.386	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.T489C	p.H163H	GATCCATCTGGAG	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22364322	22364322	+	Missense_Mutation	SNP	A	A	G	rs62000438	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	101	82	0	1	0	A|0.974;G|0.026	0.026	strong	ZNF676,NS,carcinoma,+1,1	ZNF676	146	1	NM_001001411	exon3	c.T197C	p.M66T	AATATCATTTTTT	.	PASS	Atlas-SNP
IGSF5	150084	hgsc.bcm.edu	37	21	41165462	41165462	+	Missense_Mutation	SNP	C	C	A	rs2837225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	150	124	0	0.993378	0	C|0.600;A|0.400	0.400	strong	IGSF5,NS,carcinoma,0,1	IGSF5	62	1	NM_001080444	exon8	c.C1050A	p.D350E	TGCAGACACCGCT	.	PASS	Atlas-SNP
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458200	39458200	+	Missense_Mutation	SNP	C	C	T	rs115643796	byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	142	0	0.480263	0	C|0.987;T|0.013	0.013	strong	.	KRTAP29-1	2	.	NM_001257309	exon1	c.G904A	p.G302S	TGCAGCCACTCTG	.	PASS	Atlas-SNP
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	30	85	0	0.365854	0	C|0.836;G|0.164	0.164	strong	.	CAMSAP1	142	.	NM_015447	exon7	c.G951C	p.P317P	AACATTCGGCTAA	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29840038	29840038	+	Silent	SNP	A	A	G	rs3740003	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	82	177	0	0.445652	0	A|0.678;G|0.322	0.322	strong	SVIL,NS,carcinoma,0,1	SVIL	226	1	NM_003174	exon8	c.T315C	p.I105I	CCTTGCAATTCTT	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	47	124	0	0.460784	0	C|0.484;T|0.516	0.516	strong	.	FRAS1	779	.	NM_025074	exon71	c.C11056T	p.L3686L	ATGTCACTAGCAG	.	PASS	Atlas-SNP
DZIP1L	199221	hgsc.bcm.edu	37	3	137787173	137787173	+	Missense_Mutation	SNP	G	G	A	rs11917468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	77	209	0	0.463855	0	G|0.948;A|0.052	0.052	strong	.	DZIP1L	88	.	NM_173543	exon13	c.C1652T	p.A551V	GGCTGGGCCTCTC	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30318207	30318207	+	Silent	SNP	T	T	C	rs2250574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	110	176	0	0.555556	0	A|0.007;C|0.102	0.102	strong	.	LTN1	141	.	NM_015565	exon21	c.A3828G	p.L1276L	CAGAAATAGGGAA	.	PASS	Atlas-SNP
PIN1	5300	hgsc.bcm.edu	37	19	9949152	9949152	+	Silent	SNP	G	G	A	rs2233682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	77	154	0	0.55	0	G|0.936;A|0.064	0.064	strong	PIN1,ear,carcinoma,+2,1	PIN1	7	1	NM_006221	exon2	c.G99A	p.Q33Q	CAGCCAGTGGGAG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126241335	126241335	+	Missense_Mutation	SNP	C	C	G	rs36052762	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	102	0	0.494118	0	C|0.920;G|0.080	0.080	strong	.	FAT4	1752	.	NM_024582	exon1	c.C3769G	p.Q1257E	GAAAGACAGTTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511237	195511237	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	18	635	6	0.0772532	0.00944882	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.A7214G	p.D2405G	GAAGTGTCGGTGA	.	scavenged	Atlas-SNP
TSPAN18	90139	hgsc.bcm.edu	37	11	44931308	44931308	+	Missense_Mutation	SNP	C	C	T	rs34282417	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	44	96	0	0.505747	0	C|0.995;T|0.005	0.005	strong	.	TSPAN18	38	.	NM_130783	exon4	c.C116T	p.T39I	ACCCCACCGGCTT	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193120459	193120459	+	Silent	SNP	G	G	A	rs9863164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	49	99	0	0.453704	0	G|0.974;A|0.026	0.026	strong	.	ATP13A4	154	.	NM_032279	exon30	c.C3573T	p.S1191S	TTCATTGCTCTCA	.	PASS	Atlas-SNP
ZNF516	9658	hgsc.bcm.edu	37	18	74090931	74090931	+	Silent	SNP	C	C	T	rs690353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	33	58	0	0.507692	0	C|0.903;T|0.097	0.097	strong	.	ZNF516	102	.	NM_014643	exon5	c.G3138A	p.P1046P	GGCCACCGGCTCC	.	PASS	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	37	19	50361874	50361874	+	Silent	SNP	A	A	G	rs35389621	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	43	99	0	0.505882	0	A|0.990;G|0.010	0.010	strong	.	PTOV1	41	.	NM_017432	exon10	c.A1005G	p.T335T	GGAGACACTGAAG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149485987	149485987	+	Nonsense_Mutation	SNP	T	T	A	rs893597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	90	146	0	0.473684	0	T|0.977;A|0.023	0.023	strong	.	.	.	.	NM_198455	exon29	c.T4206A	p.C1402X	CGACTGTGGCGAT	.	PASS	Atlas-SNP
IPPK	64768	hgsc.bcm.edu	37	9	95411816	95411816	+	Silent	SNP	G	G	A	rs16908484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	69	113	0	0.594828	0	G|0.986;A|0.014	0.014	strong	.	IPPK	34	.	NM_022755	exon5	c.C333T	p.Y111Y	CATAGCGTAACCA	.	PASS	Atlas-SNP
C16orf58	64755	hgsc.bcm.edu	37	16	31519174	31519174	+	Silent	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	51	64	0	0.515152	0	.	.	none	.	C16orf58	28	.	NM_022744	exon2	c.G326G	p.G109G	GCTAGGGAGCCGG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	117	81	0	1	0	G|0.825;A|0.175	0.175	strong	.	FAT4	1752	.	NM_024582	exon17	c.G13617A	p.E4539E	CAAAGAGGAGAAG	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43176832	43176832	+	Silent	SNP	A	A	G	rs2277791	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	46	112	0	0.433962	0	A|0.872;G|0.128	0.128	strong	.	RIPK4	151	.	NM_020639	exon2	c.T327C	p.A109A	CTCCGAAGCCAGC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733214	52733214	+	Missense_Mutation	SNP	A	A	C	rs200377849		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	8	290	2	0.0260586	0.00689655	.	.	weak	PCMTD1,trunk,malignant_melanoma,0,1	PCMTD1	73	1	NM_052937	exon6	c.T771G	p.N257K	TATGAAATTTCTA	.	scavenged	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31996524	31996524	+	Silent	SNP	C	C	A	rs56116673	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	823	321	570	1	0.390036	0.00175439	.	.	weak	.	C4A	15	.	NM_007293	exon26	c.C3285A	p.G1095G	AGGAGGCTCGCCT	.	PASS	Atlas-SNP
EEF1D	1936	hgsc.bcm.edu	37	8	144662353	144662353	+	Silent	SNP	G	G	A	rs1062391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	91	156	0	0.56875	0	G|0.563;A|0.437	0.437	strong	.	EEF1D	48	.	NM_001130053	exon9	c.C1734T	p.A578A	CAGCTGGGCCATG	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	37	17	66938141	66938141	+	Missense_Mutation	SNP	G	G	C	rs35643726	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	44	83	1	0.517647	0.0120482	G|0.980;C|0.020	0.020	strong	ABCA8,NS,carcinoma,+1,2	ABCA8	213	2	NM_007168	exon2	c.C35G	p.T12S	GCCCAAGTTTGTT	.	scavenged	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169580885	169580885	+	Missense_Mutation	SNP	C	C	T	rs6131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	144	126	1	0.986301	0.00793651	C|0.778;T|0.221	0.221	strong	.	SELP	132	.	NM_003005	exon7	c.G992A	p.S331N	CCTTCACTGGGGG	.	PASS	Atlas-SNP
ZC3H12D	340152	hgsc.bcm.edu	37	6	149777914	149777914	+	Missense_Mutation	SNP	G	G	T	rs200917878	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	23	61	0	0.433962	0	.	.	weak	.	ZC3H12D	21	.	NM_207360	exon4	c.C568A	p.Q190K	CGTCCTGCTCGTA	.	PASS	Atlas-SNP
LGALS2	3957	hgsc.bcm.edu	37	22	37966409	37966409	+	Missense_Mutation	SNP	G	G	A	rs73884090	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	82	150	0	0.463277	0	G|0.973;A|0.027	0.027	strong	.	LGALS2	16	.	NM_006498	exon4	c.C260T	p.T87I	TCAAAGGTCACTG	.	PASS	Atlas-SNP
EIF2S3	1968	hgsc.bcm.edu	37	X	24073785	24073785	+	Silent	SNP	A	A	G	rs56229020	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	370	169	364	0	0.456757	0	A|0.998;G|0.002	0.002	strong	.	EIF2S3	31	.	NM_001415	exon2	c.A123G	p.T41T	AGCCACAATTAAC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1103876	1103876	+	Silent	SNP	C	C	T	rs41532344	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	53	75	0	0.514563	0	C|0.898;T|0.102	0.102	strong	.	MUC2	614	.	NM_002457	exon49	c.C8163T	p.A2721A	GTACGCCGGCTGC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921127	12921127	+	Silent	SNP	A	A	G	rs12139549	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	232	185	1	0.995708	0.00540541	A|0.699;G|0.301	0.301	strong	.	PRAMEF2	85	.	NM_023014	exon4	c.A918G	p.L306L	CCTATTAGAAGAG	.	PASS	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238705	71238705	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	7	211	1	0.0267176	0.00473934	.	.	none	KRTAP5-7,NS,carcinoma,0,3	KRTAP5-7	23	3	NM_001012503	exon1	c.G359A	p.C120Y	AGCCCTGCTGCTG	.	scavenged	Atlas-SNP
UCN3	114131	hgsc.bcm.edu	37	10	5416027	5416027	+	Missense_Mutation	SNP	C	C	G	rs201708420	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	25	45	0	0.438596	0	.	.	weak	.	UCN3	13	.	NM_053049	exon2	c.C344G	p.P115R	AGAGTCCCCACCG	.	PASS	Atlas-SNP
RAD51B	5890	hgsc.bcm.edu	37	14	68292187	68292187	+	Silent	SNP	T	T	C	rs114131734	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	29	81	0	0.414286	0	T|0.991;C|0.009	0.009	strong	.	RAD51B	80	.	NM_133509	exon3	c.T91C	p.L31L	GACTTTTTATGTC	.	PASS	Atlas-SNP
SRPX	8406	hgsc.bcm.edu	37	X	38033415	38033415	+	Missense_Mutation	SNP	T	T	C	rs35474361	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	56	120	0	0.5	0	T|0.921;C|0.079	0.079	strong	.	SRPX	53	.	NM_001170751	exon3	c.A347G	p.K116R	TCACGTTTGCAGA	.	PASS	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47584869	47584869	+	Silent	SNP	C	C	T	rs73943616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	84	139	0	0.583333	0	C|0.986;T|0.014	0.014	strong	.	ZC3H4	96	.	NM_015168	exon11	c.G1341A	p.P447P	CTTACACGGGAAA	.	PASS	Atlas-SNP
MIDN	90007	hgsc.bcm.edu	37	19	1250397	1250397	+	Silent	SNP	C	C	T	rs3746107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	13	13	0	1	0	C|0.846;T|0.154	0.154	strong	.	MIDN	34	.	NM_177401	exon2	c.C102T	p.A34A	CCTCGCCATCCAC	.	PASS	Atlas-SNP
CD93	22918	hgsc.bcm.edu	37	20	23066338	23066338	+	Silent	SNP	G	G	C	rs6048539	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	24	32	0	0.521739	0	G|0.889;C|0.111	0.111	strong	.	CD93	84	.	NM_012072	exon1	c.C492G	p.P164P	CCCACAGGGGCCC	.	PASS	Atlas-SNP
ZNF695	57116	hgsc.bcm.edu	37	1	247150631	247150631	+	Missense_Mutation	SNP	T	T	C	rs77178548	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	24	46	0	0.444444	0	T|0.968;C|0.032	0.032	strong	.	ZNF695	55	.	NM_020394	exon4	c.A1186G	p.I396V	GCTGAATAAGGTA	.	PASS	Atlas-SNP
ZNF883	169834	hgsc.bcm.edu	37	9	115760381	115760381	+	Silent	SNP	G	G	A	rs113877750	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	34	100	0	0.365591	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_001101338	exon5	c.C159T	p.N53N	ATTACTGTTCCGG	.	PASS	Atlas-SNP
ZDHHC2	51201	hgsc.bcm.edu	37	8	17067959	17067959	+	Missense_Mutation	SNP	C	C	G	rs190630185	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	58	0	0.486842	0	C|0.997;G|0.003	0.003	strong	.	ZDHHC2	25	.	NM_016353	exon10	c.C920G	p.T307S	CATCTACTCCTGC	.	PASS	Atlas-SNP
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	80	146	0	0.516129	0	C|0.898;G|0.102	0.102	strong	.	HELT	34	.	NM_001029887	exon3	c.C439G	p.L147V	CAGTACCTGAGAG	.	PASS	Atlas-SNP
CWC25	54883	hgsc.bcm.edu	37	17	36963226	36963226	+	Silent	SNP	G	G	T	rs3785452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	131	137	0	1	0	G|0.860;T|0.140	0.140	strong	.	CWC25	24	.	NM_017748	exon7	c.C694A	p.R232R	AGTTCCGGACCTA	.	PASS	Atlas-SNP
CCSER1	401145	hgsc.bcm.edu	37	4	91230407	91230407	+	Silent	SNP	T	T	C	rs34445159	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	92	178	0	0.422018	0	T|0.995;C|0.005	0.005	strong	.	.	.	.	NM_001145065	exon2	c.T972C	p.Y324Y	GAAATATAGGTTA	.	PASS	Atlas-SNP
MAP4	4134	hgsc.bcm.edu	37	3	47956424	47956424	+	Missense_Mutation	SNP	C	C	T	rs1137524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	70	111	0	0.507246	0	T|0.303;G|0.116;C|0.511;N|0.000;A|0.069	0.303	strong	.	MAP4	176	.	NM_001134364	exon8	c.G1882A	p.V628I	CTGTGACGGTTTC	.	PASS	Atlas-SNP
FAM71C	196472	hgsc.bcm.edu	37	12	100042163	100042163	+	Missense_Mutation	SNP	A	A	G	rs11109969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	52	96	0	0.40625	0	A|0.738;G|0.262	0.262	strong	.	FAM71C	48	.	NM_153364	exon1	c.A211G	p.M71V	GTAACAATGGGCA	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7765495	7765495	+	Silent	SNP	G	G	T	rs2240053	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	63	127	0	0.459854	0	G|0.803;T|0.197	0.197	strong	.	AFAP1	93	.	NM_001134647	exon18	c.C2442A	p.T814T	CCCCTAGGTCCCG	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967996	49967996	+	Silent	SNP	G	G	A	rs10421522	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	40	67	0	0.506329	0	G|0.964;A|0.036	0.036	strong	.	ALDH16A1	54	.	NM_153329	exon12	c.G1545A	p.P515P	CCTGCCGGCTGGG	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102493761	102493761	+	Silent	SNP	A	A	G	rs8010870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	94	0	0.489583	0	A|0.835;G|0.165;T|0.000	0.165	strong	.	DYNC1H1	395	.	NM_001376	exon46	c.A8928G	p.L2976L	AGATCTACGGACA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1276327	1276327	+	Missense_Mutation	SNP	G	G	A	rs3829224	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	83	113	0	0.51875	0	G|0.887;A|0.113	0.113	strong	.	MUC5B	473	.	NM_002458	exon36	c.G15721A	p.A5241T	ACTGCCGCCAGTT	.	PASS	Atlas-SNP
COQ4	51117	hgsc.bcm.edu	37	9	131088076	131088076	+	Silent	SNP	G	G	A	rs2270203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	55	115	0	0.376712	0	G|0.891;A|0.109	0.109	strong	.	COQ4	20	.	NM_016035	exon4	c.G318A	p.S106S	GATTTCGACATCC	.	PASS	Atlas-SNP
ENDOD1	23052	hgsc.bcm.edu	37	11	94862340	94862340	+	Missense_Mutation	SNP	A	A	T	rs188091415	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	89	165	0	0.613793	0	A|0.998;T|0.002	0.002	strong	.	ENDOD1	26	.	NM_015036	exon2	c.A1100T	p.Q367L	CCAAGCAGGTGAT	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	37	2	86259443	86259443	+	Silent	SNP	C	C	T	rs2276626	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	222	233	0	0.986667	0	T|0.595;C|0.405;A|0.000	0.595	strong	POLR1A,NS,carcinoma,0,1	POLR1A	137	1	NM_015425	exon29	c.G4224A	p.G1408G	GGCGTCCCCCTCC	.	PASS	Atlas-SNP
OR8K1	390157	hgsc.bcm.edu	37	11	56113703	56113703	+	Silent	SNP	C	C	T	rs145394503	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	189	94	216	1	0.497355	0.00462963	C|0.993;T|0.007	0.007	strong	.	OR8K1	93	.	NM_001002907	exon1	c.C189T	p.T63T	ACACACCCCCATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513756	195513756	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	8	262	0	0.0313726	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.C4695T	p.H1565H	GGTGGTGTGACCT	.	scavenged	Atlas-SNP
PGAM4	441531	hgsc.bcm.edu	37	X	77225099	77225099	+	Missense_Mutation	SNP	C	C	T	rs6622613	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	488	248	470	1	0.508197	0.00212766	C|0.990;T|0.010	0.010	strong	.	PGAM4	28	.	NM_001029891	exon1	c.G37A	p.E13K	TGCTCTCGCCGTG	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919267	51919267	+	Silent	SNP	A	A	G	rs7258638	bycluster;byfrequency;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	29	145	0	0.163842	0	A|0.996;G|0.004	0.004	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.T909C	p.P303P	GGGTCTAGGGCCC	.	PASS	Atlas-SNP
TSSC4	10078	hgsc.bcm.edu	37	11	2424541	2424541	+	Missense_Mutation	SNP	C	C	G	rs2234279	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	92	144	0	0.502732	0	C|0.883;G|0.117	0.117	strong	.	TSSC4	19	.	NM_005706	exon2	c.C678G	p.H226Q	CAGACACGAGAGG	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33880003	33880003	+	Silent	SNP	C	C	G	rs28498569	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	70	0	0.506024	0	C|0.765;G|0.235	0.235	strong	.	SLFN14	43	.	NM_001129820	exon3	c.G1650C	p.V550V	GGAGACCACCACC	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38145918	38145918	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	15	459	0	0.0510204	0	.	.	none	.	RPGR	175	.	NM_001034853	exon15	c.G2334A	p.E778E	TCTTTCCTCCTTT	.	PASS	Atlas-SNP
UBE3A	7337	hgsc.bcm.edu	37	15	25616844	25616844	+	Silent	SNP	T	T	A	rs28528079	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	341	169	295	0	0.495601	0	T|0.958;A|0.042	0.042	strong	.	UBE3A	109	.	NM_000462	exon7	c.A486T	p.A162A	TACCAATGCCTCA	.	PASS	Atlas-SNP
FAM178B	51252	hgsc.bcm.edu	37	2	97543701	97543701	+	Missense_Mutation	SNP	G	G	A	rs34013660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	44	120	0	0.52381	0	G|0.979;A|0.021	0.021	strong	FAM178B_ENST00000417561,colon,carcinoma,+1,2	FAM178B	35	2	NM_001122646	exon16	c.C1933T	p.R645C	TGGTGCGGTGCAT	.	PASS	Atlas-SNP
C16orf58	64755	hgsc.bcm.edu	37	16	31505252	31505252	+	Silent	SNP	C	C	T	rs34231527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	78	0	0.508065	0	C|0.991;T|0.009	0.009	strong	.	C16orf58	28	.	NM_022744	exon7	c.C708A	p.S236S	CACCAGCGTCTCC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378977	31378977	+	Missense_Mutation	SNP	G	G	A	rs1051792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	178	162	0	1	0	G|0.653;A|0.347	0.347	strong	.	MICA	21	.	NM_001177519	exon3	c.G454A	p.V152M	TGGACAGTGCCCC	.	PASS	Atlas-SNP
CMPK2	129607	hgsc.bcm.edu	37	2	7005236	7005236	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	6	6	0	0.5	0	.	.	none	.	CMPK2	30	.	NM_001256478	exon1	c.C592A	p.P198T	GCGGGGGCTCCGG	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25673001	25673001	+	Silent	SNP	C	C	G	rs76419032	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	65	108	0	0.580357	0	C|0.981;G|0.019	0.019	strong	.	IFLTD1	121	.	NM_001145728	exon7	c.G807C	p.A269A	GTACCACGCAATG	.	PASS	Atlas-SNP
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195134	43195134	+	Missense_Mutation	SNP	C	C	T	rs36003980	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	43	65	0	0.565789	0	C|0.983;T|0.017	0.017	strong	.	ARFGAP3	48	.	NM_014570	exon15	c.G1444A	p.A482T	CGGGGGCGTTGGG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017316	1017316	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1388	64	1180	17	0.0461095	0.0144068	.	.	none	MUC6_ENST00000421673,right_upper_lobe,carcinoma,+1,2	MUC6	408	2	NM_005961	exon31	c.C5485A	p.P1829T	GTGATGGGGTTGG	.	scavenged	Atlas-SNP
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184082	26184082	+	Missense_Mutation	SNP	C	C	G	rs61978632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	105	225	0	0.492958	0	C|0.965;G|0.035	0.035	strong	.	HIST1H2BE	10	.	NM_003523	exon1	c.C59G	p.T20S	CCGTGACCAAGGC	.	PASS	Atlas-SNP
ITGB3	3690	hgsc.bcm.edu	37	17	45360730	45360730	+	Missense_Mutation	SNP	T	T	C	rs5918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	38	75	0	0.447059	0	T|0.884;C|0.116	0.116	strong	.	ITGB3	157	.	NM_000212	exon3	c.T176C	p.L59P	TGCCTCTGGGCTC	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175306758	175306758	+	Missense_Mutation	SNP	G	G	A	rs61731114	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	71	143	0	0.541985	0	G|0.989;A|0.011	0.011	strong	.	TNR	399	.	NM_003285	exon19	c.C3440T	p.T1147I	CTCAAAGTGTCTC	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102469273	102469273	+	Silent	SNP	T	T	C	rs75094258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	32	92	0	0.405063	0	T|0.994;C|0.006	0.006	strong	.	DYNC1H1	395	.	NM_001376	exon23	c.T4854C	p.Y1618Y	AGAATATCTGGAA	.	PASS	Atlas-SNP
ABTB2	25841	hgsc.bcm.edu	37	11	34226140	34226140	+	Silent	SNP	G	G	T	rs77165558	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	17	45	0	0.515152	0	G|0.972;T|0.028	0.028	strong	ABTB2,NS,carcinoma,-2,1	ABTB2	101	1	NM_145804	exon2	c.C981A	p.T327T	CTCCAGGGTTCGG	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21030956	21030956	+	Missense_Mutation	SNP	G	G	T	rs56750936	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	121	107	0	0.960317	0	G|0.968;T|0.032	0.032	strong	.	KIF17	130	.	NM_001122819	exon5	c.C1107A	p.S369R	GCTGGGGCTCATC	.	PASS	Atlas-SNP
EOGT	285203	hgsc.bcm.edu	37	3	69054341	69054341	+	Silent	SNP	T	T	C	rs6781612	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	23	64	0	0.38983	0	T|0.701;C|0.299	0.299	strong	.	.	.	.	NM_173654	exon7	c.A465G	p.R155R	GGTTGCTCTGCAG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79396610	79396610	+	Silent	SNP	G	G	A	rs79849142	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	110	220	1	0.5	0.00454545	G|0.984;A|0.016	0.016	strong	.	FRAS1	779	.	NM_025074	exon54	c.G7701A	p.K2567K	TGAGAAGGCAGGG	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140222430	140222430	+	Missense_Mutation	SNP	T	T	G	rs6873763	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	156	303	0	0.543554	0	T|0.933;G|0.067	0.067	strong	.	PCDHA8	366	.	NM_031856	exon1	c.T1524G	p.I508M	CTACATTTCGGTG	.	PASS	Atlas-SNP
PODN	127435	hgsc.bcm.edu	37	1	53527948	53527948	+	Silent	SNP	T	T	G	rs7513730	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	25	18	0	0.961538	0	T|0.628;G|0.372	0.372	strong	.	PODN	86	.	NM_153703	exon1	c.T57G	p.P19P	TCGGCCTGTGGGG	.	PASS	Atlas-SNP
AGRN	375790	hgsc.bcm.edu	37	1	985900	985900	+	Silent	SNP	C	C	T	rs17160776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	66	159	0	0.428571	0	C|0.953;T|0.047	0.047	strong	.	AGRN	110	.	NM_198576	exon29	c.C5070T	p.F1690F	GGACTTCGTGTCG	.	PASS	Atlas-SNP
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	158	328	0	0.486154	0	C|0.887;G|0.113	0.113	strong	.	TMPRSS11E	40	.	NM_014058	exon5	c.C474G	p.H158Q	TCCTCACTCAGTT	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45392382	45392382	+	Missense_Mutation	SNP	T	T	C	rs79393107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	31	95	0	0.392405	0	T|0.960;C|0.040	0.040	strong	.	DUOX2	137	.	NM_014080	exon24	c.A3050G	p.E1017G	ATCTTCTCTTGCA	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9888027	9888027	+	Silent	SNP	C	C	T	rs11664080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	243	127	222	0	0.522634	0	C|0.941;T|0.059	0.059	strong	.	TXNDC2	168	.	NM_001098529	exon2	c.C1551T	p.C517C	AGAGTGCGCCATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511983	195511983	+	Silent	SNP	A	A	G	rs200576215	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	79	453	1	0.282143	0.00220751	A|0.949;G|0.051	0.051	strong	.	MUC4	1505	.	NM_018406	exon2	c.T6468C	p.G2156G	GGCGTGACCTGTG	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51491866	51491866	+	Missense_Mutation	SNP	A	A	T	rs2661488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	127	235	0	0.538136	0	A|0.959;T|0.041	0.041	strong	.	PKHD1	927	.	NM_138694	exon66	c.T11714A	p.I3905N	ATATGAATATTTT	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125441359	125441359	+	Silent	SNP	T	T	C	rs10773127	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	46	155	0	0.396552	0	T|0.608;C|0.392	0.392	strong	DHX37,rectum,carcinoma,0,1	DHX37	114	1	NM_032656	exon18	c.A2331G	p.T777T	GGGGAATGTGGCC	.	PASS	Atlas-SNP
PRSS1	5644	hgsc.bcm.edu	37	7	142460764	142460764	+	Missense_Mutation	SNP	G	G	A	rs200902389		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	429	12	392	2	0.027972	0.00510204	.	.	weak	PRSS1,NS,carcinoma,0,1	PRSS1	68	1	NM_002769	exon5	c.G637A	p.V213I	CAAGGAGTTGTCT	.	scavenged	Atlas-SNP
ESX1	80712	hgsc.bcm.edu	37	X	103495007	103495007	+	Missense_Mutation	SNP	G	G	C	rs78191648	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	29	53	0	0.54717	0	G|0.948;C|0.052	0.052	strong	.	ESX1	57	.	NM_153448	exon4	c.C1123G	p.L375V	GTGGCAGAGGCGC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138379059	138379059	+	Silent	SNP	G	G	T	rs3748198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	49	70	0	0.690141	0	G|0.858;T|0.142	0.142	strong	.	.	.	.	NM_014811	exon4	c.G2703T	p.L901L	ACATCTGGCCGAA	.	PASS	Atlas-SNP
RFPL4A	342931	hgsc.bcm.edu	37	19	56273293	56273293	+	Missense_Mutation	SNP	G	G	A	rs75204738	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	897	109	790	0	0.121516	0	G|0.500;A|0.500	0.500	strong	ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	NM_001145014	exon2	c.G127A	p.D43N	GAGCCCGATGGGG	.	scavenged	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143823157	143823157	+	Missense_Mutation	SNP	T	T	C	rs3762002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	44	91	0	0.5	0	T|0.749;C|0.251	0.251	strong	.	FUCA2	28	.	NM_032020	exon5	c.A1066G	p.M356V	ACCCCATTTGCCT	.	PASS	Atlas-SNP
CT47B1	643311	hgsc.bcm.edu	37	X	120008979	120008979	+	Silent	SNP	T	T	C	rs871733	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	115	143	1	1	0.00699301	T|0.345;C|0.655	0.655	strong	.	CT47B1	67	.	NM_001145718	exon1	c.A546G	p.P182P	GCCTTCTGGGGCT	.	PASS	Atlas-SNP
CYP1B1	1545	hgsc.bcm.edu	37	2	38301803	38301803	+	Silent	SNP	C	C	G	rs9341249	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	107	0	1	0	C|0.934;G|0.066	0.066	strong	.	CYP1B1	39	.	NM_000104	exon2	c.G729C	p.V243V	GGGCATCACGTCC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48313757	48313757	+	Silent	SNP	G	G	A	rs77190804	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	55	109	0	0.416667	0	G|0.901;A|0.099	0.099	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G4494A	p.K1498K	CACAAAGCAAGTA	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	60	107	0	0.495868	0	T|0.841;C|0.159	0.159	strong	.	THBS1	106	.	NM_003246	exon18	c.T2868C	p.D956D	GACCGATTTCCGC	.	PASS	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	41	93	0	0.482353	0	C|0.824;T|0.176	0.176	strong	SLC12A5,caecum,carcinoma,0,1	SLC12A5	181	1	NM_001134771	exon18	c.C2349T	p.S783S	CCAGTCCGGGGGC	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	121016818	121016818	+	Silent	SNP	G	G	A	rs12275038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	17	0	1	0	G|0.722;A|0.278	0.278	strong	.	TECTA	329	.	NM_005422	exon11	c.G4098A	p.T1366T	TTACACGTCCTGC	.	PASS	Atlas-SNP
BMP10	27302	hgsc.bcm.edu	37	2	69093312	69093312	+	Silent	SNP	A	A	G	rs2231344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	394	203	396	1	0.515228	0.00252525	A|0.870;G|0.130	0.130	strong	.	BMP10	70	.	NM_014482	exon2	c.T726C	p.D242D	ACTGGTATCTATT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511913	4511913	+	Missense_Mutation	SNP	C	C	T	rs199927982	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	359	137	323	0	0.381616	0	C|0.988;T|0.012	0.012	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G2017A	p.D673N	CCGTGTCTACACC	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367246	142367246	+	Missense_Mutation	SNP	G	G	A	rs36092215	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	26	41	0	0.530612	0	G|0.904;A|0.096	0.096	strong	.	GPR20	43	.	NM_005293	exon2	c.C778T	p.R260C	CTTGGCGGGCGTG	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18064730	18064730	+	Silent	SNP	C	C	T	rs8077577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	49	69	0	0.583333	0	C|0.806;T|0.194	0.194	strong	.	MYO15A	268	.	NM_016239	exon56	c.C9486T	p.D3162D	CCAAGACGTGAGC	.	PASS	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77755894	77755894	+	Missense_Mutation	SNP	C	C	G	rs9912676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	42	92	0	0.362069	0	C|0.976;G|0.024	0.024	strong	.	CBX2	50	.	NM_032647	exon4	c.C582G	p.F194L	ACTCTTCCCTCCC	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137711997	137711997	+	Silent	SNP	G	G	C	rs2228560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	41	113	0	0.333333	0	A|0.009;C|0.408;G|0.583	0.408	strong	.	COL5A1	323	.	NM_000093	exon58	c.G4482C	p.P1494P	TCCTCCGGGTGAA	.	PASS	Atlas-SNP
SLC45A4	57210	hgsc.bcm.edu	37	8	142228386	142228386	+	Silent	SNP	C	C	T	rs61995881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	28	32	0	0.608696	0	C|0.986;T|0.014	0.014	strong	.	SLC45A4	71	.	NM_001080431	exon4	c.G1200A	p.P400P	GCGCGACGGCTTG	.	PASS	Atlas-SNP
POMT2	29954	hgsc.bcm.edu	37	14	77786864	77786864	+	Missense_Mutation	SNP	G	G	T	rs8177536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	27	32	0	0.658537	0	G|0.920;T|0.080	0.080	strong	.	POMT2	47	.	NM_013382	exon1	c.C161A	p.A54E	CCGACCGCCTCGA	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48703986	48703986	+	Silent	SNP	G	G	A	rs9893223	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	55	82	0	0.392857	0	G|0.876;A|0.124	0.124	strong	CACNA1G_ENST00000359106,NS,carcinoma,0,6	CACNA1G	659	6	NM_018896	exon38	c.G7008A	p.P2336P	GGCTCCGTCCAGC	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	59	129	0	0.614583	0	G|0.779;N|0.000	.	strong	.	INPP4A	205	.	NM_004027	exon5	c.G258A	p.T86T	ACAGACGGAGATC	.	PASS	Atlas-SNP
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	53	85	0	0.576087	0	G|0.601;A|0.399	0.399	strong	CD163L1,colon,carcinoma,0,2	CD163L1	238	2	NM_174941	exon10	c.C2511T	p.N837N	TCCACAGTTTAAT	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	25	56	0	0.431034	0	C|0.335;N|0.001	0.335	strong	.	HSD17B14	25	.	NM_016246	exon2	c.A91G	p.N31D	CGCTGTTCACTGA	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49376582	49376582	+	Missense_Mutation	SNP	G	G	A	rs564196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	13	25	0	0.5	0	G|0.729;A|0.271	0.271	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G92A	p.R31H	TCAGCCGCGCCTG	.	PASS	Atlas-SNP
CLCF1	23529	hgsc.bcm.edu	37	11	67135006	67135006	+	Silent	SNP	A	A	T	rs867193	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	72	133	0	0.5625	0	A|0.928;T|0.072	0.072	strong	.	CLCF1	15	.	NM_013246	exon2	c.T108A	p.P36P	GGGGCCAGGCCCT	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	50	112	0	0.515464	0	T|0.799;C|0.201	0.201	strong	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	NM_001163213	exon7	c.T882C	p.N294N	GGTGAATGGCAGC	.	PASS	Atlas-SNP
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	47	132	0	0.439252	0	G|0.975;A|0.025	0.025	strong	.	KRTAP13-3	47	.	NM_181622	exon1	c.C312T	p.S104S	GCTATTGGATCCA	.	PASS	Atlas-SNP
CCDC134	79879	hgsc.bcm.edu	37	22	42209767	42209767	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	45	99	0	0.46875	0	.	.	none	.	CCDC134	19	.	NM_024821	exon6	c.C505T	p.L169L	CAGGAGCTGGGGA	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047348	46047348	+	Missense_Mutation	SNP	C	C	T	rs62220926	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	67	148	0	0.401198	0	C|0.927;T|0.073	0.073	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.C260T	p.P87L	GCCAGCCGGCTTA	.	PASS	Atlas-SNP
GFAP	2670	hgsc.bcm.edu	37	17	42985453	42985453	+	Silent	SNP	G	G	T	rs146298944	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	70	155	0	0.469799	0	G|0.999;T|0.001	0.001	strong	GFAP,colon,carcinoma,0,1	GFAP	88	1	NM_002055	exon8	c.C1236A	p.T412T	CTCCACGGTCTTC	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214820099	214820099	+	Missense_Mutation	SNP	A	A	G	rs3748697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	116	0	0.567568	0	A|0.689;G|0.311	0.311	strong	CENPF,NS,carcinoma,0,1	CENPF	321	1	NM_016343	exon13	c.A7186G	p.N2396D	AAAGAAAATCTGA	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	316	134	311	3	0.424051	0.0096463	C|0.759;T|0.241	0.241	strong	TMEM132B,NS,carcinoma,-1,1	TMEM132B	207	1	NM_052907	exon8	c.C1973T	p.A658V	CCATCGCGGAGCT	.	scavenged	Atlas-SNP
UMPS	7372	hgsc.bcm.edu	37	3	124462808	124462808	+	Silent	SNP	C	C	T	rs13146	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	58	114	0	0.43609	0	C|0.830;A|0.001	.	strong	.	UMPS	43	.	NM_000373	exon6	c.C1320T	p.G440G	TATTGGCAAACGA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46655948	46655948	+	Missense_Mutation	SNP	T	T	C	rs6008384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	79	127	0	0.490683	0	T|0.721;C|0.279	0.279	strong	.	PKDREJ	195	.	NM_006071	exon1	c.A3272G	p.N1091S	TTGTCATTGAGCT	.	PASS	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7907189	7907189	+	Silent	SNP	C	C	T	rs3829789	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	46	99	0	0.516854	0	C|0.893;T|0.107	0.107	strong	.	GUCY2D	82	.	NM_000180	exon3	c.C741T	p.H247H	GATGCACTCGGTG	.	PASS	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	37	5	140180964	140180964	+	Missense_Mutation	SNP	C	C	A	rs7731327	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	32	75	0	0.380952	0	C|0.949;A|0.051	0.051	strong	PCDHA3_ENST00000522353,NS,carcinoma,-1,2	PCDHA3	396	2	NM_031497	exon1	c.C182A	p.P61Q	TGGTGCCGCGCCT	.	PASS	Atlas-SNP
SORD	6652	hgsc.bcm.edu	37	15	45365724	45365724	+	Missense_Mutation	SNP	C	C	T	rs76283634	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	547	198	563	2	0.361974	0.0035524	C|0.918;T|0.082	0.082	strong	.	SORD	24	.	NM_003104	exon9	c.C1070T	p.P357L	AGAATCCCTGATG	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6204161	6204161	+	Silent	SNP	G	G	A	rs17436816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	120	259	0	0.466926	0	G|0.919;A|0.081	0.081	strong	.	CHD5	267	.	NM_015557	exon12	c.C1857T	p.Y619Y	CTGGTCGTAGGGC	.	PASS	Atlas-SNP
MIA2	117153	hgsc.bcm.edu	37	14	39722023	39722023	+	Missense_Mutation	SNP	G	G	C	rs10134365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	66	0	1	0	G|0.714;C|0.286	0.286	strong	MIA2,rectum,carcinoma,0,1	MIA2	82	1	NM_054024	exon5	c.G1639C	p.D547H	TCTAAAGATAGTG	.	PASS	Atlas-SNP
NOL7	51406	hgsc.bcm.edu	37	6	13615767	13615767	+	Silent	SNP	T	T	C	rs75029999	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	32	48	0	0.477612	0	T|0.994;C|0.006	0.006	strong	.	NOL7	18	.	NM_016167	exon1	c.T177C	p.F59F	TGAGTTTGACGAT	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721870	101721870	+	Silent	SNP	G	G	A	rs146609644	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	66	176	1	0.242647	0.00568182	G|0.767;A|0.233	0.233	strong	PABPC1,rectum,carcinoma,0,1	PABPC1	76	1	NM_002568	exon8	c.C1062T	p.N354N	TCTACCGTTCATT	.	scavenged	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12414314	12414314	+	Splice_Site	SNP	C	C	G	rs138469050	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	81	178	0	0.473684	0	C|0.994;G|0.006	0.006	strong	.	VWDE	123	.	NM_001135924	exon10	c.1316+1G>C	.	AAATTACCTGCCA	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161007496	161007496	+	Missense_Mutation	SNP	G	G	C	rs7765781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	71	97	0	0.554688	0	G|0.582;C|0.418	0.418	strong	.	LPA	237	.	NM_005577	exon26	c.C4114G	p.L1372V	AAGGAAGCTCTGT	.	PASS	Atlas-SNP
FTHL17	53940	hgsc.bcm.edu	37	X	31089628	31089628	+	Missense_Mutation	SNP	T	T	A	rs7058123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	109	178	0	0.561856	0	T|0.982;A|0.018	0.018	strong	.	FTHL17	99	.	NM_031894	exon1	c.A443T	p.E148V	CCCAGCTCTTTGA	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256512	24256512	+	Silent	SNP	T	T	C	rs7005258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	56	114	0	0.421053	0	T|0.977;C|0.023	0.023	strong	.	ADAMDEC1	69	.	NM_014479	exon9	c.T888C	p.S296S	CAGTTCTAACCTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411781	105411781	+	Missense_Mutation	SNP	G	G	A	rs10438247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	323	322	270	0	0.996904	0	G|0.479;A|0.521	0.521	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C10007T	p.P3336L	GCCTTCGGCGCAG	.	PASS	Atlas-SNP
VSTM1	284415	hgsc.bcm.edu	37	19	54561792	54561792	+	Silent	SNP	G	G	A	rs11669427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	57	130	0	0.537736	0	G|0.824;A|0.176	0.176	strong	.	VSTM1	30	.	NM_198481	exon3	c.C123T	p.A41A	GCTCTCGGCTTCA	.	PASS	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546395	11546395	+	Missense_Mutation	SNP	G	G	T	rs11054277		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	434	24	597	4	0.0552995	0.00670017	.	.	weak	PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	NM_006248	exon3	c.C617A	p.P206Q	CCTTGTGGGGGTG	.	scavenged	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135358567	135358567	+	Missense_Mutation	SNP	T	T	G	rs7742542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	74	143	0	0.528571	0	T|0.538;G|0.462	0.462	strong	.	HBS1L	75	.	NM_001145207	exon5	c.A1028C	p.E343A	TCAGTTTCTTTAC	.	PASS	Atlas-SNP
SPINK4	27290	hgsc.bcm.edu	37	9	33240225	33240225	+	Missense_Mutation	SNP	G	G	A	rs706107	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	214	185	0	0.995349	0	G|0.621;A|0.379	0.379	strong	.	SPINK4	7	.	NM_014471	exon1	c.G19A	p.V7I	CAGTGGGTAATCG	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123357037	123357037	+	Silent	SNP	A	A	G	rs820463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	49	113	0	0.395161	0	A|0.732;G|0.268	0.268	strong	.	MYLK	224	.	NM_053025	exon29	c.T4842C	p.N1614N	CCCCGCATTCTCT	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48625928	48625928	+	Missense_Mutation	SNP	C	C	G	rs8076632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	39	1	1	0.025641	C|0.583;G|0.417	0.417	strong	SPATA20,NS,carcinoma,0,1	SPATA20	59	1	NM_022827	exon4	c.C310G	p.Q104E	TGGGGACAGGAAG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507926	195507926	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	17	445	6	0.265625	0.0134831	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	NM_018406	exon2	c.G10525A	p.G3509S	AAGCGCCGGTGAC	.	scavenged	Atlas-SNP
IRF2BP2	359948	hgsc.bcm.edu	37	1	234743492	234743492	+	Silent	SNP	C	C	T	rs14739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	115	87	0	0.982906	0	C|0.863;T|0.137	0.137	strong	.	IRF2BP2	37	.	NM_182972	exon2	c.G1155A	p.E385E	GAGCCCCTCTGTG	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	12705	12705	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	11	16	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.C369T	p.I123I	ACTCATCTTCCTA	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6303955	6303955	+	Silent	SNP	G	G	A	rs1046314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	42	51	0	0.583333	0	G|0.382;A|0.618	0.618	strong	.	WFS1	71	.	NM_001145853	exon8	c.G2433A	p.K811K	GTTCAAGAGCGTG	.	PASS	Atlas-SNP
EFTUD1	79631	hgsc.bcm.edu	37	15	82443824	82443824	+	Missense_Mutation	SNP	C	C	T	rs78664413	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	36	107	0	0.413793	0	C|0.942;T|0.058	0.058	strong	EFTUD1,NS,carcinoma,0,1	EFTUD1	74	1	NM_024580	exon18	c.G2971A	p.A991T	CAGTGGCCATGAT	.	PASS	Atlas-SNP
CAPS	828	hgsc.bcm.edu	37	19	5914605	5914605	+	Missense_Mutation	SNP	A	A	G	rs7249419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	35	82	0	0.443038	0	A|0.954;G|0.046	0.046	strong	.	CAPS	14	.	NM_080590	exon3	c.A115G	p.R39G	GGGAGCAGATCCC	.	PASS	Atlas-SNP
GAS2L3	283431	hgsc.bcm.edu	37	12	101018061	101018061	+	Missense_Mutation	SNP	C	C	T	rs61748063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	30	40	0	0.526316	0	C|0.995;T|0.005	0.005	strong	.	GAS2L3	76	.	NM_174942	exon10	c.C1478T	p.S493L	CACATTCAAATTC	.	PASS	Atlas-SNP
KIAA0195	9772	hgsc.bcm.edu	37	17	73488794	73488794	+	Silent	SNP	C	C	T	rs4078259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	48	0	1	0	C|0.295;T|0.705	0.705	strong	.	KIAA0195	102	.	NM_014738	exon15	c.C1836T	p.I612I	CAACATCGCCCTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228461055	228461055	+	Silent	SNP	T	T	C	rs113996842	byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	140	283	0	0.482759	0	T|0.997;C|0.003	0.003	strong	.	OBSCN	2142	.	NM_001271223	exon21	c.T6069C	p.C2023C	GAGCTGTGAGGTG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656562	46656562	+	Silent	SNP	A	A	G	rs7287371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	74	142	0	0.532374	0	A|0.942;G|0.058	0.058	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T2658C	p.Y886Y	TGTTGGATAAAAA	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	99	202	0	0.526596	0	G|0.623;A|0.377	0.377	strong	.	ATP11A	225	.	NM_032189	exon27	c.G3138A	p.S1046S	CTTTTCGCTTCTC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388370	103388370	+	Missense_Mutation	SNP	C	C	T	rs9518825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	116	202	0	0.479339	0	C|0.737;T|0.263	0.263	strong	Q8N800_HUMAN,NS,carcinoma,0,2	.	.	2	NM_001146197	exon4	c.G14677A	p.G4893S	TTCTACCTTCCCT	.	PASS	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44352690	44352690	+	Missense_Mutation	SNP	G	G	T	rs10417624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	93	0	1	0	G|0.953;T|0.047	0.047	strong	ZNF283_ENST00000324461,NS,carcinoma,+1,1	ZNF283	83	1	NM_181845	exon7	c.G1937T	p.R646I	ATGAGAGAACTCA	.	PASS	Atlas-SNP
TAF1	6872	hgsc.bcm.edu	37	X	70586196	70586196	+	Missense_Mutation	SNP	C	C	T	rs139510844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	351	183	303	1	0.521368	0.00330033	C|0.989;T|0.011	0.011	strong	.	TAF1	439	.	NM_004606	exon1	c.C32T	p.T11I	TGCGGACAGCAGC	.	PASS	Atlas-SNP
MASP2	10747	hgsc.bcm.edu	37	1	11087687	11087687	+	Missense_Mutation	SNP	C	C	T	rs12085877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	44	104	0	0.44	0	C|0.971;T|0.029	0.029	strong	MASP2,NS,carcinoma,-1,1	MASP2	71	1	NM_006610	exon11	c.G1316A	p.R439H	GTTGTGCGGGCTG	.	PASS	Atlas-SNP
TMEM82	388595	hgsc.bcm.edu	37	1	16069664	16069664	+	Missense_Mutation	SNP	T	T	C	rs61740067	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	29	67	0	0.3625	0	T|0.982;C|0.018	0.018	strong	.	TMEM82	30	.	NM_001013641	exon3	c.T311C	p.V104A	GGGCCGTGTCCAC	.	PASS	Atlas-SNP
ZNF778	197320	hgsc.bcm.edu	37	16	89289624	89289624	+	Silent	SNP	G	G	A	rs12920028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	83	209	0	0.458564	0	G|0.901;A|0.099	0.099	strong	.	ZNF778	67	.	NM_182531	exon4	c.G177A	p.L59L	TTTACTGGACCCA	.	PASS	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616668	248616668	+	Silent	SNP	C	C	T	rs144808604	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	544	205	490	0	0.376838	0	C|0.997;T|0.003	0.003	strong	.	OR2T2	73	.	NM_001004136	exon1	c.C570T	p.C190C	GTCTTGCACAGAC	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18566422	18566422	+	Missense_Mutation	SNP	C	C	T	rs146829975	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	381	149	416	0	0.391076	0	C|0.975;T|0.025	0.025	strong	.	ZNF286B	75	.	NM_001145045	exon5	c.G397A	p.E133K	ATGATTCTGCTTT	.	PASS	Atlas-SNP
ELMSAN1	91748	hgsc.bcm.edu	37	14	74203789	74203789	+	Missense_Mutation	SNP	G	G	A	rs17782124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	68	152	0	0.507463	0	G|0.856;A|0.144	0.144	strong	.	.	.	.	NM_194278	exon3	c.C1661T	p.P554L	TGTTCAGGACCCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	308	343	2	1	0.0058309	G|0.567;A|0.433	0.433	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.G3078A	p.S1026S	CAGCTCGAAAGTG	.	PASS	Atlas-SNP
C20orf118	140711	hgsc.bcm.edu	37	20	35507542	35507542	+	Silent	SNP	G	G	A	rs3748459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	69	0	0.47561	0	G|0.723;A|0.277	0.277	strong	.	C20orf118	21	.	NM_080628	exon3	c.G288A	p.R96R	CCGGCGGATGGAG	.	PASS	Atlas-SNP
MYBL2	4605	hgsc.bcm.edu	37	20	42310449	42310449	+	Missense_Mutation	SNP	G	G	A	rs150704861	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	49	135	0	0.401639	0	G|0.998;A|0.002	0.002	strong	.	MYBL2	82	.	NM_002466	exon3	c.G140A	p.R47K	TGGTGAGGCAGTT	.	PASS	Atlas-SNP
OR10AG1	282770	hgsc.bcm.edu	37	11	55735091	55735091	+	Silent	SNP	C	C	T	rs12292026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	55	115	0	0.518868	0	C|0.974;T|0.026	0.026	strong	.	OR10AG1	100	.	NM_001005491	exon1	c.G849A	p.L283L	GTTCCTCAGGGTA	.	PASS	Atlas-SNP
ST7L	54879	hgsc.bcm.edu	37	1	113068651	113068651	+	Missense_Mutation	SNP	C	C	T	rs12069022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	38	61	0	0.520548	0	C|0.963;T|0.037	0.037	strong	.	ST7L	31	.	NM_017744	exon15	c.G1712A	p.G571D	CTCAAACCTAGGT	.	PASS	Atlas-SNP
OSBPL6	114880	hgsc.bcm.edu	37	2	179226431	179226431	+	Silent	SNP	A	A	G	rs145291582	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	144	290	0	0.49827	0	A|0.995;G|0.005	0.005	strong	OSBPL6,NS,carcinoma,+1,1	OSBPL6	178	1	NM_001201480	exon14	c.A1251G	p.A417A	GTCTGCATTTAAT	.	PASS	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51742839	51742839	+	Missense_Mutation	SNP	A	A	G	rs35632246	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	133	0	0.491379	0	A|0.986;G|0.014	0.014	strong	.	CD33	55	.	NM_001772	exon7	c.A991G	p.T331A	GCCCCTACTGTGG	.	PASS	Atlas-SNP
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	76	148	0	0.481013	0	T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong	.	EPS8	70	.	NM_004447	exon20	c.G2352A	p.L784L	TACCTCCAATGCA	.	PASS	Atlas-SNP
ZC3H6	376940	hgsc.bcm.edu	37	2	113090047	113090047	+	Silent	SNP	T	T	C	rs4578863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	42	0	1	0	T|0.276;C|0.724	0.724	strong	.	ZC3H6	93	.	NM_198581	exon12	c.T3552C	p.T1184T	TCCAACTGCTTCA	.	PASS	Atlas-SNP
TRAF2	7186	hgsc.bcm.edu	37	9	139814931	139814931	+	Silent	SNP	G	G	T	rs17244166	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	29	61	0	0.376623	0	G|0.989;T|0.011	0.011	strong	.	TRAF2	46	.	NM_021138	exon8	c.G924T	p.R308R	GCACCGGCTGGAC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464474	10464474	+	Silent	SNP	G	G	T	rs113172380	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	46	56	0	0.676471	0	G|0.996;T|0.004	0.004	strong	RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	NM_178857	exon4	c.C7134A	p.L2378L	ACTTCCGAGTGCC	.	PASS	Atlas-SNP
WDR59	79726	hgsc.bcm.edu	37	16	75018874	75018874	+	Silent	SNP	G	G	A	rs12448858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	62	103	0	0.504065	0	G|0.886;A|0.114	0.114	strong	.	WDR59	66	.	NM_030581	exon1	c.C42T	p.F14F	GTCACGGAACTCT	.	PASS	Atlas-SNP
LCN15	389812	hgsc.bcm.edu	37	9	139657900	139657900	+	Silent	SNP	C	C	G	rs11145872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	20	36	0	0.625	0	C|0.994;G|0.006	0.006	strong	.	LCN15	11	.	NM_203347	exon4	c.G327C	p.V109V	GATGCGCACGTCC	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115409840	115409840	+	Missense_Mutation	SNP	C	C	T	rs2275799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	68	120	0	0.566667	0	C|0.708;T|0.292	0.292	strong	.	NRAP	208	.	NM_001261463	exon9	c.G844A	p.A282T	CCTCAGCTCCAAT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361009	107361009	+	Missense_Mutation	SNP	C	C	G	rs73508187	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	132	183	0	0.628571	0	C|0.990;G|0.010	0.010	strong	.	OR13C5	60	.	NM_001004482	exon1	c.G686C	p.S229T	GAAGAGCTAATTT	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19345802	19345802	+	Silent	SNP	C	C	T	rs2228600	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	67	118	0	0.563025	0	C|0.920;T|0.080	0.080	strong	.	NCAN	277	.	NM_004386	exon10	c.C3147T	p.D1049D	TGATGACTGCCTC	.	PASS	Atlas-SNP
CCDC42	146849	hgsc.bcm.edu	37	17	8647015	8647015	+	Missense_Mutation	SNP	G	G	A	rs9893451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	103	0	0.483051	0	G|0.924;A|0.076	0.076	strong	CCDC42,caecum,carcinoma,+1,1	CCDC42	31	1	NM_144681	exon3	c.C223T	p.R75C	CCCAGCGCAGGTT	.	PASS	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26089867	26089867	+	Silent	SNP	T	T	C	rs1060826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	48	0	1	0	T|0.303;C|0.697	0.697	strong	NOS2,NS,carcinoma,0,1	NOS2	113	1	NM_000625	exon22	c.A2757G	p.T919T	GATCTCTGTGGGC	.	PASS	Atlas-SNP
AQP2	359	hgsc.bcm.edu	37	12	50344958	50344958	+	Silent	SNP	C	C	T	rs60629501	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	43	69	0	0.518072	0	C|0.988;T|0.012	0.012	strong	.	AQP2	34	.	NM_000486	exon1	c.C345T	p.D115D	CGGGGACCTGGCT	.	PASS	Atlas-SNP
TRPC7	57113	hgsc.bcm.edu	37	5	135583342	135583342	+	Missense_Mutation	SNP	C	C	T	rs183404828	by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	3	204	1	0.012987	0.00490196	C|0.999;T|0.001	0.001	strong	TRPC7,NS,carcinoma,0,2	TRPC7	126	2	NM_020389	exon7	c.G1661A	p.R554H	GCAATGCGAGAGA	.	scavenged	Atlas-SNP
RPL31	6160	hgsc.bcm.edu	37	2	101619211	101619211	+	Silent	SNP	C	C	T	rs141007382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	114	183	0	0.520548	0	C|0.999;T|0.001	0.001	strong	.	RPL31	12	.	NM_001098577	exon2	c.C48T	p.A16A	TTCTGCCATCAAC	.	PASS	Atlas-SNP
PHYHD1	254295	hgsc.bcm.edu	37	9	131702891	131702891	+	Missense_Mutation	SNP	A	A	G	rs2273866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	86	91	0	1	0	A|0.643;G|0.357	0.357	strong	PHYHD1,NS,carcinoma,0,1	PHYHD1	29	1	NM_174933	exon10	c.A578G	p.E193G	GTCAAGAAGGATG	.	PASS	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140803241	140803241	+	Missense_Mutation	SNP	C	C	A	rs57195665	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	70	118	0	0.578512	0	C|0.900;A|0.100	0.100	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.C2447A	p.S816Y	TTATTTCTCTGCC	.	PASS	Atlas-SNP
MOK	5891	hgsc.bcm.edu	37	14	102700028	102700028	+	Missense_Mutation	SNP	T	T	C	rs34965156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	113	216	0	0.502222	0	T|0.940;C|0.060	0.060	strong	.	.	.	.	NM_014226	exon8	c.A689G	p.K230R	TACTGTTTGAACT	.	PASS	Atlas-SNP
TMEM253	643382	hgsc.bcm.edu	37	14	21570273	21570273	+	Silent	SNP	T	T	C	rs745696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	113	0	1	0	T|0.354;C|0.646	0.646	strong	.	.	.	.	NM_001146683	exon5	c.T270C	p.L90L	CCGCCTTTGGAAG	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73796917	73796917	+	Missense_Mutation	SNP	C	C	T	rs826058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	130	109	0	0.992366	0	C|0.635;T|0.365	0.365	strong	C2CD3_ENST00000334126,NS,adenoma,0,2	C2CD3	288	2	NM_015531	exon21	c.G3656A	p.R1219Q	GGTTCCCGTTCAG	.	PASS	Atlas-SNP
FHL2	2274	hgsc.bcm.edu	37	2	106002854	106002854	+	Silent	SNP	G	G	A	rs11537578	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	72	116	0	0.521739	0	G|0.989;A|0.011	0.011	strong	.	FHL2	18	.	NM_001039492	exon3	c.C120T	p.C40C	CTCCTCGCAGGTG	.	PASS	Atlas-SNP
AK8	158067	hgsc.bcm.edu	37	9	135601126	135601126	+	Silent	SNP	G	G	A	rs28477720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	89	127	0	0.760684	0	G|0.966;A|0.034	0.034	strong	.	AK8	45	.	NM_152572	exon13	c.C1389T	p.F463F	GTATTCGAAGACT	.	PASS	Atlas-SNP
KLC2	64837	hgsc.bcm.edu	37	11	66033430	66033430	+	Missense_Mutation	SNP	C	C	T	rs2276036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	111	210	0	0.470339	0	C|0.818;T|0.182	0.182	strong	.	KLC2	50	.	NM_022822	exon13	c.C1549T	p.P517S	GCCGGGCCTCGGT	.	PASS	Atlas-SNP
ARSE	415	hgsc.bcm.edu	37	X	2867651	2867651	+	Missense_Mutation	SNP	C	C	T	rs34412194	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	107	184	0	0.507109	0	C|0.969;0|0.016	.	strong	.	ARSE	43	.	NM_000047	exon6	c.G548A	p.R183H	TCCCAGCGGGCGC	.	PASS	Atlas-SNP
MIP	4284	hgsc.bcm.edu	37	12	56847384	56847384	+	Silent	SNP	G	G	A	rs36032520	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	40	85	0	0.47619	0	G|0.998;A|0.002	0.002	strong	.	MIP	39	.	NM_012064	exon2	c.C516T	p.H172H	AAAGAGGTGCCCC	.	PASS	Atlas-SNP
ZNF774	342132	hgsc.bcm.edu	37	15	90902172	90902172	+	Missense_Mutation	SNP	C	C	T	rs16944267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	19	59	0	0.413043	0	C|0.886;T|0.114	0.114	strong	.	ZNF774	35	.	NM_001004309	exon3	c.C194T	p.P65L	AGATCCCGAGGGA	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	37	78	0	0.528571	0	T|0.676;C|0.324	0.324	strong	MATN4,NS,carcinoma,0,1	MATN4	57	1	NM_030592	exon3	c.A348G	p.A116A	CTGGATTGCCAGT	.	PASS	Atlas-SNP
ARNTL2	56938	hgsc.bcm.edu	37	12	27543141	27543141	+	Missense_Mutation	SNP	G	G	C	rs74988383	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	43	100	0	0.518072	0	G|0.991;C|0.009	0.009	strong	.	ARNTL2	54	.	NM_020183	exon9	c.G888C	p.E296D	AGAAGAGCATGGA	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117131407	117131407	+	Silent	SNP	G	G	A	rs57816525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	98	168	0	0.482759	0	G|0.962;A|0.038	0.038	strong	.	IGSF3	294	.	NM_001542	exon9	c.C2409T	p.H803H	CTCCACGTGGCAG	.	PASS	Atlas-SNP
CREBRF	153222	hgsc.bcm.edu	37	5	172550204	172550204	+	Silent	SNP	C	C	T	rs1129146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	100	175	0	0.510204	0	C|0.868;T|0.132	0.132	strong	.	.	.	.	NM_153607	exon8	c.C1803T	p.L601L	TACTCTCGGTAAG	.	PASS	Atlas-SNP
CAPZA1	829	hgsc.bcm.edu	37	1	113202386	113202386	+	Silent	SNP	C	C	T	rs12074157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	35	77	0	0.406977	0	C|0.968;T|0.032	0.032	strong	CAPZA1,colon,carcinoma,0,1	CAPZA1	16	1	NM_006135	exon7	c.C570T	p.G190G	GGTTGGCGTGCTT	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143043340	143043340	+	Silent	SNP	A	A	G	rs2270658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	138	125	0	0.992806	0	A|0.867;G|0.133	0.133	strong	.	INPP4B	132	.	NM_003866	exon22	c.T2076C	p.V692V	AAATGCAACTTTC	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971108	45971108	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	18	134	1	0.104046	0.00746269	.	.	none	KRTAP10-2,caecum,carcinoma,-1,1	KRTAP10-2	21	1	NM_198693	exon1	c.G234A	p.S78S	GCAGCACGAGGGC	.	scavenged	Atlas-SNP
WWOX	51741	hgsc.bcm.edu	37	16	78458807	78458807	+	Missense_Mutation	SNP	C	C	G	rs7201683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	100	176	0	0.510204	0	C|0.956;G|0.044	0.044	strong	.	WWOX	98	.	NM_016373	exon7	c.C646G	p.L216V	TTTGCTCTACCCT	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74524757	74524757	+	Silent	SNP	T	T	G	rs58562849	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	33	73	0	0.589286	0	T|0.971;G|0.029	0.029	strong	.	CD109	170	.	NM_133493	exon30	c.T3822G	p.S1274S	AAGATCTATCCAA	.	PASS	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67266065	67266065	+	Silent	SNP	T	T	C	rs34888644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	452	223	418	1	0.493363	0.00239234	T|0.919;C|0.081	0.081	strong	.	FHOD1	86	.	NM_013241	exon14	c.A2079G	p.T693T	CAGCACTGTGGTC	.	PASS	Atlas-SNP
RHBDD1	84236	hgsc.bcm.edu	37	2	227860232	227860232	+	Silent	SNP	C	C	T	rs61745917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	95	179	0	0.505319	0	C|0.996;T|0.004	0.004	strong	.	RHBDD1	34	.	NM_001167608	exon9	c.C942T	p.S314S	CGATAGCCAGTGA	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25312895	25312895	+	Missense_Mutation	SNP	C	C	A	rs34929144	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	48	152	0	0.384	0	C|0.974;A|0.026	0.026	strong	.	THNSL1	70	.	NM_024838	exon3	c.C743A	p.A248E	TTTCAGCAAAATT	.	PASS	Atlas-SNP
C1orf112	55732	hgsc.bcm.edu	37	1	169796197	169796197	+	Missense_Mutation	SNP	T	T	C	rs142988055	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	125	242	0	0.516529	0	T|0.984;C|0.016	0.016	strong	.	C1orf112	74	.	NM_018186	exon11	c.T854C	p.F285S	GCAAGTTTCCTCC	.	PASS	Atlas-SNP
CEACAM21	90273	hgsc.bcm.edu	37	19	42083673	42083673	+	Silent	SNP	T	T	C	rs7247842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	179	152	0	0.994444	0	T|0.766;C|0.234	0.234	strong	CEACAM21_ENST00000401445,NS,carcinoma,0,1	CEACAM21	52	1	NM_033543	exon2	c.T186C	p.L62L	GAATCTTTACAGC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1265786	1265786	+	Missense_Mutation	SNP	C	C	T	rs75917341	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	607	202	506	1	0.332784	0.00197628	C|0.500;T|0.500	0.500	strong	.	MUC5B	473	.	NM_002458	exon31	c.C7676T	p.T2559M	CACCCACGGCCAC	.	PASS	Atlas-SNP
FAM221B	392307	hgsc.bcm.edu	37	9	35826058	35826058	+	Missense_Mutation	SNP	T	T	C	rs13294256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	39	114	0	0.402062	0	T|0.764;C|0.236	0.236	strong	.	FAM221B	38	.	NM_001012446	exon2	c.A101G	p.H34R	GAGATATGGTTCT	.	PASS	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75269730	75269730	+	Missense_Mutation	SNP	G	G	A	rs61729593	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	15	22	0	0.454545	0	G|0.991;A|0.009	0.009	strong	.	BCAR1	184	.	NM_001170714	exon6	c.C1205T	p.P402L	GCCGGCGGGGAGT	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060453	16060453	+	Silent	SNP	T	T	C	rs115548355	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	390	196	389	1	0.502564	0.00257069	T|0.988;C|0.012	0.012	strong	.	OR10H4	48	.	NM_001004465	exon1	c.T636C	p.C212C	AGGCTGTTTATTC	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5444061	5444061	+	Missense_Mutation	SNP	G	G	A	rs2736586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	220	276	2	0.986547	0.00724638	G|0.599;A|0.401	0.401	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.G631A	p.V211M	ATTATCGTGGATC	.	PASS	Atlas-SNP
ZNF254	9534	hgsc.bcm.edu	37	19	24310074	24310074	+	Silent	SNP	T	T	C	rs61737179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	28	59	0	0.411765	0	T|0.979;C|0.021	0.021	strong	.	ZNF254	88	.	NM_203282	exon4	c.T1272C	p.H424H	TACACATAAGATA	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1391132	1391132	+	Silent	SNP	C	C	T	rs11866635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	55	120	0	0.495495	0	C|0.927;T|0.073	0.073	strong	.	BAIAP3	88	.	NM_003933	exon7	c.C576T	p.A192A	ACAGGCCCCCACG	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324190	39324190	+	Missense_Mutation	SNP	A	A	G	rs377224840		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	73	392	1	0.439759	0.00255102	.	.	weak	.	KRTAP4-3	40	.	NM_033187	exon1	c.T235C	p.C79R	TGCAGCAACTGGA	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240560	39240560	+	Silent	SNP	T	T	C	rs200090467	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	14	97	1	0.110236	0.0103093	T|0.995;C|0.005	0.005	weak	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	NM_033061	exon1	c.T102C	p.C34C	CACCTGTTGCAGG	.	scavenged	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12443312	12443312	+	Missense_Mutation	SNP	C	C	T	rs139879021	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	14	14	0	0.5	0	C|0.996;T|0.004	0.004	strong	.	VWDE	123	.	NM_001135924	exon1	c.G31A	p.A11T	TCAGCGCGATCAC	.	PASS	Atlas-SNP
RGS8	85397	hgsc.bcm.edu	37	1	182640851	182640851	+	Silent	SNP	T	T	G	rs569956	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	217	83	283	0	0.382488	0	T|0.880;G|0.120	0.120	strong	RGS8,NS,carcinoma,0,1	RGS8	51	1	NM_033345	exon2	c.A21C	p.R7R	GAGGCTTCGGGTT	.	PASS	Atlas-SNP
BAG6	7917	hgsc.bcm.edu	37	6	31615514	31615514	+	Silent	SNP	T	T	C	rs10484558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	51	118	0	0.472222	0	T|0.937;C|0.063	0.063	strong	.	BAG6	73	.	NM_004639	exon7	c.A660G	p.T220T	TTCTGATGTTTGA	.	PASS	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	12	26	0	0.521739	0	A|0.534;C|0.466	0.466	strong	.	PAPOLB	93	.	NM_020144	exon1	c.T57G	p.N19K	GTAGCGATTCGGC	.	PASS	Atlas-SNP
PYROXD2	84795	hgsc.bcm.edu	37	10	100148176	100148176	+	Missense_Mutation	SNP	A	A	G	rs2147896	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	48	113	0	0.484848	0	T|0.003;G|0.526	0.526	strong	.	PYROXD2	43	.	NM_032709	exon13	c.T1382C	p.M461T	TAGGGCATGTACT	.	PASS	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	37	19	59074429	59074429	+	Silent	SNP	C	C	T	rs2228162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	11	16	0	0.44	0	C|0.839;T|0.161	0.161	strong	.	MZF1	37	.	NM_198055	exon6	c.G1215A	p.T405T	GGTGTGCGTAAGC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32046832	32046832	+	Silent	SNP	C	C	T	rs61998180	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	71	86	0	0.518248	0	C|0.987;T|0.013	0.013	weak	TNXB_ENST00000375247,NS,carcinoma,0,1	TNXB	553	1	NM_019105	exon11	c.G4353A	p.P1451P	GGACACCGGGCCC	.	PASS	Atlas-SNP
PGLYRP3	114771	hgsc.bcm.edu	37	1	153276449	153276449	+	Missense_Mutation	SNP	T	T	C	rs41264632	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	38	71	1	0.506667	0.0140845	T|0.982;C|0.018	0.018	strong	PGLYRP3,NS,carcinoma,0,1	PGLYRP3	55	1	NM_052891	exon4	c.A413G	p.E138G	AGACCCTCTGCAG	.	scavenged	Atlas-SNP
WDR4	10785	hgsc.bcm.edu	37	21	44283574	44283574	+	Silent	SNP	C	C	T	rs11911090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	102	187	1	0.545455	0.00534759	C|0.895;T|0.105	0.105	strong	.	WDR4	35	.	NM_018669	exon4	c.G429A	p.G143G	CAGGTGCCCCAGC	.	PASS	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	37	1	153740285	153740285	+	Silent	SNP	G	G	A	rs61736048	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	38	74	0	0.5	0	G|0.983;A|0.017	0.017	strong	.	INTS3	83	.	NM_023015	exon21	c.G2226A	p.T742T	CCTCACGCCCTCC	.	PASS	Atlas-SNP
PTRF	284119	hgsc.bcm.edu	37	17	40556951	40556951	+	Silent	SNP	C	C	T	rs112332573	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	92	135	0	0.534884	0	C|0.981;T|0.019	0.019	strong	.	PTRF	48	.	NM_012232	exon2	c.G927A	p.A309A	GGAGCGCGCGTAC	.	PASS	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	37	9	130485476	130485476	+	Missense_Mutation	SNP	A	A	C	rs115363266	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	62	118	0	0.62	0	A|0.962;C|0.038	0.038	strong	.	TTC16	55	.	NM_144965	exon7	c.A736C	p.K246Q	CTCCAGAAGATGG	.	PASS	Atlas-SNP
TAS1R3	83756	hgsc.bcm.edu	37	1	1269488	1269488	+	Missense_Mutation	SNP	G	G	A	rs112507608	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	29	71	0	0.47541	0	G|0.933;A|0.067	0.067	strong	.	TAS1R3	39	.	NM_152228	exon6	c.G2203A	p.A735T	GCGCACGCCACCA	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609806	32609806	+	Missense_Mutation	SNP	C	C	T	rs707952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	254	196	0	1	0	C|0.785;T|0.215	0.215	strong	.	HLA-DQA1	52	.	NM_002122	exon3	c.C389T	p.T130I	CCAACACCCTCAT	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261778	39261778	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	23	127	1	0.270588	0.00787402	.	.	none	KRTAP4-9,NS,carcinoma,0,1	KRTAP4-9	110	1	NM_001146041	exon1	c.A138G	p.V46V	TTGTGTATCCAGC	.	scavenged	Atlas-SNP
TOP2B	7155	hgsc.bcm.edu	37	3	25679738	25679738	+	Silent	SNP	T	T	C	rs60422476	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	123	179	0	0.554054	0	T|0.700;C|0.300	0.300	strong	.	TOP2B	98	.	NM_001068	exon5	c.A444G	p.V148V	TTTCTCTACCTTG	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721705	101721705	+	Missense_Mutation	SNP	G	G	T	rs201017624	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	264	48	200	0	0.181818	0	G|0.944;T|0.057	0.057	strong	.	PABPC1	76	.	NM_002568	exon8	c.C1227A	p.F409L	TGCCATGAAGTAA	.	PASS	Atlas-SNP
RFX4	5992	hgsc.bcm.edu	37	12	107114548	107114548	+	Silent	SNP	G	G	A	rs73391388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	66	165	0	0.423077	0	G|0.988;A|0.012	0.012	strong	.	RFX4	218	.	NM_001206691	exon13	c.G1272A	p.K424K	TGCCAAGAGACAA	.	PASS	Atlas-SNP
UGT1A4	54657	hgsc.bcm.edu	37	2	234627992	234627992	+	Missense_Mutation	SNP	A	A	T	rs45540231	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	411	215	374	0	0.523114	0	A|0.980;T|0.020	0.020	strong	.	UGT1A4	63	.	NM_007120	exon1	c.A526T	p.I176F	AGGTACATTCCAT	.	PASS	Atlas-SNP
PMEPA1	56937	hgsc.bcm.edu	37	20	56227514	56227514	+	Silent	SNP	T	T	C	rs6025698	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	106	0	1	0	T|0.715;C|0.285	0.285	strong	PMEPA1,NS,lymphoid_neoplasm,0,1	PMEPA1	29	1	NM_020182	exon4	c.A459G	p.S153S	CCCGTCTGACAGC	.	PASS	Atlas-SNP
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940052	70940052	+	Missense_Mutation	SNP	C	C	T	rs33998366	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	24	52	0	0.461538	0	C|0.961;T|0.039	0.039	strong	.	SUPV3L1	61	.	NM_003171	exon1	c.C5T	p.S2F	CGATGTCCTTCTC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415469	105415469	+	Missense_Mutation	SNP	T	T	C	rs11846918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	359	357	289	0	0.994429	0	T|0.581;C|0.419	0.419	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A6319G	p.M2107V	CTCTCATTTCCAC	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1391419	1391419	+	Silent	SNP	T	T	C	rs73485660	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	65	124	0	0.515873	0	T|0.989;C|0.011	0.011	strong	.	BAIAP3	88	.	NM_003933	exon8	c.T765C	p.P255P	CCTGCCTGCCAAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	10792	10792	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	9	9	6	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.A33G	p.L11L	TATATTACTACCA	.	PASS	Atlas-SNP
SOS1	6654	hgsc.bcm.edu	37	2	39294787	39294787	+	Silent	SNP	T	T	G	rs7609455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	75	135	0	0.471698	0	T|0.952;G|0.048	0.048	strong	.	SOS1	134	.	NM_005633	exon2	c.A195C	p.R65R	AGCACTTCGGGGC	.	PASS	Atlas-SNP
ZNF354C	30832	hgsc.bcm.edu	37	5	178507069	178507069	+	Missense_Mutation	SNP	T	T	C	rs1445846	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	278	118	296	0	0.42446	0	T|0.268;C|0.731	0.731	strong	.	ZNF354C	77	.	NM_014594	exon5	c.T1636C	p.F546L	AGATTTTTTAAAG	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	40	122	0	0.384615	0	A|0.637;G|0.363	0.363	strong	SLC9A11,NS,carcinoma,-2,1	.	.	1	NM_178527	exon13	c.T1482C	p.N494N	CATATCATTATGT	.	PASS	Atlas-SNP
KCNK15	60598	hgsc.bcm.edu	37	20	43374694	43374694	+	Missense_Mutation	SNP	T	T	C	rs144556326	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	15	41	0	0.405405	0	T|0.981;C|0.019	0.019	strong	.	KCNK15	19	.	NM_022358	exon1	c.T143C	p.L48P	GCGCTCTCCGGAG	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18565915	18565915	+	Missense_Mutation	SNP	G	G	A	rs73291461	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	299	130	330	0	0.434783	0	G|0.943;A|0.057	0.057	strong	.	ZNF286B	75	.	NM_001145045	exon5	c.C904T	p.R302C	ATTCACGGCATTC	.	PASS	Atlas-SNP
ANXA2	302	hgsc.bcm.edu	37	15	60690089	60690089	+	Silent	SNP	A	A	G	rs12904657	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	4	11	1	0.266667	0.0909091	A|0.203;G|0.797	0.797	strong	ANXA2,rectum,carcinoma,0,1	ANXA2	28	1	NM_001002858	exon1	c.T24C	p.C8C	GTCTCCACACCCC	.	scavenged	Atlas-SNP
TBC1D13	54662	hgsc.bcm.edu	37	9	131565554	131565554	+	Missense_Mutation	SNP	T	T	C	rs1572912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	163	161	0	0.981928	0	T|0.535;C|0.464	0.464	strong	.	TBC1D13	27	.	NM_018201	exon8	c.T569C	p.V190A	ACTCTGTGCCATC	.	PASS	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140218212	140218212	+	Missense_Mutation	SNP	G	G	A	rs56750318	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	29	86	0	0.298969	0	G|0.957;A|0.043	0.043	strong	.	EXD3	86	.	NM_017820	exon19	c.C2149T	p.R717C	TGACACGCACGTT	.	PASS	Atlas-SNP
UBXN6	80700	hgsc.bcm.edu	37	19	4446164	4446164	+	Missense_Mutation	SNP	G	G	A	rs34179017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	50	97	0	0.490196	0	G|0.992;A|0.008	0.008	strong	.	UBXN6	27	.	NM_025241	exon10	c.C1082T	p.A361V	TACACCGCCCCCA	.	PASS	Atlas-SNP
RAB17	64284	hgsc.bcm.edu	37	2	238494742	238494742	+	Missense_Mutation	SNP	A	A	G	rs3751112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	79	123	0	0.572464	0	A|0.726;G|0.274	0.274	strong	.	RAB17	17	.	NM_022449	exon2	c.T56C	p.V19A	TTGAACACACGGG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4791012	4791012	+	Missense_Mutation	SNP	C	C	T	rs146706676	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	80	0	0.453333	0	C|0.999;T|0.001	0.001	strong	.	OR51F1	60	.	NM_001004752	exon1	c.G136A	p.V46M	GGATCACGCTGTT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17283657	17283657	+	Silent	SNP	C	C	T	rs2279006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	30	46	0	0.625	0	C|0.845;T|0.155	0.155	strong	.	MYO9B	264	.	NM_001130065	exon13	c.C2025T	p.I675I	GCTCATCGGCATG	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36349721	36349721	+	Silent	SNP	G	G	A	rs57079408	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	104	246	1	0.483721	0.00406504	G|0.994;A|0.006	0.006	strong	.	KIRREL2	170	.	NM_199180	exon4	c.G477A	p.L159L	ATTGCTGTGGTTC	.	PASS	Atlas-SNP
CKAP2L	150468	hgsc.bcm.edu	37	2	113514180	113514180	+	Silent	SNP	T	T	C	rs17042342	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	66	186	0	0.461538	0	T|0.919;C|0.081	0.081	strong	.	CKAP2L	54	.	NM_152515	exon4	c.A768G	p.V256V	TGATTTTACTGGG	.	PASS	Atlas-SNP
SCGB1D2	10647	hgsc.bcm.edu	37	11	62010863	62010863	+	Missense_Mutation	SNP	C	C	T	rs2232950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	112	224	0	0.568528	0	C|0.614;N|0.000	.	strong	.	SCGB1D2	11	.	NM_006551	exon2	c.C158T	p.P53L	CCCCTCCGGAAGC	.	PASS	Atlas-SNP
MBOAT2	129642	hgsc.bcm.edu	37	2	9013424	9013424	+	Missense_Mutation	SNP	C	C	T	rs34573615	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	61	97	0	0.642105	0	C|0.994;T|0.006	0.006	strong	.	MBOAT2	36	.	NM_138799	exon8	c.G697A	p.V233I	GAACAACCGCAGT	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3215030	3215030	+	Silent	SNP	C	C	A	rs9964300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	20	15	0	0.625	0	C|0.932;A|0.068	0.068	strong	.	MYOM1	192	.	NM_003803	exon2	c.G192T	p.A64A	GGCGGACGCCCGA	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2029196	2029196	+	Silent	SNP	G	G	A	rs10964470	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	56	91	0	0.504505	0	G|0.950;A|0.050	0.050	strong	.	SMARCA2	313	.	NM_139045	exon2	c.G174A	p.P58P	TATGCCGACGATG	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393330	393330	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	31	69	0	0.413333	0	.	.	none	IRF4_ENST00000380956,NS,lymphoid_neoplasm,-2,2	IRF4	65	2	NM_001195286	exon2	c.C178A	p.Q60K	GGCAAGCAGGACT	.	PASS	Atlas-SNP
POPDC2	64091	hgsc.bcm.edu	37	3	119378872	119378872	+	Silent	SNP	G	G	A	rs1880040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	63	137	0	0.422819	0	G|0.616;A|0.384	0.384	strong	.	POPDC2	36	.	NM_022135	exon1	c.C399T	p.C133C	CTCCTCGCAGCAG	.	PASS	Atlas-SNP
ACOT1	641371	hgsc.bcm.edu	37	14	74008304	74008304	+	Missense_Mutation	SNP	G	G	A	rs146335256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	257	241	0	0.996124	0	G|0.989;A|0.011	0.011	strong	.	ACOT1	12	.	NM_001037161	exon2	c.G565A	p.A189T	GCTCTGGCTTACT	.	PASS	Atlas-SNP
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628622	51628622	+	Missense_Mutation	SNP	A	A	C	rs16988910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	28	60	0	0.518519	0	A|0.895;C|0.105	0.105	strong	.	SIGLEC9	85	.	NM_001198558	exon1	c.A391C	p.K131Q	AATTATAAACATC	.	PASS	Atlas-SNP
RSBN1L	222194	hgsc.bcm.edu	37	7	77325919	77325919	+	Missense_Mutation	SNP	G	G	A	rs79095281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	39	60	0	0.58209	0	G|0.973;A|0.027	0.027	strong	.	RSBN1L	74	.	NM_198467	exon1	c.G133A	p.V45I	AAGAAGGTCCGGA	.	PASS	Atlas-SNP
C14orf2	9556	hgsc.bcm.edu	37	14	104381502	104381502	+	Missense_Mutation	SNP	T	T	C	rs1053419	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	33	83	0	0.428571	0	T|0.809;C|0.191;A|0.000	0.191	strong	.	C14orf2	7	.	NM_001127393	exon3	c.A76G	p.I26V	TCCATATGTTTTT	.	PASS	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44172496	44172496	+	Silent	SNP	T	T	C	rs145963884	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	54	96	0	0.415385	0	T|0.999;C|0.001	0.001	strong	.	LRPPRC	105	.	NM_133259	exon22	c.A2271G	p.V757V	TGCCAATACTCTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100675512	100675512	+	Missense_Mutation	SNP	G	G	A	rs10259584	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	66	148	0	0.507692	0	G|0.868;A|0.132	0.132	strong	.	MUC17	804	.	NM_001040105	exon3	c.G815A	p.G272E	CTAGTGGAGGAAG	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	37	19	12805525	12805525	+	Silent	SNP	G	G	C	rs10416965	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	41	70	0	0.5	0	G|0.921;C|0.079	0.079	strong	.	FBXW9	30	.	NM_032301	exon3	c.C561G	p.L187L	CAGACAGAGTGAC	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84212779	84212779	+	Missense_Mutation	SNP	G	G	A	rs2230131	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	36	61	0	0.514286	0	G|0.840;A|0.160	0.160	strong	.	TAF1C	60	.	NM_005679	exon14	c.C2378T	p.P793L	GAGGGCGGGGTCG	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2050564	2050564	+	Silent	SNP	G	G	A	rs34460811	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	21	53	0	0.396226	0	G|0.991;A|0.009	0.009	strong	.	MYOM2	251	.	NM_003970	exon21	c.G2727A	p.A909A	AGAGGCGAGACCA	.	PASS	Atlas-SNP
PFN4	375189	hgsc.bcm.edu	37	2	24342505	24342505	+	Silent	SNP	T	T	C	rs1056122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	23	42	0	0.511111	0	T|0.709;C|0.291	0.291	strong	.	PFN4	16	.	NM_199346	exon4	c.A303G	p.V101V	AGTTGCTACCAGA	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525285	248525285	+	Missense_Mutation	SNP	T	T	C	rs28637620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	914	373	964	1	0.408096	0.00103734	T|0.811;C|0.189	0.189	strong	.	OR2T4	126	.	NM_001004696	exon1	c.T403C	p.F135L	ATGTTCTTCTACG	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113386950	113386950	+	Silent	SNP	T	T	C	rs2285932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	48	41	0	0.979592	0	T|0.189;C|0.811	0.811	strong	.	OAS3	63	.	NM_006187	exon6	c.T1314C	p.I438I	GGCCATTGACATC	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24184088	24184088	+	Silent	SNP	G	G	T	rs113950884	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	106	217	0	0.490741	0	G|0.998;T|0.002	0.002	strong	.	ADAM28	100	.	NM_014265	exon10	c.G912T	p.T304T	TGGAACGACTGTG	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1255206	1255206	+	Silent	SNP	C	C	T	rs28365123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	38	67	0	0.584615	0	C|0.953;T|0.047	0.047	strong	.	CACNA1H	317	.	NM_021098	exon11	c.C2544T	p.G848G	CTGCGGCCCTCTG	.	PASS	Atlas-SNP
SPSB2	84727	hgsc.bcm.edu	37	12	6982162	6982162	+	Splice_Site	SNP	C	C	T	rs11064437	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	43	41	0	1	0	C|0.840;T|0.160	0.160	strong	.	SPSB2	11	.	.	.	.	.	AGGGAGCTGGGAG	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1533513	1533513	+	Silent	SNP	A	A	G	rs2251226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	240	220	0	1	0	A|0.379;G|0.621	0.621	strong	.	INTS1	145	.	NM_001080453	exon15	c.T1945C	p.L649L	CCTCCAAAATGGG	.	PASS	Atlas-SNP
EPHA7	2045	hgsc.bcm.edu	37	6	93982100	93982100	+	Silent	SNP	C	C	T	rs34302170	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	92	224	0	0.528736	0	C|0.963;T|0.037	0.037	strong	.	EPHA7	251	.	NM_004440	exon6	c.G1365A	p.L455L	CCGCTGCAGTACT	.	PASS	Atlas-SNP
TREML1	340205	hgsc.bcm.edu	37	6	41117586	41117586	+	Missense_Mutation	SNP	T	T	G	rs34254490	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	77	138	0	0.52027	0	T|0.975;G|0.025	0.025	strong	.	TREML1	20	.	NM_178174	exon6	c.A692C	p.H231P	CTAATGTGTGGTA	.	PASS	Atlas-SNP
TSPYL1	7259	hgsc.bcm.edu	37	6	116600774	116600774	+	Missense_Mutation	SNP	C	C	G	rs3749895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	12	21	0	0.545455	0	C|0.657;G|0.343	0.343	strong	TSPYL1,NS,carcinoma,0,1	TSPYL1	28	1	NM_003309	exon1	c.G220C	p.A74P	CCGCGGCATCCTG	.	PASS	Atlas-SNP
NFAM1	150372	hgsc.bcm.edu	37	22	42793873	42793873	+	Silent	SNP	A	A	G	rs5996153	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	105	99	0	1	0	A|0.848;G|0.152	0.152	strong	.	NFAM1	12	.	NM_145912	exon4	c.T654C	p.S218S	GTAGACAGATTCT	.	PASS	Atlas-SNP
CACTIN	58509	hgsc.bcm.edu	37	19	3614538	3614538	+	Silent	SNP	C	C	T	rs60651483	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	107	159	0	0.597765	0	C|0.890;T|0.110	0.110	strong	.	.	.	.	NM_021231	exon7	c.G1212A	p.S404S	GAACACCGACTGC	.	PASS	Atlas-SNP
WRAP73	49856	hgsc.bcm.edu	37	1	3548136	3548136	+	Silent	SNP	T	T	C	rs2760321	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	54	64	0	1	0	T|0.138;C|0.862	0.862	strong	.	WRAP73	43	.	NM_017818	exon11	c.A1134G	p.A378A	CTGAAATGCGCGC	.	PASS	Atlas-SNP
CCT8L2	150160	hgsc.bcm.edu	37	22	17071899	17071899	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	94	148	0	0.543353	0	.	.	none	CCT8L2,NS,carcinoma,-2,2	CCT8L2	150	2	NM_014406	exon1	c.C1542T	p.L514L	AGTCACGAGCTGT	.	PASS	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19570146	19570146	+	Silent	SNP	G	G	A	rs6661253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	129	203	0	0.503906	0	G|0.959;A|0.041	0.041	strong	.	.	.	.	NM_001271427	exon4	c.C342T	p.I114I	GCCCCCGATGTTA	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109740128	109740128	+	Silent	SNP	C	C	G	rs61756684	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	24	75	0	0.333333	0	C|0.975;G|0.025	0.025	strong	.	KIAA1324	77	.	NM_020775	exon16	c.C2154G	p.V718V	CAATGTCACTGAC	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149755340	149755340	+	Silent	SNP	G	G	T	rs7701163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	70	117	0	0.48951	0	G|0.910;T|0.090	0.090	strong	.	TCOF1	154	.	NM_001135243	exon12	c.G1761T	p.G587G	CAAGGGGCCCCCT	.	PASS	Atlas-SNP
PLOD1	5351	hgsc.bcm.edu	37	1	12024235	12024235	+	Silent	SNP	C	C	T	rs1130529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	63	0	0.522388	0	C|0.687;N|0.001	.	strong	.	PLOD1	75	.	NM_000302	exon12	c.C1206T	p.N402N	CAGGAACGTCATT	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	15	9	0	0.394737	0	A|0.873;G|0.127	0.127	strong	PKD1,right_upper_lobe,carcinoma,+2,1	PKD1	184	1	NM_000296	exon20	c.T7708C	p.L2570L	TGGCCAAAGACCT	.	scavenged	Atlas-SNP
ZNF354C	30832	hgsc.bcm.edu	37	5	178505831	178505831	+	Missense_Mutation	SNP	A	A	G	rs57271258	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	99	187	0	0.553073	0	A|0.974;G|0.026	0.026	strong	ZNF354C,caecum,carcinoma,0,1	ZNF354C	77	1	NM_014594	exon5	c.A398G	p.E133G	AGAGCGAGATAGA	.	PASS	Atlas-SNP
ZNF444	55311	hgsc.bcm.edu	37	19	56671359	56671359	+	Missense_Mutation	SNP	C	C	G	rs145075834	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	6	21	0	1	0	C|0.987;G|0.013	0.013	strong	.	ZNF444	15	.	NM_018337	exon5	c.C773G	p.T258S	GCAAGACCTTCTA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	98	169	0	0.586826	0	C|0.507;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.C5493T	p.P1831P	TCTACCCTCTTTG	.	PASS	Atlas-SNP
OR4A47	403253	hgsc.bcm.edu	37	11	48510777	48510777	+	Missense_Mutation	SNP	G	G	A	rs7103992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	297	155	277	0	0.521886	0	G|0.441;A|0.559	0.559	strong	.	OR4A47	72	.	NM_001005512	exon1	c.G433A	p.V145M	CTGGTAGTGTCCT	.	PASS	Atlas-SNP
C16orf88	400506	hgsc.bcm.edu	37	16	19726124	19726124	+	Silent	SNP	G	G	A	rs58543897	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	54	91	0	0.504673	0	G|0.972;A|0.028	0.028	strong	.	C16orf88	41	.	NM_001012991	exon2	c.C234T	p.C78C	CTCCTCGCAAAGG	.	PASS	Atlas-SNP
PYROXD2	84795	hgsc.bcm.edu	37	10	100147060	100147060	+	Silent	SNP	A	A	G	rs4345897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	32	67	0	0.380952	0	A|0.541;G|0.459	0.459	strong	.	PYROXD2	43	.	NM_032709	exon14	c.T1452C	p.F484F	GCAATCAAACACT	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19753479	19753479	+	Splice_Site	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	3	263	0	0.0116279	0	.	.	none	TUBA3C,NS,carcinoma,-2,1	TUBA3C	166	1	NM_006001	exon3	c.226+2T>C	.	GCACCTACCGACC	.	scavenged	Atlas-SNP
DNAJC30	84277	hgsc.bcm.edu	37	7	73097720	73097720	+	Missense_Mutation	SNP	G	G	C	rs28494095	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	26	44	0	0.590909	0	G|0.897;C|0.103	0.103	strong	.	DNAJC30	12	.	NM_032317	exon1	c.C34G	p.L12V	GTAACAGCCGCTG	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2255311	2255311	+	Missense_Mutation	SNP	C	C	G	rs7250822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	196	82	145	0	0.418367	0	C|0.836;G|0.164	0.164	strong	.	JSRP1	18	.	NM_144616	exon2	c.G3C	p.M1I	CATGGACATGGCT	.	PASS	Atlas-SNP
MYO1B	4430	hgsc.bcm.edu	37	2	192256874	192256874	+	Missense_Mutation	SNP	G	G	A	rs200814325	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	3	175	1	0.0163934	0.00571429	G|0.999;A|0.001	0.001	weak	MYO1B_ENST00000392318,rectum,carcinoma,-1,3	MYO1B	160	3	NM_012223	exon19	c.G2023A	p.V675M	ATTCCCGTGGAAG	.	scavenged	Atlas-SNP
TDP1	55775	hgsc.bcm.edu	37	14	90429858	90429858	+	Missense_Mutation	SNP	G	G	A	rs28365054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	54	80	0	0.545455	0	G|0.892;A|0.108	0.108	strong	.	TDP1	47	.	NM_018319	exon3	c.G400A	p.A134T	GCTCCCGCCTGCC	.	PASS	Atlas-SNP
HOXD9	3235	hgsc.bcm.edu	37	2	176988765	176988765	+	Silent	SNP	C	C	T	rs35649704	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	170	86	162	0	0.505882	0	C|0.987;T|0.013	0.013	strong	.	HOXD9	49	.	NM_014213	exon2	c.C921T	p.N307N	CTTCAACATGTAC	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207890818	207890818	+	Missense_Mutation	SNP	G	G	A	rs113806677	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	112	262	0	0.533333	0	G|0.976;A|0.024	0.024	strong	CR1L_ENST00000508064,NS,carcinoma,-1,1	CR1L	97	1	NM_175710	exon11	c.G1424A	p.C475Y	TCTTTTGTCCAAA	.	PASS	Atlas-SNP
LRRC38	126755	hgsc.bcm.edu	37	1	13802373	13802373	+	Missense_Mutation	SNP	G	G	A	rs2940315	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	51	98	0	0.490385	0	G|0.944;A|0.056	0.056	strong	.	LRRC38	12	.	NM_001010847	exon2	c.C826T	p.L276F	TCTGGAGGCACTG	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100732321	100732321	+	Silent	SNP	C	C	T	rs11760747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	12	10	0	0.521739	0	C|0.857;T|0.143	0.143	strong	.	TRIM56	123	.	NM_030961	exon3	c.C1728T	p.N576N	CCCCAACGGCGAA	.	PASS	Atlas-SNP
PSMC3IP	29893	hgsc.bcm.edu	37	17	40725379	40725379	+	Missense_Mutation	SNP	A	A	T	rs2292754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	89	168	0	0.442786	0	A|0.948;T|0.052	0.052	strong	.	PSMC3IP	23	.	NM_016556	exon6	c.T487A	p.Y163N	CTCTGTACACCTA	.	PASS	Atlas-SNP
SH3D19	152503	hgsc.bcm.edu	37	4	152065197	152065197	+	Silent	SNP	C	C	T	rs3736502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	64	122	0	0.5	0	C|0.913;T|0.087	0.087	strong	.	SH3D19	54	.	NM_001009555	exon13	c.G1317A	p.G439G	TACATCCCCACGC	.	PASS	Atlas-SNP
CXXC11	285093	hgsc.bcm.edu	37	2	242814463	242814463	+	Silent	SNP	A	A	T	rs28523279	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	71	134	0	0.533835	0	A|0.731;T|0.269	0.269	strong	.	.	.	.	NM_173821	exon2	c.A756T	p.S252S	GGATTCAGTGGCC	.	PASS	Atlas-SNP
C1orf168	199920	hgsc.bcm.edu	37	1	57186000	57186000	+	Silent	SNP	G	G	A	rs76493848	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	41	103	0	0.476744	0	G|0.987;A|0.013	0.013	strong	.	C1orf168	102	.	NM_001004303	exon18	c.C1977T	p.Y659Y	TTTGTCGTACTGA	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801738	14801738	+	Missense_Mutation	SNP	G	G	C	rs16932300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	311	167	263	1	0.536977	0.00380228	G|0.839;C|0.161	0.161	strong	.	FREM1	261	.	NM_144966	exon21	c.C3606G	p.S1202R	GTCTTTGCTAAAC	.	PASS	Atlas-SNP
SRP68	6730	hgsc.bcm.edu	37	17	74060168	74060168	+	Silent	SNP	T	T	C	rs58471646	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	115	222	1	0.421245	0.0045045	T|0.925;C|0.075	0.075	strong	SRP68,rectum,carcinoma,-1,1	SRP68	61	1	NM_014230	exon4	c.A450G	p.R150R	CCGTTTTCGGGGT	.	scavenged	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371328	240371328	+	Silent	SNP	G	G	A	rs71646895	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	50	137	1	0.280899	0.00729927	G|0.835;A|0.165	0.165	strong	FMN2,colon,carcinoma,0,2	FMN2	451	2	NM_020066	exon5	c.G3216A	p.A1072A	CGGAGCGGGCATA	.	scavenged	Atlas-SNP
KCNK4	50801	hgsc.bcm.edu	37	11	64066999	64066999	+	Missense_Mutation	SNP	C	C	T	rs953778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	17	32	0	0.607143	0	C|0.772;T|0.228	0.228	strong	.	KCNK4	22	.	NM_033310	exon7	c.C983T	p.P328L	CTCAGCCGCCTTC	.	PASS	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	37	19	1079968	1079968	+	Silent	SNP	G	G	A	rs34047143	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	42	78	0	0.5	0	G|0.962;A|0.038	0.038	strong	.	HMHA1	78	.	NM_001258328	exon13	c.G1602A	p.A534A	GACGGCGCCGCTG	.	PASS	Atlas-SNP
GNMT	27232	hgsc.bcm.edu	37	6	42930877	42930877	+	Silent	SNP	G	G	A	rs147291064	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	65	0	0.47561	0	G|0.993;A|0.007	0.007	strong	.	GNMT	13	.	NM_018960	exon4	c.G519A	p.L173L	CCTACTGGTCATT	.	PASS	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188327555	188327555	+	Missense_Mutation	SNP	T	T	C	rs7645635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	52	116	0	0.468468	0	T|0.786;C|0.214	0.214	strong	.	LPP	72	.	NM_005578	exon6	c.T1036C	p.Y346H	GGGATGTATCCAG	.	PASS	Atlas-SNP
VN1R4	317703	hgsc.bcm.edu	37	19	53770746	53770746	+	Missense_Mutation	SNP	C	C	A	rs140031028	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	301	178	232	1	0.591362	0.00431034	A|0.055;C|0.945;G|0.001	0.055	strong	VN1R4,mouth,carcinoma,0,1	VN1R4	65	1	NM_173857	exon1	c.G173T	p.R58L	TTACAGCGGAGAG	.	PASS	Atlas-SNP
TRMU	55687	hgsc.bcm.edu	37	22	46731689	46731689	+	Missense_Mutation	SNP	G	G	T	rs11090865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	21	13	0	0.583333	0	G|0.890;T|0.110	0.110	strong	.	TRMU	23	.	NM_018006	exon1	c.G28T	p.A10S	GTGTGCGCCCTGT	.	PASS	Atlas-SNP
BCMO1	53630	hgsc.bcm.edu	37	16	81301571	81301571	+	Silent	SNP	A	A	G	rs7202895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	49	110	0	0.426087	0	A|0.850;G|0.150	0.150	strong	.	BCMO1	53	.	NM_017429	exon6	c.A678G	p.P226P	CATCCCATCCCGC	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128378009	128378009	+	Missense_Mutation	SNP	G	G	A	rs199900811	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	120	205	0	0.508475	0	G|0.997;A|0.003	0.003	strong	.	MYO7B	359	.	NM_001080527	exon26	c.G3415A	p.G1139S	TGCCTCGGCTGCT	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158623092	158623092	+	Missense_Mutation	SNP	T	T	A	rs145054175	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	62	137	2	0.5	0.0145985	T|0.996;A|0.004	0.004	strong	SPTA1,NS,carcinoma,+1,1	SPTA1	720	1	NM_003126	exon22	c.A3160T	p.T1054S	GCTGGGTGATGTT	.	scavenged	Atlas-SNP
SIGLEC12	89858	hgsc.bcm.edu	37	19	51994926	51994926	+	Missense_Mutation	SNP	T	T	C	rs7245807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	71	113	0	0.572581	0	T|0.956;C|0.044	0.044	strong	.	SIGLEC12	243	.	NM_053003	exon8	c.A1757G	p.Y586C	TACTCATAGCCGA	.	PASS	Atlas-SNP
LONRF2	164832	hgsc.bcm.edu	37	2	100916306	100916306	+	Silent	SNP	A	A	G	rs2033748	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	96	0	1	0	A|0.270;G|0.730	0.730	strong	.	LONRF2	62	.	NM_198461	exon5	c.T1140C	p.F380F	CTCTTCAAAGTGT	.	PASS	Atlas-SNP
PTPN7	5778	hgsc.bcm.edu	37	1	202129826	202129826	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	73	175	0	0.450617	0	.	.	none	.	PTPN7	31	.	NM_002832	exon1	c.A110G	p.Q37R	CCCTCCTGTGCCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124401117	124401117	+	Silent	SNP	C	C	T	rs61749063	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	39	75	0	0.52	0	C|0.957;T|0.043	0.043	strong	.	DNAH10	888	.	NM_207437	exon62	c.C10482T	p.N3494N	TGACAACGTCTTA	.	PASS	Atlas-SNP
PRNP	5621	hgsc.bcm.edu	37	20	4680217	4680217	+	Silent	SNP	A	A	G	rs8124214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	70	87	0	0.551181	0	A|0.956;G|0.044	0.044	strong	.	PRNP	31	.	NM_000311	exon2	c.A351G	p.A117A	TGCAGCAGCTGGG	.	PASS	Atlas-SNP
PDIA6	10130	hgsc.bcm.edu	37	2	10942687	10942687	+	Silent	SNP	C	C	T	rs4758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	87	177	0	0.497143	0	C|0.523;T|0.477	0.477	strong	.	PDIA6	31	.	NM_005742	exon2	c.G99A	p.S33S	GAAATTCGATGGA	.	PASS	Atlas-SNP
SDR42E1	93517	hgsc.bcm.edu	37	16	82034435	82034435	+	Missense_Mutation	SNP	C	C	G	rs6564956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	37	0	1	0	C|0.924;G|0.076	0.076	strong	.	SDR42E1	26	.	NM_145168	exon2	c.G29C	p.S10T	AGGACACTTTCCT	.	PASS	Atlas-SNP
XRCC1	7515	hgsc.bcm.edu	37	19	44047550	44047550	+	Silent	SNP	T	T	C	rs3547	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	21	47	0	0.428571	0	T|0.344;C|0.656	0.656	strong	.	XRCC1	47	.	NM_006297	exon17	c.A1896G	p.Q632Q	TCAGGCTTGCGGC	.	PASS	Atlas-SNP
TCF20	6942	hgsc.bcm.edu	37	22	42610099	42610099	+	Missense_Mutation	SNP	T	T	C	rs34030679	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	88	175	0	0.536585	0	T|0.901;C|0.099	0.099	strong	.	TCF20	164	.	NM_181492	exon1	c.A1213G	p.M405V	AACCCATAGGCAC	.	PASS	Atlas-SNP
PTGFR	5737	hgsc.bcm.edu	37	1	78959081	78959081	+	Missense_Mutation	SNP	T	T	C	rs115994459	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	61	126	0	0.429577	0	T|0.995;C|0.005	0.005	strong	.	PTGFR	121	.	NM_000959	exon2	c.T653C	p.L218S	CATTGTTGTGCAA	.	PASS	Atlas-SNP
CEMP1	752014	hgsc.bcm.edu	37	16	2580912	2580912	+	Missense_Mutation	SNP	T	T	C	rs13331643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	79	0	1	0	T|0.955;C|0.045	0.045	strong	.	CEMP1	17	.	NM_001048212	exon1	c.A163G	p.K55E	ACCCCTTAGGAAG	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	37	138	0	0.327434	0	T|0.860;C|0.140	0.140	strong	.	KIF5C	166	.	NM_004522	exon7	c.T531C	p.P177P	GAGCCCTGAGGAA	.	PASS	Atlas-SNP
CGN	57530	hgsc.bcm.edu	37	1	151496718	151496718	+	Missense_Mutation	SNP	C	C	T	rs16833336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	34	67	0	0.4	0	C|0.961;T|0.039	0.039	strong	CGN,colon,carcinoma,-1,2	CGN	106	2	NM_020770	exon7	c.C1285T	p.R429C	ATGAAGCGCCTCT	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74521948	74521948	+	Silent	SNP	G	G	T	rs61063525	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	84	187	0	0.435233	0	G|0.971;T|0.029	0.029	strong	.	CD109	170	.	NM_133493	exon29	c.G3723T	p.T1241T	GCCAACGGCAGTT	.	PASS	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41966699	41966699	+	Silent	SNP	A	A	G	rs78683283	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	48	75	0	0.527473	0	A|0.974;G|0.026	0.026	strong	.	PDZRN4	346	.	NM_001164595	exon10	c.A2118G	p.G706G	TGGAGGATTCCGG	.	PASS	Atlas-SNP
OGT	8473	hgsc.bcm.edu	37	X	70777435	70777435	+	Silent	SNP	G	G	A	rs34739713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	90	156	0	0.486486	0	G|0.947;A|0.053	0.053	strong	.	OGT	207	.	NM_181672	exon12	c.G1515A	p.V505V	TTCTGTGCATCCT	.	PASS	Atlas-SNP
WDR64	128025	hgsc.bcm.edu	37	1	241886717	241886717	+	Silent	SNP	C	C	T	rs10926547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	56	105	0	0.41791	0	C|0.922;T|0.078	0.078	strong	.	WDR64	234	.	NM_144625	exon9	c.C1143T	p.V381V	ACATGTCGTCAGC	.	PASS	Atlas-SNP
FTHL17	53940	hgsc.bcm.edu	37	X	31089629	31089629	+	Nonsense_Mutation	SNP	C	C	A	rs7057057	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	109	179	0	0.561856	0	C|0.982;A|0.018	0.018	strong	.	FTHL17	99	.	NM_031894	exon1	c.G442T	p.E148X	CCAGCTCTTTGAT	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	11	193	0	0.0482456	0	T|0.999;C|0.001	0.001	weak	CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	NM_000106	exon7	c.A1064G	p.Y355C	GTGGTGTAGGGCA	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276603	152276603	+	Missense_Mutation	SNP	C	C	T	rs111939167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	581	297	609	0	0.511188	0	T|1.000;|0.000	1.000	weak	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G10759A	p.G3587S	CGTGACCGGCTCT	.	PASS	Atlas-SNP
BRD4	23476	hgsc.bcm.edu	37	19	15355540	15355540	+	Missense_Mutation	SNP	G	G	A	rs149185763	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	71	107	0	0.5	0	A|0.001;G|0.999	0.001	strong	.	BRD4	172	.	NM_058243	exon12	c.C2192T	p.P731L	CTCCCGGGGTGCC	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34174737	34174737	+	Silent	SNP	A	A	G	rs10914765	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	52	94	0	0.495238	0	A|0.972;G|0.028	0.028	strong	.	CSMD2	946	.	NM_052896	exon22	c.T3408C	p.I1136I	CAGCTGAATTCCC	.	PASS	Atlas-SNP
CYP2C8	1558	hgsc.bcm.edu	37	10	96818106	96818106	+	Missense_Mutation	SNP	T	T	A	rs11572103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	73	138	0	0.536765	0	T|0.950;A|0.050	0.050	strong	.	CYP2C8	73	.	NM_000770	exon5	c.A805T	p.I269F	TTTTGATCAGGAA	.	PASS	Atlas-SNP
NCOA5	57727	hgsc.bcm.edu	37	20	44691350	44691350	+	Silent	SNP	T	T	G	rs1537028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	124	304	0	0.454212	0	A|0.003;C|0.002	.	strong	.	NCOA5	58	.	NM_020967	exon8	c.A1329C	p.T443T	CGTCACTGTGCCA	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7231736	7231736	+	Missense_Mutation	SNP	G	G	T	rs116295722	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	58	104	0	0.527273	0	G|0.997;T|0.003	0.003	strong	.	RREB1	242	.	NM_001003700	exon10	c.G3404T	p.S1135I	CCAGCAGCCCAGA	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	61	114	0	0.488	0	G|0.805;A|0.195	0.195	strong	PZP_ENST00000381997,NS,carcinoma,+1,2	PZP	422	2	NM_002864	exon24	c.C3008T	p.T1003M	TCCTGCGTCAGCT	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294703	124294703	+	Missense_Mutation	SNP	T	T	C	rs10750270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	28	65	0	0.538462	0	T|0.675;C|0.325	0.325	strong	.	OR8B4	60	.	NM_001005196	exon1	c.A65G	p.E22G	TGGAGCTCTGGCT	.	PASS	Atlas-SNP
SCARB2	950	hgsc.bcm.edu	37	4	77102148	77102148	+	Missense_Mutation	SNP	G	G	C	rs143558324	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	33	61	0	0.540984	0	G|0.999;C|0.001	0.001	strong	.	SCARB2	47	.	NM_005506	exon3	c.C382G	p.P128A	TTTTAGGGTCTCC	.	PASS	Atlas-SNP
MAS1L	116511	hgsc.bcm.edu	37	6	29455333	29455333	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	3	98	0	0.0361446	0	.	.	none	MAS1L,NS,carcinoma,+1,1	MAS1L	66	1	NM_052967	exon1	c.T347C	p.V116A	GCAGCGACCAGGT	.	scavenged	Atlas-SNP
TCHHL1	126637	hgsc.bcm.edu	37	1	152060495	152060495	+	Missense_Mutation	SNP	C	C	T	rs76137589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	51	127	0	0.425	0	C|0.985;T|0.015	0.015	strong	.	TCHHL1	132	.	NM_001008536	exon2	c.G125A	p.G42E	AAGTCCCCAAACT	.	PASS	Atlas-SNP
GPATCH4	54865	hgsc.bcm.edu	37	1	156565389	156565389	+	Silent	SNP	C	C	T	rs145851878	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	130	237	0	0.457746	0	C|0.988;T|0.012	0.012	strong	.	GPATCH4	34	.	NM_015590	exon8	c.G744A	p.K248K	CCTTTTCTTCTTC	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19338942	19338942	+	Missense_Mutation	SNP	G	G	A	rs10426537	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	27	63	0	0.421875	0	G|0.973;A|0.027	0.027	strong	.	NCAN	277	.	NM_004386	exon8	c.G2513A	p.S838N	CCCCCAGTGATGC	.	PASS	Atlas-SNP
TRIB1	10221	hgsc.bcm.edu	37	8	126448674	126448674	+	Missense_Mutation	SNP	G	G	T	rs16900603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	75	114	0	0.559702	0	G|0.974;T|0.026	0.026	strong	.	TRIB1	73	.	NM_025195	exon3	c.G1080T	p.E360D	TCCAGAGTACCAG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20844383	20844383	+	Silent	SNP	C	C	T	rs2228042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	244	129	212	0	0.528689	0	T|0.040;G|0.128;C|0.828;A|0.004	0.040	strong	.	TEP1	224	.	NM_007110	exon42	c.G6129A	p.T2043T	TGGCCGCGTCAGC	.	PASS	Atlas-SNP
NAPG	8774	hgsc.bcm.edu	37	18	10539774	10539774	+	Missense_Mutation	SNP	C	C	T	rs2228300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	48	132	0	0.417391	0	C|0.965;T|0.035	0.035	strong	.	NAPG	18	.	NM_003826	exon6	c.C274T	p.P92S	AAACTACCAGAGG	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	105263979	105263979	+	Silent	SNP	C	C	T	rs10461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	74	170	0	0.445783	0	C|0.553;T|0.447	0.447	strong	.	RIMS2	1357	.	NM_001100117	exon24	c.C3981T	p.A1327A	CTTGGCCCCTCTG	.	PASS	Atlas-SNP
GPRASP2	114928	hgsc.bcm.edu	37	X	101970662	101970662	+	Missense_Mutation	SNP	A	A	G	rs113336462	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	64	130	0	0.407643	0	A|0.986;G|0.014	0.014	strong	.	GPRASP2	89	.	NM_138437	exon4	c.A865G	p.S289G	GAGGCCAGCAACC	.	PASS	Atlas-SNP
ZSWIM4	65249	hgsc.bcm.edu	37	19	13936385	13936385	+	Missense_Mutation	SNP	C	C	T	rs62620757	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	51	146	0	0.504951	0	C|0.892;T|0.108	0.108	strong	.	ZSWIM4	69	.	NM_023072	exon11	c.C1886T	p.T629M	TGCACACGGTACT	.	PASS	Atlas-SNP
ADCY7	113	hgsc.bcm.edu	37	16	50344627	50344627	+	Silent	SNP	C	C	T	rs140505854		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	71	127	0	0.5	0	C|1.000;T|0.000	0.000	weak	.	ADCY7	90	.	NM_001114	exon18	c.C2190T	p.F730F	GGGCTTCATCGCC	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305775	+	Missense_Mutation	SNP	T	T	C	rs141265645	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	53	137	0	0.609195	0	.	.	weak	KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	NM_033188	exon1	c.A245G	p.Q82R	GTGGTCTGGCAGC	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1703982	1703982	+	Missense_Mutation	SNP	C	C	T	rs9913923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	207	100	251	0	0.483092	0	C|0.863;T|0.137	0.137	strong	.	SMYD4	50	.	NM_052928	exon5	c.G706A	p.G236S	ATAAGCCGATGGA	.	PASS	Atlas-SNP
HMHB1	57824	hgsc.bcm.edu	37	5	143200053	143200053	+	Missense_Mutation	SNP	C	C	T	rs161557	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	83	192	0	0.432292	0	C|0.720;T|0.280	0.280	strong	.	HMHB1	3	.	NM_021182	exon2	c.C46T	p.H16Y	TCTCTGCATGTTT	.	PASS	Atlas-SNP
MTMR4	9110	hgsc.bcm.edu	37	17	56584508	56584508	+	Missense_Mutation	SNP	T	T	C	rs2302190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	60	157	0	0.405405	0	T|0.709;C|0.291	0.291	strong	.	MTMR4	91	.	NM_004687	exon9	c.A838G	p.S280G	CCTCGCTGGTATC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678560	100678560	+	Missense_Mutation	SNP	C	C	A	rs77199586	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	30	105	0	0.211268	0	C|0.936;A|0.064	0.064	strong	MUC17,NS,carcinoma,-1,2	MUC17	804	2	NM_001040105	exon3	c.C3863A	p.T1288K	GCACCACGCTGGT	.	PASS	Atlas-SNP
OR8H3	390152	hgsc.bcm.edu	37	11	55890066	55890066	+	Missense_Mutation	SNP	G	G	A	rs61732941		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	390	160	368	0	0.410256	0	G|0.986;A|0.014	0.014	weak	.	OR8H3	92	.	NM_001005201	exon1	c.G218A	p.S73N	ACCTCAGTTACTC	.	PASS	Atlas-SNP
FEZ2	9637	hgsc.bcm.edu	37	2	36810586	36810586	+	Silent	SNP	T	T	C	rs14291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	106	119	1	1	0.00840336	T|0.567;C|0.433	0.433	strong	.	FEZ2	13	.	NM_001042548	exon3	c.A402G	p.T134T	ATCTGATGTATCA	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65300305	65300305	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	78	142	0	0.46988	0	.	.	none	.	JAK1	209	.	NM_002227	exon25	c.A3405G	p.Q1135Q	GGATGGTTGGAAT	.	PASS	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	37	5	35779447	35779447	+	Missense_Mutation	SNP	A	A	C	rs2277044	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	18	43	0	0.473684	0	A|0.949;C|0.051	0.051	strong	SPEF2_ENST00000356031,NS,carcinoma,+1,1	SPEF2	324	1	NM_024867	exon30	c.A4446C	p.K1482N	ACCTAAAGGTAGG	.	PASS	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	37	12	93150102	93150102	+	Missense_Mutation	SNP	T	T	C	rs924326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	331	327	396	2	0.987915	0.00505051	T|0.427;C|0.573	0.573	strong	.	PLEKHG7	38	.	NM_001004330	exon8	c.T635C	p.M212T	AACACATGGCAGA	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	70	0	0.45	0	T|0.710;G|0.290	0.290	strong	.	NTAN1	21	.	NM_173474	exon8	c.A576C	p.A192A	AAAGGATGCTCTG	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129293256	129293256	+	Missense_Mutation	SNP	T	T	C	rs2255703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	94	106	0	1	0	T|0.496;C|0.504	0.504	strong	PLXND1,colon,carcinoma,0,1	PLXND1	149	1	NM_015103	exon12	c.A2608G	p.M870V	TCCACATGCACAG	.	PASS	Atlas-SNP
ARHGAP23	57636	hgsc.bcm.edu	37	17	36623157	36623157	+	Silent	SNP	G	G	A	rs12326006	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	70	0	1	0	G|0.964;A|0.036	0.036	strong	.	ARHGAP23	48	.	NM_001199417	exon7	c.G1233A	p.L411L	GGGCCTGGATGAC	.	PASS	Atlas-SNP
PRR25	388199	hgsc.bcm.edu	37	16	855732	855732	+	Missense_Mutation	SNP	C	C	T	rs115484509	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	68	53	0	1	0	C|0.977;T|0.023	0.023	strong	PRR25,NS,carcinoma,+1,1	PRR25	27	1	NM_001013638	exon1	c.C290T	p.A97V	GAACAGCGCAGCC	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79220224	79220224	+	Missense_Mutation	SNP	G	G	C	rs2725405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	30	47	0	0.588235	0	G|0.561;C|0.439	0.439	strong	.	SLC38A10	133	.	NM_001037984	exon16	c.C2492G	p.A831G	AGCTTGGCCTGGG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906903	129906903	+	Silent	SNP	C	C	T	rs3740424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	107	206	0	0.479821	0	C|0.970;T|0.030	0.030	strong	.	MKI67	363	.	NM_002417	exon13	c.G3201A	p.T1067T	CTTAAACGTTCTG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38375666	38375666	+	Missense_Mutation	SNP	C	C	T	rs73027451	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	64	114	0	0.516129	0	C|0.835;T|0.166	0.166	strong	.	WDR87	191	.	NM_031951	exon6	c.G8528A	p.R2843Q	CCATACCGGGCAA	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs62112127	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	36	0	1	0	T|0.624;C|0.376	0.376	strong	.	PSG8	101	.	NM_001130168	exon1	c.A30G	p.T10T	GCGCTGTGTGCAG	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200978412	200978412	+	Silent	SNP	C	C	T	rs7556510	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	62	140	0	0.43662	0	C|0.922;T|0.078	0.078	strong	.	KIF21B	208	.	NM_017596	exon2	c.G246A	p.T82T	CAGCACCGTGGCA	.	PASS	Atlas-SNP
CRELD2	79174	hgsc.bcm.edu	37	22	50315971	50315971	+	Missense_Mutation	SNP	C	C	G	rs73891177	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	57	0	1	0	C|0.933;G|0.067	0.067	strong	.	CRELD2	57	.	NM_001135101	exon6	c.C619G	p.P207A	TCTTACCCGCCTT	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77920563	77920563	+	Silent	SNP	G	G	T	rs2510045	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	79	118	0	0.490683	0	G|0.761;T|0.239	0.239	strong	.	USP35	179	.	NM_020798	exon10	c.G1662T	p.P554P	CTCTCCGCCCGAG	.	PASS	Atlas-SNP
ALDH3A1	218	hgsc.bcm.edu	37	17	19642952	19642952	+	Missense_Mutation	SNP	G	G	C	rs2228100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	112	82	0	1	0	G|0.662;C|0.338	0.338	strong	.	ALDH3A1	40	.	NM_001135168	exon7	c.C985G	p.P329A	TCACCGGGGACTG	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257831	110257831	+	Missense_Mutation	SNP	T	T	C	rs2227963	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	585	287	545	1	0.490598	0.00183486	T|0.847;C|0.153	0.153	strong	GSTM5,scalp,carcinoma,0,13	GSTM5	89	13	NM_000851	exon7	c.T536C	p.L179P	CCTTCCTAAACTT	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85436868	85436868	+	Missense_Mutation	SNP	G	G	C	rs597480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	200	250	0	1	0	G|0.491;C|0.509	0.509	strong	.	SYTL2	231	.	NM_206927	exon1	c.C632G	p.A211G	GTATCAGCAAAAT	.	PASS	Atlas-SNP
SLC3A1	6519	hgsc.bcm.edu	37	2	44547672	44547672	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	3	119	0	0.0230769	0	.	.	none	SLC3A1,NS,carcinoma,-1,1	SLC3A1	62	1	NM_000341	exon10	c.A1952G	p.N651S	AACACAACACGAA	.	scavenged	Atlas-SNP
CTSG	1511	hgsc.bcm.edu	37	14	25045386	25045386	+	Missense_Mutation	SNP	C	C	G	rs61737123	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	37	77	0	0.445783	0	C|0.969;G|0.031	0.031	strong	.	CTSG	63	.	NM_001911	exon1	c.G44C	p.G15A	TCAGCCCCAGTGG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39264083	39264083	+	Missense_Mutation	SNP	C	C	G	rs7329939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	64	112	0	0.561404	0	C|0.947;G|0.053	0.053	strong	.	FREM2	385	.	NM_207361	exon1	c.C2602G	p.L868V	TTCACTCTCACTC	.	PASS	Atlas-SNP
SGSM1	129049	hgsc.bcm.edu	37	22	25270455	25270455	+	Silent	SNP	G	G	C	rs9624633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	81	140	0	0.515924	0	G|0.883;C|0.117	0.117	strong	.	SGSM1	150	.	NM_133454	exon13	c.G1365C	p.R455R	AGGCCGGTCCATG	.	PASS	Atlas-SNP
OR8B2	26595	hgsc.bcm.edu	37	11	124253042	124253042	+	Silent	SNP	G	G	A	rs79763748		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	87	242	0	0.497143	0	.	.	weak	.	OR8B2	42	.	NM_001005468	exon1	c.C198T	p.L66L	GAAGGAGAGATTG	.	PASS	Atlas-SNP
RHBDF1	64285	hgsc.bcm.edu	37	16	113027	113027	+	Missense_Mutation	SNP	G	G	A	rs78541046	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	80	96	0	0.571429	0	G|0.996;A|0.004	0.004	strong	.	RHBDF1	54	.	NM_022450	exon5	c.C616T	p.R206C	GCTTGCGCCGCCG	.	PASS	Atlas-SNP
OR51V1	283111	hgsc.bcm.edu	37	11	5221132	5221132	+	Missense_Mutation	SNP	G	G	A	rs61736992	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	58	117	0	0.557692	0	G|0.975;A|0.025	0.025	strong	.	OR51V1	77	.	NM_001004760	exon1	c.C799T	p.L267F	TTGTGAGGCTAAT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744722	54744722	+	Missense_Mutation	SNP	T	T	C	rs66585874	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	302	20	273	1	0.0662252	0.003663	CATCAGGATGTT|0.500;GATCAGGATGTC|0.500	.	alt	LILRA6,NS,carcinoma,+2,1	LILRA6	75	1	NM_024318	exon5	c.A940G	p.N314D	GGATGTTCAGGGG	.	scavenged	Atlas-SNP
UBE2L3	7332	hgsc.bcm.edu	37	22	21965298	21965298	+	Silent	SNP	C	C	G	rs61133050	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	459	203	446	0	0.442266	0	C|0.964;G|0.036	0.036	strong	.	UBE2L3	11	.	NM_001256355	exon3	c.C450G	p.A150A	TAGTGCCGAAAAC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	G	A	rs199733185		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	550	18	510	0	0.0327273	0	.	.	weak	SIRPA_ENST00000400068,NS,carcinoma,0,5	SIRPA	83	5	NM_001040022	exon4	c.G697A	p.V233I	GCCCACGTCACCT	.	scavenged	Atlas-SNP
CYP11B1	1584	hgsc.bcm.edu	37	8	143958291	143958291	+	Silent	SNP	C	C	T	rs6419	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	24	140	1	0.130435	0.00714286	C|0.025;T|0.975	0.975	strong	CYP11B1,right_lower_lobe,carcinoma,0,1	CYP11B1	128	1	NM_000497	exon4	c.G606A	p.L202L	AAGAGCCAAGTTG	.	scavenged	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125592065	125592065	+	Silent	SNP	C	C	A	rs10018651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	93	185	0	0.458128	0	C|0.743;A|0.257	0.257	strong	.	ANKRD50	136	.	NM_020337	exon4	c.G2367T	p.A789A	CATAGACGCTGCT	.	PASS	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190649	209190649	+	Silent	SNP	A	A	G	rs999891	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	103	0	0.990654	0	A|0.882;G|0.118	0.118	strong	PIKFYVE,colon,carcinoma,+1,1	PIKFYVE	223	1	NM_015040	exon20	c.A3114G	p.R1038R	TAAACGAAAGACT	.	PASS	Atlas-SNP
RNF151	146310	hgsc.bcm.edu	37	16	2018580	2018580	+	Missense_Mutation	SNP	G	G	A	rs62038784	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	44	73	0	0.571429	0	G|0.970;A|0.030	0.030	strong	.	RNF151	12	.	NM_174903	exon4	c.G392A	p.R131Q	AGCACCGGCAGCA	.	PASS	Atlas-SNP
FKRP	79147	hgsc.bcm.edu	37	19	47258842	47258842	+	Silent	SNP	C	C	T	rs2287717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	71	121	0	0.522059	0	C|0.859;T|0.141	0.141	strong	.	FKRP	16	.	NM_024301	exon4	c.C135T	p.A45A	TGCTGCCGGCCCC	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114175004	114175004	+	Silent	SNP	C	C	T	rs2260334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	67	135	0	0.475177	0	C|0.768;T|0.232	0.232	strong	.	TMCO3	77	.	NM_017905	exon8	c.C1299T	p.A433A	CATGGCCGTCATG	.	PASS	Atlas-SNP
CYFIP1	23191	hgsc.bcm.edu	37	15	22925851	22925851	+	Silent	SNP	C	C	T	rs4134802	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	57	91	0	0.553398	0	C|0.769;T|0.231	0.231	strong	.	CYFIP1	159	.	NM_014608	exon2	c.C69T	p.P23P	CCTGCCCGACCAG	.	PASS	Atlas-SNP
DHDDS	79947	hgsc.bcm.edu	37	1	26786627	26786627	+	Missense_Mutation	SNP	G	G	A	rs3816539	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	59	149	1	0.427536	0.00671141	G|0.637;A|0.363	0.363	strong	DHDDS,NS,carcinoma,0,2	DHDDS	33	2	NM_024887	exon8	c.G757A	p.V253M	CATAGCGTGCTTC	.	scavenged	Atlas-SNP
DNAI2	64446	hgsc.bcm.edu	37	17	72306239	72306239	+	Silent	SNP	C	C	G	rs144035254	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	30	69	0	0.416667	0	C|0.996;G|0.004	0.004	strong	.	DNAI2	102	.	NM_023036	exon11	c.C1431G	p.T477T	AACCACCCTGCTG	.	PASS	Atlas-SNP
KCNA7	3743	hgsc.bcm.edu	37	19	49573518	49573518	+	Silent	SNP	G	G	A	rs3810188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	29	84	0	0.439394	0	G|0.856;A|0.144	0.144	strong	.	KCNA7	30	.	NM_031886	exon2	c.C1173T	p.P391P	AATGACGGGCACT	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1245062	1245062	+	Silent	SNP	C	C	T	rs59794024	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	34	80	0	0.441558	0	C|0.967;T|0.033	0.033	strong	.	CACNA1H	317	.	NM_021098	exon3	c.C390T	p.S130S	CGGCTCCGAGCGC	.	PASS	Atlas-SNP
MAPK4	5596	hgsc.bcm.edu	37	18	48248453	48248453	+	Silent	SNP	T	T	C	rs16952476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	24	66	0	0.4	0	T|0.971;C|0.029	0.029	strong	.	MAPK4	75	.	NM_002747	exon4	c.T837C	p.P279P	GCTCCCTGAAGTG	.	PASS	Atlas-SNP
LSM14A	26065	hgsc.bcm.edu	37	19	34706531	34706531	+	Missense_Mutation	SNP	A	A	G	rs73929373	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	43	105	0	0.467391	0	A|0.908;G|0.092	0.092	strong	.	LSM14A	44	.	NM_001114093	exon6	c.A746G	p.N249S	CAGAAAATGAGCA	.	PASS	Atlas-SNP
TGFB1	7040	hgsc.bcm.edu	37	19	41858921	41858921	+	Missense_Mutation	SNP	G	G	A	rs1800470	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	8	5	1	0	0.625	0	G|0.436;A|0.564	0.564	strong	.	TGFB1	27	.	NM_000660	exon1	c.C29T	p.P10L	AGCAGCGGCAGCA	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85992390	85992390	+	Missense_Mutation	SNP	G	G	T	rs12262099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	56	115	0	0.391608	0	G|0.815;T|0.185	0.185	strong	.	LRIT1	73	.	NM_015613	exon4	c.C1165A	p.P389T	CAGCGGGTTTGGG	.	PASS	Atlas-SNP
GPR176	11245	hgsc.bcm.edu	37	15	40094431	40094431	+	Silent	SNP	C	C	T	rs76578471	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	21	39	0	0.446809	0	C|0.989;T|0.011	0.011	strong	.	GPR176	41	.	NM_007223	exon3	c.G450A	p.L150L	CCTCTCCAGTGGA	.	PASS	Atlas-SNP
DHRS1	115817	hgsc.bcm.edu	37	14	24768220	24768220	+	Silent	SNP	G	G	T	rs150092528		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	25	59	0	0.362319	0	G|1.000;T|0.000	0.000	weak	.	DHRS1	21	.	NM_138452	exon2	c.C93A	p.G31G	TGTGGCGCCTGCT	.	PASS	Atlas-SNP
TAPT1	202018	hgsc.bcm.edu	37	4	16215451	16215451	+	Silent	SNP	C	C	T	rs6823623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	61	142	0	0.429577	0	C|0.863;T|0.137	0.137	strong	TAPT1,colon,carcinoma,-1,1	TAPT1	31	1	NM_153365	exon2	c.G270A	p.K90K	TGTATACTTGGCC	.	PASS	Atlas-SNP
OR2T6	254879	hgsc.bcm.edu	37	1	248550970	248550970	+	Missense_Mutation	SNP	A	A	G	rs7417616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	72	112	0	0.576	0	A|0.702;G|0.298	0.298	strong	.	OR2T6	101	.	NM_001005471	exon1	c.A61G	p.N21D	ACTCACAATAAAT	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108281862	108281862	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	4	77	0	0.0571429	0	.	.	none	.	FER	100	.	NM_005246	exon11	c.C1268T	p.S423F	TTGAATCTATTCG	.	PASS	Atlas-SNP
ZCCHC14	23174	hgsc.bcm.edu	37	16	87451273	87451273	+	Silent	SNP	G	G	T	rs56283442	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	17	18	0	0.653846	0	G|0.859;T|0.141	0.141	strong	.	ZCCHC14	87	.	NM_015144	exon8	c.C765A	p.S255S	GGCGGCGGAGCCG	.	PASS	Atlas-SNP
CEBPZ	10153	hgsc.bcm.edu	37	2	37454998	37454998	+	Silent	SNP	A	A	G	rs1803251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	36	61	0	0.529412	0	A|0.912;G|0.088	0.088	strong	.	CEBPZ	68	.	NM_005760	exon2	c.T1338C	p.N446N	CATTTGATTTAAA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159672419	159672419	+	Silent	SNP	G	G	C	rs551392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	67	122	0	0.449664	0	G|0.777;C|0.222	0.222	strong	.	FNDC1	250	.	NM_032532	exon17	c.G4920C	p.L1640L	CAGCCTGGATGAA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207753621	207753621	+	Missense_Mutation	SNP	A	A	G	rs2274567	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	120	214	0	0.528634	0	A|0.785;G|0.214	0.214	strong	.	CR1	354	.	NM_000651	exon30	c.A4973G	p.H1658R	GTGAGCATACCCC	.	PASS	Atlas-SNP
ATXN1L	342371	hgsc.bcm.edu	37	16	71885423	71885423	+	Missense_Mutation	SNP	A	A	G	rs61747555	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	51	109	0	0.463636	0	A|0.828;G|0.172	0.172	strong	.	ATXN1L	18	.	NM_001137675	exon3	c.A1780G	p.S594G	CAGGCCAGCTGTG	.	PASS	Atlas-SNP
OR5H15	403274	hgsc.bcm.edu	37	3	97887970	97887970	+	Missense_Mutation	SNP	C	C	T	rs72933946	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	514	16	509	3	0.0311284	0.00589391	C|0.965;A|0.035	.	alt	OR5H15,NS,carcinoma,-2,1	OR5H15	70	1	NM_001005515	exon1	c.C427T	p.R143W	TGCATCCGGCTAT	.	scavenged	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263345	80263345	+	Missense_Mutation	SNP	A	A	C	rs1138358	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	87	211	0	0.414286	0	A|0.600;C|0.400	0.400	strong	.	BCL2A1	28	.	NM_001114735	exon1	c.T117G	p.N39K	CGCAACATTTTGT	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32035634	32035634	+	Silent	SNP	G	G	A	rs61746537		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	115	215	0	0.497835	0	G|0.987;A|0.013	0.013	weak	TNXB_ENST00000375247,NS,carcinoma,-2,2	TNXB	553	2	NM_019105	exon18	c.C6348T	p.T2116T	GGGGACGGTCCAG	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	43	0	1	0	T|0.888;C|0.112	0.112	strong	.	RAI1	121	.	NM_030665	exon3	c.T4311C	p.P1437P	GCAGCCTGGGGGG	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43926573	43926573	+	Missense_Mutation	SNP	C	C	T	rs2227275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	50	101	0	0.403226	0	C|0.757;T|0.243	0.243	strong	.	MATN4	57	.	NM_003833	exon8	c.G1564A	p.G522S	TGCTGCCTCTGAG	.	PASS	Atlas-SNP
NSMCE1	197370	hgsc.bcm.edu	37	16	27268779	27268779	+	Missense_Mutation	SNP	G	G	C	rs7195194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	51	89	0	0.536842	0	G|0.913;C|0.087	0.087	strong	NSMCE1,NS,carcinoma,0,1	NSMCE1	28	1	NM_145080	exon2	c.C113G	p.T38R	CAGTGCGTCTGCA	.	PASS	Atlas-SNP
ME2	4200	hgsc.bcm.edu	37	18	48458662	48458662	+	Missense_Mutation	SNP	G	G	A	rs649224	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	266	260	0	1	0	G|0.838;A|0.162	0.162	strong	.	ME2	49	.	NM_001168335	exon13	c.G1349A	p.G450E	CATTTGGGCCAGT	.	PASS	Atlas-SNP
EGFL7	51162	hgsc.bcm.edu	37	9	139564668	139564668	+	Missense_Mutation	SNP	G	G	A	rs2297538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	30	79	0	0.3	0	G|0.800;A|0.200	0.200	strong	.	EGFL7	11	.	NM_016215	exon8	c.G457A	p.V153I	CGCTGCGTCAACA	.	PASS	Atlas-SNP
NELFA	7469	hgsc.bcm.edu	37	4	1985668	1985668	+	Silent	SNP	G	G	A	rs2234574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	66	70	0	0.52381	0	G|0.977;A|0.023	0.023	strong	.	.	.	.	NM_005663	exon9	c.C1242T	p.V414V	AGGGGCGACAGCC	.	PASS	Atlas-SNP
CLDN23	137075	hgsc.bcm.edu	37	8	8559917	8559917	+	Silent	SNP	G	G	A	rs61754917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	7	6	6	0	0.857143	0	G|0.995;A|0.005	0.005	strong	.	CLDN23	5	.	NM_194284	exon1	c.G9A	p.T3T	GCGGACGCCGGTG	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46761497	46761497	+	Missense_Mutation	SNP	C	C	G	rs12165943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	99	101	0	0.99	0	C|0.641;G|0.359	0.359	strong	.	CELSR1	242	.	NM_014246	exon31	c.G8390C	p.C2797S	TCCTTGCAGCTCC	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444026	20444026	+	Missense_Mutation	SNP	T	T	G	rs3861513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	191	191	180	0	1	0	T|0.767;G|0.233	0.233	strong	.	OR4K15	82	.	NM_001005486	exon1	c.T349G	p.S117A	ACTATTTCTTTTG	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33744465	33744465	+	Missense_Mutation	SNP	A	A	G	rs73428967	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	80	143	0	0.454545	0	A|0.997;G|0.003	0.003	strong	.	ELP2	70	.	NM_001242875	exon19	c.A1984G	p.I662V	GCTATCATTCTTT	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22273687	22273687	+	Silent	SNP	T	T	C	rs6558052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	75	149	0	0.457317	0	T|0.748;C|0.252	0.252	strong	SLC39A14_ENST00000381237,NS,malignant_melanoma,+2,2	SLC39A14	59	2	NM_001135153	exon7	c.T1041C	p.H347H	CCTCCATAATTTC	.	PASS	Atlas-SNP
SHC2	25759	hgsc.bcm.edu	37	19	422229	422229	+	Missense_Mutation	SNP	C	C	T	rs61750917	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	62	128	0	0.455882	0	C|0.981;T|0.019	0.019	strong	SHC2,colon,carcinoma,0,1	SHC2	47	1	NM_012435	exon11	c.G1537A	p.V513I	TGGTGACGCTGTC	.	PASS	Atlas-SNP
DCAF4L2	138009	hgsc.bcm.edu	37	8	88885256	88885256	+	Missense_Mutation	SNP	G	G	A	rs146716352	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	87	199	0	0.47027	0	G|0.997;A|0.003	0.003	strong	.	DCAF4L2	187	.	NM_152418	exon1	c.C944T	p.S315F	TAGGCGGAGTTAT	.	PASS	Atlas-SNP
KIAA1671	85379	hgsc.bcm.edu	37	22	25570285	25570285	+	Silent	SNP	C	C	T	rs56351192	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	155	184	0	0.99359	0	C|0.981;T|0.019	0.019	strong	.	KIAA1671	28	.	NM_001145206	exon6	c.C4728T	p.S1576S	TCTGTCCTCCCAA	.	PASS	Atlas-SNP
CAPS	828	hgsc.bcm.edu	37	19	5914625	5914625	+	Silent	SNP	G	G	A	rs7248090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	42	87	0	0.442105	0	G|0.953;A|0.047	0.047	strong	.	CAPS	14	.	NM_080590	exon3	c.G135A	p.E45E	TGATGAGTTCCGG	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31678534	31678534	+	Silent	SNP	T	T	C	rs2070326	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	70	109	0	0.526316	0	T|0.784;C|0.216	0.216	strong	.	.	.	.	NM_182519	exon8	c.T1072C	p.L358L	GGGATATTGGGAA	.	PASS	Atlas-SNP
DDX24	57062	hgsc.bcm.edu	37	14	94526812	94526812	+	Silent	SNP	C	C	T	rs11845400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	118	197	0	0.517544	0	C|0.952;T|0.048	0.048	strong	.	DDX24	82	.	NM_020414	exon5	c.G1545A	p.Q515Q	AGGAGCCTGATGC	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135369532	135369532	+	Missense_Mutation	SNP	T	T	C	rs3747881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	28	44	0	0.491228	0	T|0.851;C|0.149	0.149	strong	.	SYCE1	81	.	NM_001143763	exon9	c.A548G	p.K183R	ATCTCCTTTGCCA	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30672342	30672342	+	Missense_Mutation	SNP	A	A	G	rs3130645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	416	201	392	1	0.483173	0.00255102	A|0.872;G|0.128	0.128	strong	.	MDC1	218	.	NM_014641	exon10	c.T4618C	p.S1540P	AGGTGGAAGGCTG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46264805	46264805	+	Missense_Mutation	SNP	C	C	T	rs2230781	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	87	134	0	0.56129	0	C|0.981;T|0.019	0.019	strong	.	NCOA3	156	.	NM_001174088	exon12	c.C1705T	p.P569S	ACCCAACCAAGTA	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54844790	54844790	+	Silent	SNP	C	C	T	rs2229506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	97	205	0	0.482587	0	C|0.859;G|0.000;T|0.140	0.140	strong	.	SPTBN1	378	.	NM_003128	exon6	c.C612T	p.D204D	GAGGGACGGCATG	.	PASS	Atlas-SNP
PYCR2	29920	hgsc.bcm.edu	37	1	226108200	226108200	+	Silent	SNP	C	C	T	rs73131849	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	67	116	0	0.531746	0	C|0.808;T|0.192	0.192	strong	.	PYCR2	13	.	NM_013328	exon7	c.G918A	p.G306G	GAGCTTCCCTGGG	.	PASS	Atlas-SNP
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	82	180	0	0.465909	0	C|0.573;N|0.000	.	strong	.	PPFIA2	207	.	NM_001220476	exon9	c.G1125A	p.L375L	CTGCCGCAGGATA	.	PASS	Atlas-SNP
LGALS16	148003	hgsc.bcm.edu	37	19	40148584	40148584	+	Missense_Mutation	SNP	T	T	C	rs10403702	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	71	107	0	0.577236	0	T|0.912;C|0.088	0.088	strong	.	LGALS16	6	.	NM_001190441	exon2	c.T77C	p.L26P	GGACACTGATCGA	.	PASS	Atlas-SNP
PTCHD2	57540	hgsc.bcm.edu	37	1	11561164	11561164	+	Missense_Mutation	SNP	G	G	A	rs41274528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	67	112	0	0.492647	0	G|0.885;A|0.115	0.115	strong	.	PTCHD2	193	.	NM_020780	exon2	c.G115A	p.G39R	CAACCTGGGGCAG	.	PASS	Atlas-SNP
ANKRD24	170961	hgsc.bcm.edu	37	19	4216829	4216829	+	Missense_Mutation	SNP	G	G	A	rs61738959	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	14	35	0	0.482759	0	G|0.982;A|0.018	0.018	strong	.	ANKRD24	180	.	NM_133475	exon18	c.G1672A	p.G558R	GTTAACGGAGCCG	.	PASS	Atlas-SNP
CASS4	57091	hgsc.bcm.edu	37	20	55027509	55027509	+	Missense_Mutation	SNP	C	C	T	rs34899200	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	45	82	0	0.517241	0	C|0.984;T|0.016	0.016	strong	CASS4,rectum,adenoma,-1,1	CASS4	121	1	NM_020356	exon5	c.C1277T	p.S426L	CTTCCTCGGAGGA	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783596	140783596	+	Silent	SNP	C	C	T	rs1363448	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	197	181	1	1	0.00552486	C|0.540;T|0.460	0.460	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.C1077T	p.D359D	AGAAGACGCACCT	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84582124	84582124	+	Missense_Mutation	SNP	G	G	T	rs4842838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	47	52	0	1	0	G|0.348;T|0.652	0.652	strong	.	ADAMTSL3	290	.	NM_207517	exon16	c.G1981T	p.V661L	ACATGCGTGGGAG	.	PASS	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188327461	188327461	+	Silent	SNP	C	C	T	rs1059380	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	93	94	0	1	0	C|0.403;T|0.597	0.597	strong	.	LPP	72	.	NM_005578	exon6	c.C942T	p.D314D	CTCTGACCCTACC	.	PASS	Atlas-SNP
ARNTL2	56938	hgsc.bcm.edu	37	12	27543028	27543028	+	Splice_Site	SNP	G	G	A	rs113615248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	78	172	0	0.516556	0	G|0.991;A|0.009	0.009	strong	.	ARNTL2	54	.	NM_001248005	exon7	c.665-1G>A	.	ACGAAAGCTGGTT	.	PASS	Atlas-SNP
PELI2	57161	hgsc.bcm.edu	37	14	56763743	56763743	+	Silent	SNP	G	G	T	rs112097284	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	76	0	0.478873	0	G|0.979;T|0.021	0.021	strong	.	PELI2	55	.	NM_021255	exon6	c.G1122T	p.S374S	GTGCTCGGAGAAG	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031024	32031024	+	Silent	SNP	C	C	T	rs4449357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	208	98	210	0	0.471154	0	C|0.655;T|0.345	0.345	strong	.	ZNF860	96	.	NM_001137674	exon2	c.C453T	p.I151I	GCCTATCAAAGAT	.	PASS	Atlas-SNP
CPM	1368	hgsc.bcm.edu	37	12	69326547	69326547	+	Missense_Mutation	SNP	C	C	T	rs7978197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	56	106	0	0.466667	0	C|0.819;T|0.181	0.181	strong	CPM,NS,carcinoma,-1,1	CPM	30	1	NM_001005502	exon2	c.G71A	p.R24H	TCCTGGCGGTGGT	.	PASS	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158369025	158369025	+	Missense_Mutation	SNP	T	T	C	rs6662597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	53	96	0	0.582418	0	T|0.985;C|0.015	0.015	strong	.	OR10T2	76	.	NM_001004475	exon1	c.A232G	p.I78V	GGATGATGACAAA	.	PASS	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	37	8	106813518	106813518	+	Missense_Mutation	SNP	C	C	G	rs11993776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	48	151	0	0.352941	0	C|0.817;G|0.183	0.183	strong	.	ZFPM2	219	.	NM_012082	exon8	c.C1208G	p.A403G	CAAGTGCAACTGA	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25672945	25672945	+	Missense_Mutation	SNP	T	T	C	rs34326830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	81	169	0	0.522581	0	T|0.980;C|0.020	0.020	strong	.	IFLTD1	121	.	NM_001145728	exon7	c.A863G	p.E288G	TTAAATTCAACGT	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15793238	15793238	+	Silent	SNP	C	C	T	rs144258147	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	342	74	270	0	0.216374	0	C|0.990;T|0.010	0.010	strong	.	CYP4F12	89	.	NM_023944	exon6	c.C565T	p.L189L	AGTTGTCTGGACA	.	PASS	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58152182	58152182	+	Missense_Mutation	SNP	G	G	A	rs34897843	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	115	251	0	0.475207	0	G|0.991;A|0.009	0.009	strong	.	ZNF211	78	.	NM_001265597	exon5	c.G523A	p.D175N	AATGCCGACTCCT	.	PASS	Atlas-SNP
CC2D1A	54862	hgsc.bcm.edu	37	19	14030689	14030689	+	Silent	SNP	T	T	C	rs10410239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	217	242	1	0.990868	0.00413223	T|0.665;C|0.335	0.335	strong	.	CC2D1A	67	.	NM_017721	exon12	c.T1281C	p.G427G	GGTGGGTGTCCTG	.	PASS	Atlas-SNP
CDH19	28513	hgsc.bcm.edu	37	18	64235877	64235877	+	Missense_Mutation	SNP	G	G	A	rs114375304	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	49	107	0	0.457944	0	G|0.980;A|0.020	0.020	strong	CDH19,NS,carcinoma,-1,1	CDH19	141	1	NM_021153	exon3	c.C266T	p.T89I	ATAAAAGTACTTC	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10713765	10713765	+	Silent	SNP	T	T	C	rs284294	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	29	57	0	0.517857	0	T|0.453;C|0.547	0.547	strong	CASZ1,colon,carcinoma,0,1	CASZ1	150	1	NM_001079843	exon11	c.A2349G	p.S783S	GGGGATTGAGCCA	.	PASS	Atlas-SNP
SLC12A4	6560	hgsc.bcm.edu	37	16	67984589	67984589	+	Silent	SNP	A	A	G	rs11542821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	78	144	0	0.484472	0	A|0.851;G|0.149	0.149	strong	.	SLC12A4	81	.	NM_001145962	exon10	c.T1428C	p.G476G	GCAGGCACCAAAG	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	37	4	2896419	2896419	+	Silent	SNP	G	G	A	rs112813723	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	148	240	0	0.503401	0	G|0.988;A|0.012	0.012	strong	.	ADD1	56	.	NM_014190	exon6	c.G702A	p.V234V	GGACGTGAAGTGC	.	PASS	Atlas-SNP
PLEKHO2	80301	hgsc.bcm.edu	37	15	65157482	65157482	+	Missense_Mutation	SNP	C	C	T	rs2010875	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	40	68	0	0.416667	0	T|0.220;G|0.000;C|0.779	0.220	strong	.	PLEKHO2	50	.	NM_025201	exon6	c.C868T	p.P290S	GCAGAACCGTCCC	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57378150	57378150	+	Silent	SNP	C	C	T	rs1620073	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	221	110	181	0	0.497738	0	C|0.905;T|0.095	0.095	strong	C8A,NS,carcinoma,+2,1	C8A	103	1	NM_000562	exon10	c.C1455T	p.R485R	GCGCCGCGCCTTG	.	PASS	Atlas-SNP
MCM5	4174	hgsc.bcm.edu	37	22	35802661	35802661	+	Missense_Mutation	SNP	C	C	G	rs2307340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	33	66	0	0.559322	0	C|0.945;G|0.055	0.055	strong	.	MCM5	54	.	NM_006739	exon5	c.C539G	p.T180S	CCCTCACCAACAT	.	PASS	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	37	1	32279629	32279629	+	Missense_Mutation	SNP	G	G	A	rs6669563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	73	146	0	0.536765	0	G|0.624;A|0.376	0.376	strong	SPOCD1,NS,carcinoma,0,2	SPOCD1	109	2	NM_144569	exon2	c.C1306T	p.R436W	TGCCCCGGTCTTG	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3352294	3352294	+	Missense_Mutation	SNP	A	A	G	rs1488689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	135	259	0	0.494505	0	A|0.769;G|0.231	0.231	strong	.	SPATA22	49	.	NM_032598	exon6	c.T479C	p.I160T	TCAGGTATTCTTA	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96098373	96098373	+	Missense_Mutation	SNP	C	C	T	rs17517578	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	105	231	0	0.450644	0	C|0.868;T|0.132	0.132	strong	.	NOC3L	67	.	NM_022451	exon18	c.G2083A	p.A695T	GCAGAGCATGCAG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76447617	76447617	+	Silent	SNP	A	A	G	rs34002770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	125	237	0	0.468165	0	A|0.969;G|0.031	0.031	strong	.	DNAH17	347	.	NM_173628	exon66	c.T10668C	p.D3556D	GAGTCCATCCCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515726	195515726	+	Missense_Mutation	SNP	G	G	C	rs55697302	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	136	226	0	0.494545	0	G|0.942;C|0.058	0.058	strong	.	MUC4	1505	.	NM_018406	exon2	c.C2725G	p.Q909E	GAGTCTGGGCCAT	.	PASS	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	37	22	31535995	31535995	+	Missense_Mutation	SNP	C	C	G	rs2074734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	82	145	0	0.525641	0	C|0.889;G|0.111	0.111	strong	.	PLA2G3	85	.	NM_015715	exon1	c.G346C	p.E116Q	ATGCCTCCCACTG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	74	132	0	0.578125	0	A|0.813;G|0.187	0.187	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon5	c.T558C	p.Y186Y	TGGCCAATAGCGG	.	PASS	Atlas-SNP
ZNF230	7773	hgsc.bcm.edu	37	19	44514859	44514859	+	Missense_Mutation	SNP	C	C	T	rs147553354	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	50	110	0	0.416667	0	C|0.998;T|0.002	0.002	strong	.	ZNF230	44	.	NM_006300	exon5	c.C668T	p.P223L	AGAAACCATTCAA	.	PASS	Atlas-SNP
DHRS4L1	728635	hgsc.bcm.edu	37	14	24505722	24505722	+	Missense_Mutation	SNP	C	C	G	rs8005834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	36	104	0	0.367347	0	C|0.569;G|0.431	0.431	strong	.	.	.	.	NM_001082488	exon1	c.C13G	p.R5G	AAGGCGCGGCTAC	.	PASS	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282960	59282960	+	Missense_Mutation	SNP	C	C	G	rs113146895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	82	176	0	0.485207	0	C|0.979;G|0.021	0.021	strong	.	OR4D9	47	.	NM_001004711	exon1	c.C575G	p.T192S	CTGACACCTTCAC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149498893	149498893	+	Missense_Mutation	SNP	A	A	G	rs77858430	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	47	121	0	0.505376	0	A|0.897;G|0.103	0.103	strong	.	.	.	.	NM_198455	exon50	c.A7345G	p.M2449V	TTCATGATGCCTA	.	PASS	Atlas-SNP
DNAH12	201625	hgsc.bcm.edu	37	3	57528503	57528503	+	Missense_Mutation	SNP	A	A	G	rs9311651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	46	101	0	0.425926	0	A|0.760;G|0.240	0.240	strong	.	DNAH12	182	.	NM_198564	exon2	c.T95C	p.V32A	GTATCAACGCCTA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919145	12919145	+	Missense_Mutation	SNP	G	G	A	rs149655365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	100	156	0	0.512821	0	G|0.957;A|0.043	0.043	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.G281A	p.R94H	AGGATCGCCCCAG	.	PASS	Atlas-SNP
CDPF1	150383	hgsc.bcm.edu	37	22	46644168	46644168	+	Missense_Mutation	SNP	A	A	G	rs9627281	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	33	55	0	0.52381	0	A|0.682;G|0.318	0.318	strong	.	.	.	.	NM_207327	exon2	c.T14C	p.V5A	CACTCTACATGGG	.	PASS	Atlas-SNP
SEPT9	10801	hgsc.bcm.edu	37	17	75471762	75471762	+	Silent	SNP	G	G	A	rs312821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	44	66	0	0.53012	0	G|0.937;A|0.063	0.063	strong	.	SEPT9	105	.	NM_001113495	exon1	c.G162A	p.T54T	GCCCACGCTGGGC	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	220	5	205	1	0.0227273	0.00487805	C|0.996;T|0.004	0.004	strong	UBB,bladder,carcinoma,0,2	UBB	30	2	NM_018955	exon2	c.C270T	p.T90T	CATCACCCTGGAA	.	scavenged	Atlas-SNP
MRPL46	26589	hgsc.bcm.edu	37	15	89008072	89008072	+	Silent	SNP	T	T	G	rs16941885	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	73	140	0	0.5	0	T|0.925;G|0.075	0.075	strong	.	MRPL46	13	.	NM_022163	exon3	c.A451C	p.R151R	GCTTCCTGTTCAG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92616006	92616006	+	Silent	SNP	C	C	T	rs58474174	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	47	140	0	0.408696	0	C|0.976;T|0.024	0.024	strong	.	FAT3	1822	.	NM_001008781	exon23	c.C12384T	p.Y4128Y	GGGCTACGTGGGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73551088	73551088	+	Silent	SNP	G	G	A	rs55964031	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	44	80	1	0.488889	0.0125	G|0.974;A|0.026	0.026	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon45	c.G6249A	p.P2083P	CTGCCCGCCTGGT	.	scavenged	Atlas-SNP
PPFIA1	8500	hgsc.bcm.edu	37	11	70200529	70200529	+	Silent	SNP	C	C	T	rs17853270	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	62	49	0	0.984127	0	C|0.855;T|0.145	0.145	strong	.	PPFIA1	114	.	NM_177423	exon17	c.C2286T	p.V762V	CACCGTCAGCCAC	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	160977167	160977167	+	Silent	SNP	G	G	T	rs375904594		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	361	33	342	2	0.0914127	0.00584795	.	.	weak	LPA,right_upper_lobe,carcinoma,-1,1	LPA	237	1	NM_005577	exon31	c.C4863A	p.G1621G	ACTCTGGCCATTA	.	scavenged	Atlas-SNP
APTX	54840	hgsc.bcm.edu	37	9	32984803	32984803	+	Missense_Mutation	SNP	C	C	T	rs150886026	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	63	108	0	0.5625	0	C|0.994;T|0.006	0.006	strong	.	APTX	44	.	NM_001195248	exon6	c.G638A	p.R213H	TGGTAACGGGCCT	.	PASS	Atlas-SNP
ZNF324	25799	hgsc.bcm.edu	37	19	58982447	58982447	+	Silent	SNP	A	A	G	rs61742224	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	95	1	0.509804	0.0105263	A|0.942;G|0.058	0.058	strong	ZNF324,NS,carcinoma,0,1	ZNF324	46	1	NM_014347	exon4	c.A588G	p.K196K	GCAGAAACCATGT	.	scavenged	Atlas-SNP
GALNT18	374378	hgsc.bcm.edu	37	11	11292700	11292700	+	Silent	SNP	G	G	C	rs10831567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	52	64	0	1	0	G|0.596;C|0.404	0.404	strong	GALNTL4,NS,carcinoma,0,1	.	.	1	NM_198516	exon11	c.C1815G	p.L605L	GGACGCGAGGCTC	.	PASS	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	37	22	31478942	31478942	+	Silent	SNP	G	G	A	rs73408133	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	38	76	0	0.38	0	G|0.963;A|0.037	0.037	strong	.	SMTN	219	.	NM_001207017	exon1	c.G36A	p.A12A	ACTGGCGGCCAAG	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62018164	62018164	+	Silent	SNP	A	A	C	rs2227906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	89	98	0	1	0	A|0.808;C|0.192	0.192	strong	.	SCN4A	205	.	NM_000334	exon24	c.T5478G	p.T1826T	GCGCACAGTCTGC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81242184	81242184	+	Silent	SNP	T	T	C	rs9927930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	21	37	0	0.446809	0	T|0.951;C|0.049	0.049	strong	.	PKD1L2	361	.	NM_001076780	exon4	c.A672G	p.S224S	CTGGCATGACTGT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15496730	15496730	+	Missense_Mutation	SNP	A	A	G	rs8078150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	240	253	0	0.995851	0	A|0.688;G|0.312	0.312	strong	.	CDRT1	83	.	NM_006382	exon11	c.T1927C	p.F643L	CATTGAAGAAATT	.	PASS	Atlas-SNP
AKAP2	11217	hgsc.bcm.edu	37	9	112811038	112811038	+	Missense_Mutation	SNP	C	C	T	rs78923754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	10	2	0	0.833333	0	C|0.917;T|0.083	0.083	strong	.	AKAP2	98	.	NM_001004065	exon1	c.C59T	p.P20L	GACCCCCGGAGTC	.	PASS	Atlas-SNP
AIP	9049	hgsc.bcm.edu	37	11	67258362	67258362	+	Silent	SNP	C	C	A	rs35665586	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	70	149	0	0.472973	0	C|0.995;A|0.005	0.005	strong	.	AIP	26	.	NM_003977	exon6	c.C891A	p.A297A	CCCAGCCCTGGCG	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769228	43769228	+	Silent	SNP	A	A	C	rs10506226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	75	144	0	0.614754	0	A|0.790;C|0.210	0.210	strong	.	ADAMTS20	635	.	NM_025003	exon36	c.T5400G	p.T1800T	GAAAACAGTGTAT	.	PASS	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080523	5080523	+	Missense_Mutation	SNP	A	A	G	rs144077173	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	47	87	0	0.516484	0	A|0.999;G|0.001	0.001	strong	.	OR52E2	63	.	NM_001005164	exon1	c.T335C	p.M112T	GACTCCATAAGTG	.	PASS	Atlas-SNP
ANKRD45	339416	hgsc.bcm.edu	37	1	173596257	173596257	+	Missense_Mutation	SNP	A	A	T	rs12059066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	53	67	0	0.981481	0	A|0.814;T|0.186	0.186	strong	.	ANKRD45	36	.	NM_198493	exon4	c.T538A	p.L180I	CAGCTAAAGAGAC	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672746	3672746	+	Silent	SNP	G	G	A	rs34921899	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	22	39	0	0.536585	0	G|0.979;A|0.021	0.021	strong	.	SIGLEC1	210	.	NM_023068	exon16	c.C4134T	p.A1378A	AGATAGGGCCAGC	.	PASS	Atlas-SNP
KDM1A	23028	hgsc.bcm.edu	37	1	23395037	23395037	+	Silent	SNP	T	T	C	rs145865107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	71	98	0	0.546154	0	T|0.998;C|0.002	0.002	strong	.	KDM1A	49	.	NM_001009999	exon11	c.T1185C	p.P395P	GGTTCCTAAAGAG	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	C	rs5749080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	69	96	0	0.64486	0	A|0.198;C|0.000;G|0.802	0.000	strong	.	CCDC157	86	.	NM_001017437	exon4	c.G330C	p.A110A	GGCTGCGGGGCCC	.	PASS	Atlas-SNP
ZDHHC20	253832	hgsc.bcm.edu	37	13	21987823	21987823	+	Missense_Mutation	SNP	G	G	A	rs151151710	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	25	58	0	0.490196	0	G|0.994;A|0.006	0.006	strong	ZDHHC20_ENST00000382466,NS,carcinoma,0,2	ZDHHC20	36	2	NM_153251	exon4	c.C338T	p.A113V	GGTAAAGCTCTTG	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20873695	20873695	+	Missense_Mutation	SNP	A	A	G	rs148090256	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	29	64	0	0.508772	0	A|0.994;G|0.006	0.006	strong	TEP1,caecum,carcinoma,0,1	TEP1	224	1	NM_007110	exon4	c.T785C	p.M262T	TTGTTCATGTTTA	.	PASS	Atlas-SNP
PET112	5188	hgsc.bcm.edu	37	4	152682046	152682046	+	Missense_Mutation	SNP	G	G	T	rs11556167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	62	87	0	0.48062	0	G|0.857;T|0.143	0.143	strong	.	PET112	43	.	NM_004564	exon1	c.C89A	p.A30D	GTCGGAGCCCCTC	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38377417	38377417	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	11	82	0	0.148649	0	.	.	none	.	WDR87	191	.	NM_031951	exon6	c.G6777A	p.E2259E	CTCCTCCTCCTCC	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77660550	77660550	+	Silent	SNP	T	T	C	rs61745983	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	58	136	0	0.439394	0	T|0.978;C|0.022	0.022	strong	.	SHROOM3	134	.	NM_020859	exon5	c.T1224C	p.D408D	CCTTGATCAGAAA	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64216815	64216815	+	Missense_Mutation	SNP	C	C	T	rs8178847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	49	145	0	0.371212	0	C|0.927;T|0.073	0.073	strong	.	APOH	45	.	NM_000042	exon5	c.G461A	p.R154H	TAAACACGAAGTG	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3425731	3425731	+	Missense_Mutation	SNP	G	G	A	rs35775829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	87	133	0	0.494318	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_016030	exon4	c.G1244A	p.G415E	AGAGCGGGCTGCT	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30342933	30342933	+	Missense_Mutation	SNP	C	C	A	rs61748614	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	35	84	0	0.507246	0	C|0.971;A|0.029	0.029	strong	.	LTN1	141	.	NM_015565	exon8	c.G1254T	p.Q418H	GATGGACTGAGGG	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124288213	124288213	+	Missense_Mutation	SNP	G	G	A	rs77726895	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	23	61	0	0.621622	0	G|0.980;A|0.020	0.020	strong	.	DNAH10	888	.	NM_207437	exon16	c.G2266A	p.G756S	GGTATCGGTGACT	.	PASS	Atlas-SNP
ECM1	1893	hgsc.bcm.edu	37	1	150484004	150484004	+	Silent	SNP	G	G	A	rs11801190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	45	85	0	0.478723	0	G|0.878;A|0.122	0.122	strong	.	ECM1	96	.	NM_001202858	exon7	c.G861A	p.T287T	CTGCACGCGGCAG	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117114223	117114223	+	Silent	SNP	T	T	A	rs6924002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	88	214	1	0.468085	0.0046729	T|0.683;A|0.317	0.317	strong	.	GPRC6A	152	.	NM_148963	exon6	c.A1863T	p.T621T	AACAGGTGTGTTC	.	PASS	Atlas-SNP
LZTS1	11178	hgsc.bcm.edu	37	8	20107325	20107325	+	Missense_Mutation	SNP	G	G	C	rs114929298	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	71	135	0	0.586777	0	G|0.995;C|0.005	0.005	strong	.	LZTS1	72	.	NM_021020	exon3	c.C1699G	p.L567V	GTGCCAGCTGCTG	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32756807	32756807	+	Silent	SNP	G	G	C	rs78565810	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	86	198	0	0.398148	0	G|0.978;C|0.022	0.022	strong	.	RFPL3	91	.	NM_001098535	exon2	c.G942C	p.G314G	TCCTGGGGAGGCC	.	PASS	Atlas-SNP
RGS8	85397	hgsc.bcm.edu	37	1	182640848	182640848	+	Silent	SNP	G	G	A	rs115960776	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	80	286	0	0.372093	0	G|0.981;A|0.019	0.019	strong	.	RGS8	51	.	NM_033345	exon2	c.C24T	p.S8S	AGAGAGGCTTCGG	.	PASS	Atlas-SNP
HERC6	55008	hgsc.bcm.edu	37	4	89338691	89338691	+	Missense_Mutation	SNP	A	A	G	rs190243300	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	24	53	0	0.40678	0	A|0.998;G|0.002	0.002	strong	.	HERC6	104	.	NM_017912	exon13	c.A1673G	p.N558S	ACTGTAATGTTAA	.	PASS	Atlas-SNP
SERPINB3	6317	hgsc.bcm.edu	37	18	61323228	61323228	+	Missense_Mutation	SNP	C	C	G	rs61748838	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	230	121	232	0	0.526087	0	C|0.940;G|0.060	0.060	strong	SERPINB3,caecum,carcinoma,0,1	SERPINB3	90	1	NM_006919	exon8	c.G836C	p.R279P	TCGACACGTGTCT	.	PASS	Atlas-SNP
BRD3	8019	hgsc.bcm.edu	37	9	136913355	136913355	+	Silent	SNP	T	T	C	rs464826	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	86	0	1	0	T|0.288;C|0.712	0.712	strong	.	BRD3	82	.	NM_007371	exon6	c.A936G	p.L312L	GTAGCGTAGGTGC	.	PASS	Atlas-SNP
UGGT1	56886	hgsc.bcm.edu	37	2	128870784	128870784	+	Silent	SNP	A	A	G	rs149605444	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	290	132	243	0	0.455172	0	A|0.995;G|0.005	0.005	strong	.	UGGT1	126	.	NM_020120	exon6	c.A648G	p.S216S	TATATCAAAAAGC	.	PASS	Atlas-SNP
AGL	178	hgsc.bcm.edu	37	1	100353654	100353654	+	Silent	SNP	A	A	C	rs34230588	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	21	61	0	0.42	0	A|0.994;C|0.006	0.006	strong	.	AGL	137	.	NM_000644	exon21	c.A2802C	p.A934A	ATATGCAGGTCTT	.	PASS	Atlas-SNP
LAIR2	3904	hgsc.bcm.edu	37	19	55019379	55019379	+	Missense_Mutation	SNP	T	T	A	rs34429135	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	55	107	0	0.433071	0	T|0.943;A|0.057	0.057	strong	.	LAIR2	30	.	NM_002288	exon3	c.T344A	p.F115Y	GTGACTTCCTGGA	.	PASS	Atlas-SNP
ARSH	347527	hgsc.bcm.edu	37	X	2933057	2933057	+	Silent	SNP	T	T	C	rs143359225	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	115	195	0	0.506608	0	T|0.952;C|0.048	0.048	strong	.	ARSH	72	.	NM_001011719	exon4	c.T387C	p.C129C	TCACTGTTACCAC	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129275206	129275206	+	Silent	SNP	C	C	T	rs11920311	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	106	245	0	0.527363	0	C|0.790;T|0.210	0.210	strong	.	PLXND1	149	.	NM_015103	exon36	c.G5727A	p.Q1909Q	CACCACCTGCTCA	.	PASS	Atlas-SNP
PRKAR2B	5577	hgsc.bcm.edu	37	7	106791447	106791447	+	Silent	SNP	G	G	A	rs3729878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	95	201	0	0.454545	0	G|0.953;A|0.047	0.047	strong	.	PRKAR2B	34	.	NM_002736	exon7	c.G822A	p.L274L	GTCACTGCCATTC	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49951377	49951377	+	Missense_Mutation	SNP	C	C	T	rs59261129	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	32	51	0	0.5	0	C|0.914;T|0.086	0.086	strong	.	KCNH3	88	.	NM_012284	exon15	c.C2893T	p.R965C	CACCCTCGTCCGG	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45503121	45503121	+	Missense_Mutation	SNP	G	G	A	rs2071152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	28	76	0	0.394366	0	G|0.661;A|0.339	0.339	strong	.	TRAPPC10	109	.	NM_003274	exon14	c.G2176A	p.V726M	GCCCACGTGCTGA	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57758732	57758732	+	Missense_Mutation	SNP	C	C	A	rs2923144	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	25	38	0	0.480769	0	C|0.891;A|0.109	0.109	strong	.	CCDC135	97	.	NM_032269	exon12	c.C1743A	p.N581K	GTCAAACCCCCGG	.	PASS	Atlas-SNP
CDKN1B	1027	hgsc.bcm.edu	37	12	12871099	12871099	+	Missense_Mutation	SNP	T	T	G	rs2066827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	21	37	0	0.512195	0	T|0.661;G|0.339	0.339	strong	.	CDKN1B	48	.	NM_004064	exon1	c.T326G	p.V109G	AGGATGTCAGCGG	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73550969	73550969	+	Missense_Mutation	SNP	G	G	A	rs10466026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	44	92	1	0.44898	0.0108696	G|0.661;A|0.339	0.339	strong	CDH23,colon,carcinoma,0,2	CDH23	365	2	NM_022124	exon45	c.G6130A	p.E2044K	CTGGCTGAGGACA	.	scavenged	Atlas-SNP
MESP2	145873	hgsc.bcm.edu	37	15	90320146	90320146	+	Silent	SNP	G	G	A	rs28546919	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	6	0	0	1	.	A|1.000;|0.000	1.000	weak	.	MESP2	20	.	NM_001039958	exon1	c.G558A	p.Q186Q	GGGGCAGGGGCAG	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27473066	27473066	+	Silent	SNP	A	A	G	rs13077400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	67	109	0	0.492647	0	A|0.800;G|0.200	0.200	strong	.	SLC4A7	119	.	NM_003615	exon7	c.T846C	p.L282L	ATGACCAAGAAGA	.	PASS	Atlas-SNP
GPCPD1	56261	hgsc.bcm.edu	37	20	5556512	5556512	+	Missense_Mutation	SNP	G	G	A	rs2273373	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	325	147	326	0	0.452308	0	G|0.899;A|0.101	0.101	strong	GPCPD1,NS,carcinoma,+1,1	GPCPD1	52	1	NM_019593	exon9	c.C818T	p.T273I	GGAAGAGTAAGAA	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71234960	71234960	+	Missense_Mutation	SNP	A	A	G	rs9455142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	22	65	0	0.366667	0	A|0.974;G|0.026	0.026	strong	.	FAM135A	181	.	NM_001162529	exon13	c.A2173G	p.I725V	CTTTCTATTGGAG	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	225	222	0	0.991189	0	G|0.712;A|0.288	0.288	strong	.	FKBP15	128	.	NM_015258	exon26	c.C3286T	p.L1096L	GGGACAGTCTTGT	.	PASS	Atlas-SNP
MASTL	84930	hgsc.bcm.edu	37	10	27475444	27475444	+	Silent	SNP	T	T	C	rs10741130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	57	98	0	0.513514	0	T|0.404;C|0.596	0.596	strong	.	MASTL	81	.	NM_001172303	exon12	c.T2619C	p.T873T	CCTGACTGTATCT	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	98	91	0	1	0	A|0.517;G|0.483	0.483	strong	.	GPATCH1	79	.	NM_018025	exon15	c.A2171G	p.H724R	AAGAGCATGCACC	.	PASS	Atlas-SNP
CLCN5	1184	hgsc.bcm.edu	37	X	49854942	49854942	+	Silent	SNP	C	C	T	rs34173954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	270	262	1	1	0.00381679	C|0.910;T|0.090	0.090	strong	.	CLCN5	137	.	NM_001127898	exon13	c.C1914T	p.P638P	ATACCCCTTTCTT	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2554836	2554836	+	Silent	SNP	A	A	G	rs16943442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	68	157	0	0.447368	0	A|0.881;G|0.119	0.119	strong	.	METTL4	40	.	NM_022840	exon4	c.T661C	p.L221L	CCACCAATTGTAA	.	PASS	Atlas-SNP
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	15	18	0	0.625	0	G|0.964;C|0.036	0.036	strong	.	FAM25A	4	.	NM_001146157	exon2	c.G103C	p.V35L	AAGGAGGTGGTGG	.	PASS	Atlas-SNP
PANX1	24145	hgsc.bcm.edu	37	11	93913392	93913392	+	Missense_Mutation	SNP	G	G	T	rs74549886	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	56	136	0	0.434109	0	G|0.968;T|0.032	0.032	strong	.	PANX1	38	.	NM_015368	exon4	c.G1170T	p.E390D	GAGAGAGGAGCAG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109644616	109644616	+	Silent	SNP	C	C	T	rs17848814	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	87	157	1	0.488764	0.00636943	C|0.914;T|0.086	0.086	strong	ACACB,NS,carcinoma,0,1	ACACB	330	1	NM_001093	exon19	c.C3015T	p.N1005N	CACCAACGTCATG	.	scavenged	Atlas-SNP
ILDR1	286676	hgsc.bcm.edu	37	3	121712271	121712271	+	Missense_Mutation	SNP	C	C	T	rs34883204	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	56	85	1	0.54902	0.0117647	C|0.960;T|0.040	0.040	strong	ILDR1_ENST00000344209,colon,carcinoma,-1,2	ILDR1	120	2	NM_001199799	exon7	c.G1325A	p.R442H	TGACAGCGGCTCC	.	scavenged	Atlas-SNP
BHMT	635	hgsc.bcm.edu	37	5	78421959	78421959	+	Missense_Mutation	SNP	G	G	A	rs3733890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	118	192	0	0.538813	0	G|0.715;A|0.285	0.285	strong	.	BHMT	53	.	NM_001713	exon6	c.G716A	p.R239Q	CTGCCCGACTGAA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158623103	158623103	+	Missense_Mutation	SNP	G	G	A	rs116297260	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	65	134	0	0.5	0	G|0.995;A|0.005	0.005	strong	.	SPTA1	720	.	NM_003126	exon22	c.C3149T	p.P1050L	TTTCCTGGCTCTT	.	PASS	Atlas-SNP
DACT1	51339	hgsc.bcm.edu	37	14	59112732	59112732	+	Missense_Mutation	SNP	C	C	T	rs17832998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	17	17	0	0.515152	0	C|0.713;T|0.287	0.287	strong	.	DACT1	119	.	NM_016651	exon4	c.C1391T	p.A464V	AACATGCTCGGTG	.	PASS	Atlas-SNP
KRT4	3851	hgsc.bcm.edu	37	12	53207628	53207628	+	Missense_Mutation	SNP	G	G	A	rs2638525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	84	0	0.522388	0	G|0.795;A|0.205	0.205	strong	.	KRT4	110	.	NM_002272	exon1	c.C215T	p.A72V	AAGCAGGCACCTT	.	PASS	Atlas-SNP
SEMA6A	57556	hgsc.bcm.edu	37	5	115827506	115827506	+	Silent	SNP	G	G	A	rs34096390	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	91	153	1	0.399123	0.00653595	G|0.979;A|0.021	0.021	strong	SEMA6A,NS,carcinoma,-2,1	SEMA6A	93	1	NM_020796	exon7	c.C465T	p.F155F	ATCCCCGAATGGT	.	scavenged	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160735775	160735775	+	Missense_Mutation	SNP	C	C	T	rs77761086	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	35	117	0	0.380435	0	C|0.994;T|0.006	0.006	strong	.	LY75	151	.	NM_002349	exon9	c.G1510A	p.D504N	CCTCATCTGGAGG	.	PASS	Atlas-SNP
SENP5	205564	hgsc.bcm.edu	37	3	196613075	196613075	+	Silent	SNP	C	C	T	rs34533379	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	81	0	1	0	C|0.751;T|0.249	0.249	strong	.	SENP5	68	.	NM_152699	exon2	c.C1023T	p.D341D	TTTAGACGAAGCA	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52636843	52636843	+	Silent	SNP	G	G	A	rs10564	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	44	95	0	0.517647	0	G|0.964;A|0.036	0.036	strong	KRT7,colon,carcinoma,+1,1	KRT7	48	1	NM_005556	exon6	c.G906A	p.R302R	CCTCCGGAATACC	.	PASS	Atlas-SNP
RCBTB1	55213	hgsc.bcm.edu	37	13	50123622	50123622	+	Silent	SNP	G	G	C	rs3751384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	90	100	0	0.978261	0	G|0.453;C|0.547	0.547	strong	.	RCBTB1	34	.	NM_018191	exon9	c.C1017G	p.P339P	GACGGCGGGAGTG	.	PASS	Atlas-SNP
DIS3L2	129563	hgsc.bcm.edu	37	2	232995462	232995462	+	Silent	SNP	A	A	G	rs75061164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	72	121	0	0.533333	0	A|0.984;G|0.016	0.016	strong	.	DIS3L2	77	.	NM_001257282	exon7	c.A735G	p.Q245Q	TGTCCAAATGGCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511212	195511212	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	269	11	760	4	0.0408922	0.00526316	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7239G	p.H2413Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31526531	31526531	+	Missense_Mutation	SNP	G	G	A	rs77034974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	103	200	0	0.451754	0	G|0.974;A|0.026	0.026	strong	.	DROSHA	130	.	NM_013235	exon4	c.C509T	p.P170L	TAGCCCGGAGGGT	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4952511	4952511	+	Missense_Mutation	SNP	C	C	T	rs115478590	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	90	128	0	0.5625	0	C|0.996;T|0.004	0.004	strong	.	PPL	168	.	NM_002705	exon4	c.G334A	p.E112K	CACGCTCCTTCAG	.	PASS	Atlas-SNP
CAMSAP3	57662	hgsc.bcm.edu	37	19	7682267	7682267	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	3	78	0	0.0340909	0	.	.	none	KIAA1543,NS,carcinoma,0,3	CAMSAP3	131	3	NM_001080429	exon17	c.C3349T	p.R1117W	CGCGAACGGGACT	.	scavenged	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167097739	167097739	+	Missense_Mutation	SNP	C	C	A	rs2281959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	31	72	0	0.525424	0	C|0.639;A|0.361	0.361	strong	.	DUSP27	235	.	NM_001080426	exon5	c.C3371A	p.T1124N	GAAGCACTGACAG	.	PASS	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	37	4	31144189	31144189	+	Silent	SNP	C	C	T	rs148629328	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	54	102	0	0.473684	0	C|0.997;T|0.003	0.003	strong	.	PCDH7	215	.	NM_001173523	exon3	c.C3486T	p.R1162R	GGTCCGCACTTCT	.	PASS	Atlas-SNP
WNK4	65266	hgsc.bcm.edu	37	17	40947163	40947163	+	Silent	SNP	G	G	A	rs2290042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	139	337	0	0.505455	0	G|0.918;A|0.082	0.082	strong	.	WNK4	182	.	NM_032387	exon14	c.G2724A	p.P908P	TCCTCCGTGCCCC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88783449	88783449	+	Silent	SNP	C	C	G	rs8057031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	85	98	0	1	0	C|0.318;G|0.682	0.682	strong	.	PIEZO1	79	.	NM_001142864	exon45	c.G6642C	p.L2214L	CAGCTTCAGGGTG	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115392919	115392919	+	Missense_Mutation	SNP	T	T	A	rs2270182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	103	214	0	0.504902	0	T|0.718;A|0.282	0.282	strong	.	NRAP	208	.	NM_001261463	exon16	c.A1556T	p.N519I	AACTTATTTTTCT	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113941002	113941002	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	3	176	0	0.0131004	0	.	.	none	PSD4,NS,carcinoma,+2,1	PSD4	74	1	NM_012455	exon2	c.C969T	p.P323P	TGTGCCCATCTAT	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78925716	78925716	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	3	92	0	0.0306122	0	.	.	none	PCSK5_ENST00000545128,NS,carcinoma,-1,2	PCSK5	329	2	NM_001190482	exon29	c.C3752T	p.P1251L	TGCAGCCGGGCCA	.	scavenged	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55817676	55817676	+	Silent	SNP	G	G	A	rs12973169	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	35	72	0	0.432099	0	G|0.889;A|0.111	0.111	strong	.	BRSK1	192	.	NM_032430	exon17	c.G1947A	p.K649K	GTACAAGGCCAGT	.	PASS	Atlas-SNP
ROCK2	9475	hgsc.bcm.edu	37	2	11484212	11484212	+	Silent	SNP	C	C	A	rs368832806		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	35	28	0	0.660377	0	.	.	weak	ROCK2_ENST00000315872,NS,carcinoma,-2,2	ROCK2	224	2	NM_004850	exon1	c.G51T	p.A17A	CCCCGGCGCGGTC	.	PASS	Atlas-SNP
ZNF610	162963	hgsc.bcm.edu	37	19	52869312	52869312	+	Silent	SNP	T	T	C	rs162120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	139	206	0	1	0	T|0.181;C|0.819	0.819	strong	.	ZNF610	84	.	NM_001161426	exon6	c.T681C	p.T227T	CCATACTGCAGAG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92538351	92538351	+	Silent	SNP	C	C	T	rs56843577	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	81	172	0	0.455056	0	C|0.988;T|0.012	0.012	strong	.	FAT3	1822	.	NM_001008781	exon10	c.C8929T	p.L2977L	CTGGGCCTGGTGC	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78032677	78032677	+	Silent	SNP	C	C	T	rs61734950	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	60	122	0	0.582524	0	C|0.972;T|0.028	0.028	strong	.	CCDC40	198	.	NM_017950	exon9	c.C1338T	p.L446L	CCAGCTCACCACT	.	PASS	Atlas-SNP
NEURL4	84461	hgsc.bcm.edu	37	17	7226082	7226082	+	Silent	SNP	G	G	A	rs116452797	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	52	72	0	0.52	0	G|0.999;A|0.001	0.001	strong	.	NEURL4	192	.	NM_032442	exon16	c.C2697T	p.T899T	CTTCTCGGTGGCA	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801418	27801418	+	Missense_Mutation	SNP	C	C	A	rs1919126	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	282	293	0	1	0	C|0.365;A|0.635	0.635	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1979A	p.A660E	AGTCTGCAGAATT	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27462651	27462651	+	Silent	SNP	T	T	C	rs61741874	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	45	84	0	0.529412	0	A|0.000;C|0.070;G|0.000;T|0.929	0.070	strong	.	CAD	199	.	NM_004341	exon34	c.T5481C	p.T1827T	TGCCACTAGTGAG	.	PASS	Atlas-SNP
RDX	5962	hgsc.bcm.edu	37	11	110118459	110118459	+	Silent	SNP	T	T	C	rs139953187	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	99	193	0	0.607362	0	T|0.989;C|0.011	0.011	strong	.	RDX	59	.	NM_001260493	exon10	c.A1059G	p.Q353Q	TTCAATTTGTTTT	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31409252	31409252	+	Silent	SNP	A	A	G	rs2241337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	110	219	0	0.443548	0	A|0.696;G|0.304	0.304	strong	.	DROSHA	130	.	NM_013235	exon32	c.T3765C	p.N1255N	ATCCTGATTCAAA	.	PASS	Atlas-SNP
CP	1356	hgsc.bcm.edu	37	3	148901300	148901300	+	Missense_Mutation	SNP	C	C	T	rs115552500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	83	0	0.522388	0	C|0.987;T|0.013	0.013	strong	.	CP	112	.	NM_000096	exon13	c.G2378A	p.R793H	GGAACACGGAATG	.	PASS	Atlas-SNP
MRPL46	26589	hgsc.bcm.edu	37	15	89002888	89002888	+	Missense_Mutation	SNP	G	G	T	rs146290179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	53	114	0	0.434426	0	G|1.000;T|0.000	0.000	weak	.	MRPL46	13	.	NM_022163	exon4	c.C796A	p.P266T	ATTTTGGTTTCAA	.	PASS	Atlas-SNP
MASP2	10747	hgsc.bcm.edu	37	1	11106648	11106648	+	Missense_Mutation	SNP	G	G	A	rs56392418	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	50	109	0	0.384615	0	G|0.964;A|0.036	0.036	strong	.	MASP2	71	.	NM_139208	exon3	c.C377T	p.P126L	GTGAACGGCTTCT	.	PASS	Atlas-SNP
FUT4	2526	hgsc.bcm.edu	37	11	94278713	94278713	+	Silent	SNP	C	C	T	rs2230274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	47	156	0	0.408696	0	C|0.940;T|0.060	0.060	strong	FUT4,NS,carcinoma,0,1	FUT4	17	1	NM_002033	exon1	c.C1414T	p.L472L	TCGTACCTGCTTT	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622563	121622563	+	Silent	SNP	G	G	A	rs1621388	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	55	98	0	0.528846	0	G|0.649;A|0.351	0.351	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon13	c.G1746A	p.P582P	GTTTCCGAAGAGT	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53504721	53504721	+	Silent	SNP	T	T	C	rs10748	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	133	134	0	1	0	T|0.470;C|0.530	0.530	strong	.	RBL2	115	.	NM_005611	exon17	c.T2590C	p.L864L	GATGAATTGAGGA	.	PASS	Atlas-SNP
TCF7L1	83439	hgsc.bcm.edu	37	2	85510654	85510654	+	Missense_Mutation	SNP	T	T	A	rs115942112	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	57	106	0	0.435115	0	T|0.989;A|0.011	0.011	strong	.	TCF7L1	44	.	NM_031283	exon4	c.T478A	p.S160T	GTCCCCTCCAGCG	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30955043	30955043	+	Missense_Mutation	SNP	G	G	A	rs9262385	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	10	152	4	0.0540541	0.0263158	G|0.992;A|0.008	0.008	strong	MUC21,NS,neuroblastoma,0,1	MUC21	98	1	NM_001010909	exon2	c.G1091A	p.G364E	ACTCTGGGTCCAG	.	scavenged	Atlas-SNP
NUAK2	81788	hgsc.bcm.edu	37	1	205273142	205273142	+	Silent	SNP	G	G	C	rs41264881	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	73	106	0	0.579365	0	G|0.874;C|0.126	0.126	strong	NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	NM_030952	exon7	c.C1323G	p.P441P	GAGCAGGGGGGCA	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	37	4	438067	438067	+	Silent	SNP	C	C	T	rs73070365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	58	139	0	0.414286	0	C|0.943;T|0.057	0.057	strong	.	ZNF721	205	.	NM_133474	exon3	c.A189A	p.V63V	AACTCCCTTCTGC	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6267523	6267523	+	Silent	SNP	C	C	T	rs58587405	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	152	214	0	0.517007	0	C|0.966;T|0.034	0.034	strong	.	RNF207	45	.	NM_207396	exon3	c.C276T	p.G92G	GGATGGCGTGGAG	.	PASS	Atlas-SNP
ASB2	51676	hgsc.bcm.edu	37	14	94401102	94401102	+	Missense_Mutation	SNP	C	C	T	rs35858830	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	41	96	0	0.465909	0	C|0.985;T|0.015	0.015	strong	.	ASB2	71	.	NM_001202429	exon10	c.G1808A	p.R603Q	CGAACCCGCAGTC	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21011346	21011346	+	Silent	SNP	A	A	G	rs12028811	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	91	206	1	0.452736	0.00485437	A|0.831;G|0.169	0.169	strong	KIF17,caecum,carcinoma,-1,1	KIF17	130	1	NM_001122819	exon10	c.T2187C	p.T729T	GTCATCAGTCAGC	.	scavenged	Atlas-SNP
CCDC92	80212	hgsc.bcm.edu	37	12	124421764	124421764	+	Silent	SNP	C	C	T	rs34241686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	10	13	0	0.454545	0	C|0.996;T|0.004	0.004	strong	.	CCDC92	18	.	NM_025140	exon5	c.G837A	p.P279P	GCGGGCCGGGCTG	.	PASS	Atlas-SNP
MICALL1	85377	hgsc.bcm.edu	37	22	38302469	38302469	+	Missense_Mutation	SNP	C	C	T	rs146549351	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	4	4	5	0	1	0	C|0.942;T|0.058	0.058	strong	.	MICALL1	53	.	NM_033386	exon1	c.C40T	p.R14C	TGCCGCCGCCAGT	.	PASS	Atlas-SNP
PAQR5	54852	hgsc.bcm.edu	37	15	69682021	69682021	+	Silent	SNP	G	G	A	rs12438855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	86	173	0	0.49711	0	G|0.960;A|0.040	0.040	strong	PAQR5,caecum,carcinoma,+1,1	PAQR5	35	1	NM_001104554	exon6	c.G414A	p.T138T	ATACACGTTCCCG	.	PASS	Atlas-SNP
IGLL1	3543	hgsc.bcm.edu	37	22	23917176	23917176	+	Silent	SNP	G	G	A	rs115303391	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	72	110	0	0.467532	0	G|0.965;A|0.035	0.035	strong	.	IGLL1	27	.	NM_020070	exon2	c.C300T	p.S100S	GGTCCCGCTGCCA	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117248218	117248218	+	Silent	SNP	T	T	C	rs611349	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	60	106	0	0.508475	0	T|0.757;C|0.243	0.243	strong	.	RFX6	141	.	NM_173560	exon17	c.T1914C	p.G638G	TGCTGGTCATCTG	.	PASS	Atlas-SNP
MED14	9282	hgsc.bcm.edu	37	X	40551993	40551993	+	Silent	SNP	G	G	A	rs10127014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	128	178	0	0.542373	0	G|0.966;A|0.034	0.034	strong	.	MED14	108	.	NM_004229	exon14	c.C1812T	p.T604T	TTTCCCGGTTTTT	.	PASS	Atlas-SNP
HAPLN2	60484	hgsc.bcm.edu	37	1	156593928	156593928	+	Missense_Mutation	SNP	G	G	T	rs149573918	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	99	170	0	0.464789	0	G|0.986;T|0.014	0.014	strong	.	HAPLN2	20	.	NM_021817	exon4	c.G415T	p.V139L	GAGAGCGTGGCGC	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31276811	31276811	+	Missense_Mutation	SNP	G	G	A	rs1143679	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	50	115	0	0.434783	0	G|0.914;A|0.086	0.086	strong	.	ITGAM	137	.	NM_000632	exon3	c.G230A	p.R77H	CCATCCGCCTGCA	.	PASS	Atlas-SNP
GUCA1C	9626	hgsc.bcm.edu	37	3	108627024	108627024	+	Missense_Mutation	SNP	T	T	C	rs16854916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	52	101	0	0.452174	0	T|0.982;C|0.018	0.018	strong	.	GUCA1C	39	.	NM_005459	exon4	c.A475G	p.M159V	TTGCCATGCCATT	.	PASS	Atlas-SNP
C16orf82	162083	hgsc.bcm.edu	37	16	27078547	27078547	+	Silent	SNP	G	G	C	rs114049498	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	28	61	0	0.424242	0	G|0.968;C|0.032	0.032	strong	.	.	.	.	NM_001145545	exon1	c.G231C	p.P77P	GCACCCGAGGCCA	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61722645	61722645	+	Silent	SNP	C	C	A	rs1109748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	68	155	0	0.503704	0	C|0.838;A|0.162	0.162	strong	.	BEST1	85	.	NM_004183	exon3	c.C219A	p.I73I	CTACATCCAGCTC	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227348245	227348245	+	Missense_Mutation	SNP	G	G	A	rs34614709	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	136	311	0	0.445902	0	G|0.995;A|0.005	0.005	strong	.	CDC42BPA	528	.	NM_003607	exon6	c.C692T	p.T231M	TTTACCGTTCCAT	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	567	22	953	2	0.0388007	0.00209864	C|0.840;T|0.160	0.160	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.C408T	p.Y136Y	CTTCTACGTGACA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515025	195515025	+	Silent	SNP	A	A	G	rs199975352	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	438	161	136	1	0.36758	0.00735294	A|0.960;G|0.040	0.040	strong	MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	NM_018406	exon2	c.T3426C	p.T1142T	TGAGGAAGTGTCG	.	scavenged	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171553209	171553209	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	133	254	0	0.488971	0	.	.	none	.	.	.	.	NM_015172	exon29	c.C7518T	p.S2506S	ACAATCCGGTCTT	.	PASS	Atlas-SNP
ALDH1L2	160428	hgsc.bcm.edu	37	12	105433523	105433523	+	Silent	SNP	T	T	A	rs4964317	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	85	155	0	0.578231	0	T|0.687;A|0.313	0.313	strong	.	ALDH1L2	71	.	NM_001034173	exon17	c.A2013T	p.G671G	AGTGGATCCAGTG	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	37	12	1965369	1965369	+	Silent	SNP	G	G	A	rs2286372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	49	108	0	0.597561	0	G|0.840;A|0.160	0.160	strong	.	CACNA2D4	220	.	NM_172364	exon21	c.C2035T	p.L679L	GGGCCAGGTCTGG	.	PASS	Atlas-SNP
EFCAB12	90288	hgsc.bcm.edu	37	3	129137245	129137245	+	Missense_Mutation	SNP	T	T	G	rs116798859	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	41	72	0	0.602941	0	T|0.975;G|0.025	0.025	strong	.	.	.	.	NM_207307	exon3	c.A533C	p.Q178P	TGGAGCTGGGGCA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17303774	17303774	+	Missense_Mutation	SNP	T	T	G	rs1545620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	44	39	0	0.977778	0	T|0.363;G|0.637	0.637	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon21	c.T3031G	p.S1011A	CAGGCCTCATGGA	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111641825	111641825	+	Missense_Mutation	SNP	G	G	A	rs1538660	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	202	144	222	1	0.712871	0.0045045	G|0.773;A|0.227	0.227	strong	.	IKBKAP	122	.	NM_003640	exon33	c.C3473T	p.P1158L	CCGTGGGGTACCT	.	PASS	Atlas-SNP
GPC4	2239	hgsc.bcm.edu	37	X	132438872	132438872	+	Missense_Mutation	SNP	C	C	A	rs1129980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	47	125	0	0.38843	0	C|0.574;A|0.426	0.426	strong	.	GPC4	58	.	NM_001448	exon7	c.G1173T	p.E391D	CAGTTTCTCCTTG	.	PASS	Atlas-SNP
ZCCHC18	644353	hgsc.bcm.edu	37	X	103359334	103359334	+	Missense_Mutation	SNP	C	C	T	rs61745269	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	148	314	0	0.571429	0	C|0.962;T|0.038	0.038	strong	.	.	.	.	NM_001143978	exon3	c.C532T	p.L178F	CAACAGCTTCTTT	.	PASS	Atlas-SNP
PPFIBP1	8496	hgsc.bcm.edu	37	12	27842052	27842052	+	Silent	SNP	G	G	A	rs61730962	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	84	137	0	0.502994	0	G|0.949;A|0.051	0.051	strong	.	PPFIBP1	153	.	NM_177444	exon26	c.G2619A	p.L873L	CCTTCTGATTGGG	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8518143	8518143	+	Silent	SNP	T	T	C	rs7026388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	250	144	217	0	0.576	0	C|0.268;N|0.000	0.268	strong	.	PTPRD	1348	.	NM_130392	exon10	c.A1248G	p.A416A	GGATGGTGCTTGC	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57378149	57378149	+	Missense_Mutation	SNP	G	G	T	rs1620075	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	109	179	1	0.5	0.00558659	T|0.096;G|0.903;A|0.001	0.096	strong	C8A,NS,carcinoma,+1,1	C8A	103	1	NM_000562	exon10	c.G1454T	p.R485L	TGCGCCGCGCCTT	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	495	20	446	0	0.040404	0	C|0.996;G|0.003;T|0.001	0.003	strong	FLG,right_upper_lobe,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.G6748C	p.E2250Q	GTCCCTCACTGTC	.	scavenged	Atlas-SNP
ARMC1	55156	hgsc.bcm.edu	37	8	66517549	66517549	+	Silent	SNP	T	T	C	rs16932266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	103	190	0	0.533679	0	T|0.984;C|0.016	0.016	strong	.	ARMC1	22	.	NM_018120	exon6	c.A606G	p.S202S	CTTGGTTGATGCT	.	PASS	Atlas-SNP
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857798	140857798	+	Silent	SNP	T	T	C	rs1423148	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	90	90	0	1	0	A|0.002;C|0.545	0.545	strong	.	PCDHGC3	173	.	NM_032402	exon1	c.T2115C	p.F705F	GGGGTTTGTGGTC	.	PASS	Atlas-SNP
SNAP23	8773	hgsc.bcm.edu	37	15	42820589	42820589	+	Silent	SNP	G	G	A	rs1060291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	41	91	0	0.493976	0	G|0.678;A|0.322	0.322	strong	SNAP23,colon,carcinoma,+1,1	SNAP23	15	1	NM_003825	exon6	c.G396A	p.T132T	AACAACGGGAGCA	.	PASS	Atlas-SNP
SFXN4	119559	hgsc.bcm.edu	37	10	120920588	120920588	+	Silent	SNP	T	T	C	rs10749291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	80	0	0.448718	0	T|0.515;C|0.485	0.485	strong	.	SFXN4	24	.	NM_213649	exon4	c.A258G	p.Q86Q	AGCTTCTTGTATC	.	PASS	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170684548	170684548	+	Silent	SNP	G	G	A	rs79036304	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	16	9	26	0	0.5625	0	G|0.940;A|0.060	0.060	strong	.	UBR3	182	.	NM_172070	exon1	c.G531A	p.V177V	CAACGTGATGCGG	.	PASS	Atlas-SNP
ZSWIM3	140831	hgsc.bcm.edu	37	20	44506418	44506418	+	Silent	SNP	G	G	A	rs1045493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	56	101	0	0.424242	0	G|0.506;A|0.494	0.494	strong	.	ZSWIM3	96	.	NM_080752	exon2	c.G1221A	p.R407R	CTTTCGGGAACAG	.	PASS	Atlas-SNP
HSPA8	3312	hgsc.bcm.edu	37	11	122931337	122931337	+	Silent	SNP	T	T	C	rs147610984	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	56	118	0	0.424242	0	T|0.989;C|0.011	0.011	strong	.	HSPA8	168	.	NM_006597	exon3	c.A375G	p.T125T	CATCTTTGTCAGA	.	PASS	Atlas-SNP
SLC22A5	6584	hgsc.bcm.edu	37	5	131721174	131721174	+	Silent	SNP	A	A	G	rs274558	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	71	173	0	0.482993	0	A|0.579;G|0.421	0.421	strong	.	SLC22A5	34	.	NM_003060	exon4	c.A807G	p.L269L	GGTGCTATGCGTG	.	PASS	Atlas-SNP
COQ5	84274	hgsc.bcm.edu	37	12	120954490	120954490	+	Missense_Mutation	SNP	C	C	T	rs3742049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	68	171	2	0.357895	0.0116959	C|0.846;T|0.154	0.154	strong	COQ5,NS,carcinoma,0,1	COQ5	26	1	NM_032314	exon3	c.G454A	p.A152T	CTTTGGCAATTTC	.	scavenged	Atlas-SNP
NOL9	79707	hgsc.bcm.edu	37	1	6614230	6614230	+	Silent	SNP	G	G	A	rs10864625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	33	59	0	0.478261	0	G|0.815;A|0.185	0.185	strong	.	NOL9	49	.	NM_024654	exon1	c.C333T	p.L111L	GATGAGGAGAGGC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	974	509	482	1	0.522587	0.00207469	A|0.030;G|0.970	0.970	strong	FLG,brain,glioma,+2,1	FLG	900	1	NM_002016	exon3	c.T6355C	p.Y2119H	GATCATAATGGGA	.	PASS	Atlas-SNP
ZNF433	163059	hgsc.bcm.edu	37	19	12127370	12127370	+	Silent	SNP	G	G	A	rs79787738	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	72	167	0	0.447205	0	G|0.994;A|0.006	0.006	strong	.	ZNF433	49	.	NM_001080411	exon4	c.C312T	p.C104C	GCTTTCGCATGAT	.	PASS	Atlas-SNP
VEGFA	7422	hgsc.bcm.edu	37	6	43738977	43738977	+	Silent	SNP	C	C	T	rs25648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	21	21	0	0.456522	0	C|0.876;T|0.124	0.124	strong	.	VEGFA	21	.	NM_001171622	exon1	c.C534T	p.S178S	GGCCTCCGAAACC	.	PASS	Atlas-SNP
ADCY8	114	hgsc.bcm.edu	37	8	132002770	132002770	+	Silent	SNP	G	G	A	rs2228950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	36	79	0	0.571429	0	G|0.701;A|0.299	0.299	strong	.	ADCY8	291	.	NM_001115	exon2	c.C979T	p.L327L	TGAATAGCACTGC	.	PASS	Atlas-SNP
SYNGAP1	8831	hgsc.bcm.edu	37	6	33408542	33408542	+	Silent	SNP	G	G	A	rs411136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	32	76	0	0.405063	0	G|0.608;A|0.392	0.392	strong	SYNGAP1_ENST00000293748,NS,carcinoma,0,2	SYNGAP1	202	2	NM_006772	exon11	c.G1713A	p.S571S	TGCTTCGTGGCGG	.	PASS	Atlas-SNP
TBC1D9	23158	hgsc.bcm.edu	37	4	141600320	141600320	+	Silent	SNP	A	A	G	rs4956329	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	65	91	0	0.52	0	A|0.352;G|0.648	0.648	strong	.	TBC1D9	198	.	NM_015130	exon5	c.T627C	p.L209L	CTTCTCAAGCTGA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149486294	149486294	+	Missense_Mutation	SNP	A	A	G	rs855691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	47	58	0	0.580247	0	T|0.003;G|0.087	0.087	strong	.	.	.	.	NM_198455	exon30	c.A4270G	p.S1424G	ACTTGCAGCTCCG	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971478	57971478	+	Missense_Mutation	SNP	A	A	G	rs11229281	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	398	181	391	0	0.454774	0	A|0.913;G|0.087	0.087	strong	.	OR1S2	119	.	NM_001004459	exon1	c.T176C	p.I59T	GCCACAATGATGA	.	PASS	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	37	19	37697988	37697988	+	Missense_Mutation	SNP	T	T	C	rs145040657	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	39	76	0	0.506494	0	T|1.000;C|0.000	0.000	strong	.	ZNF585B	91	.	NM_152279	exon2	c.A26G	p.Q9R	GATTTCTGGGGTG	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18237661	18237661	+	Silent	SNP	C	C	T	rs1013062	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	215	115	224	0	0.534884	0	C|0.837;T|0.163	0.163	strong	.	DEK	31	.	NM_003472	exon8	c.G849A	p.K283K	TGCTTTCTTAACA	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123801856	123801856	+	Silent	SNP	T	T	C	rs61751328	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	73	152	0	0.486667	0	T|0.907;C|0.093	0.093	strong	.	SBNO1	138	.	NM_001167856	exon20	c.A2847G	p.Q949Q	ATCTGCTTGTAAT	.	PASS	Atlas-SNP
EOMES	8320	hgsc.bcm.edu	37	3	27758756	27758756	+	Silent	SNP	G	G	A	rs6783101	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	99	197	0	0.466981	0	G|0.963;A|0.037	0.037	strong	.	EOMES	65	.	NM_005442	exon6	c.C1866T	p.P622P	GGAAGGGGGTGTC	.	PASS	Atlas-SNP
RAET1E	135250	hgsc.bcm.edu	37	6	150210681	150210681	+	Missense_Mutation	SNP	G	G	A	rs9371533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	118	248	0	0.435424	0	G|0.403;A|0.597	0.597	strong	RAET1E,NS,carcinoma,+1,2	RAET1E	20	2	NM_139165	exon3	c.C425T	p.T142I	CCATTGGTGGCGA	.	PASS	Atlas-SNP
COG7	91949	hgsc.bcm.edu	37	16	23403744	23403744	+	Silent	SNP	A	A	G	rs8057712	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	59	127	0	0.44697	0	A|0.910;G|0.090	0.090	strong	COG7,NS,malignant_melanoma,-2,1	COG7	62	1	NM_153603	exon16	c.T2103C	p.P701P	CAGCTCAGGGATC	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117392110	117392110	+	Silent	SNP	A	A	G	rs35503235	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	28	85	0	0.35	0	A|0.969;G|0.031	0.031	strong	.	DSCAML1	286	.	NM_020693	exon6	c.T1128C	p.H376H	GGTCACATGAAGG	.	PASS	Atlas-SNP
PPIAL4G	644591	hgsc.bcm.edu	37	1	143767730	143767730	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1225	155	1116	0	0.126531	0	.	.	none	.	PPIAL4G	22	.	NM_001123068	exon1	c.G119A	p.S40N	CCAGTGCTCAGAG	.	PASS	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	33	51	0	0.52381	0	G|0.746;A|0.254	0.254	strong	TMEM204,NS,carcinoma,0,1	TMEM204	29	1	NM_024600	exon2	c.G321A	p.T107T	GGCCACGGCCGCG	.	PASS	Atlas-SNP
OR6B1	135946	hgsc.bcm.edu	37	7	143701516	143701516	+	Missense_Mutation	SNP	C	C	T	rs7787378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	83	151	0	0.471591	0	C|0.853;N|0.000	.	strong	OR6B1,NS,carcinoma,-1,3	OR6B1	60	3	NM_001005281	exon1	c.C427T	p.R143C	TGCTTCCGCCTCG	.	PASS	Atlas-SNP
GRM8	2918	hgsc.bcm.edu	37	7	126173902	126173902	+	Missense_Mutation	SNP	G	G	C	rs61753365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	54	99	1	0.486486	0.010101	G|0.968;C|0.032	0.032	strong	GRM8,NS,carcinoma,+2,1	GRM8	377	1	NM_000845	exon8	c.C1534G	p.P512A	ACGCCGGGTGAGT	.	scavenged	Atlas-SNP
ZNF331	55422	hgsc.bcm.edu	37	19	54080999	54080999	+	Silent	SNP	A	A	G	rs1056393	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	79	117	0	0.526667	0	A|0.890;G|0.110	0.110	strong	.	ZNF331	66	.	NM_001253801	exon5	c.A1185G	p.G395G	TTATGGATCGAGC	.	PASS	Atlas-SNP
TMEM64	169200	hgsc.bcm.edu	37	8	91638019	91638019	+	Silent	SNP	T	T	C	rs61741096	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	68	156	0	0.450331	0	T|0.996;C|0.004	0.004	strong	.	TMEM64	31	.	NM_001008495	exon3	c.A1023G	p.V341V	ACAAGCTACAATA	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38800164	38800164	+	Missense_Mutation	SNP	G	G	A	rs9357283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	46	101	0	0.393162	0	G|0.840;A|0.160	0.160	strong	DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	NM_001206927	exon31	c.G4255A	p.E1419K	TCTGTGGAAGTTT	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47087371	47087371	+	Silent	SNP	G	G	A	rs1048156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	125	170	0	0.462963	0	G|0.870;A|0.130	0.130	strong	PPYR1,mouth,carcinoma,0,1	PPYR1	54	1	NM_005972	exon3	c.G588A	p.A196A	CCTGGCGGATAAG	.	PASS	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	37	19	54803504	54803504	+	Missense_Mutation	SNP	A	A	C	rs6509862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	90	165	0	0.523256	0	A|0.646;C|0.354	0.354	strong	.	LILRA3	65	.	NM_001172654	exon3	c.T320G	p.L107R	TCTGAGAGGCCTG	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694613	139694613	+	Missense_Mutation	SNP	C	C	A	rs35342663	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	9	6	0	0.818182	0	C|0.929;A|0.071	0.071	strong	.	KIAA1984	39	.	NM_001039374	exon4	c.C430A	p.L144M	CTGCGGCTGCTGC	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640893	3640893	+	Missense_Mutation	SNP	C	C	A	rs79448721	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	343	168	308	0	0.489796	0	C|0.990;A|0.010	0.010	strong	.	SLX4	173	.	NM_032444	exon12	c.G2746T	p.A916S	TGGCGGCCTCATC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73377069	73377069	+	Silent	SNP	C	C	T	rs7903475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	52	112	0	0.481481	0	C|0.932;T|0.068	0.068	strong	.	CDH23	365	.	NM_052836	exon11	c.C1053T	p.S351S	CAGCTCCGAGTAC	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765161	66765161	+	Missense_Mutation	SNP	A	A	T	rs200185441		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	6	62	0	0.0857143	0	.	.	weak	.	AR	249	.	NM_000044	exon1	c.A173T	p.Q58L	TGCTGCAGCAGCA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058968	79058968	+	Silent	SNP	T	T	C	rs112827102	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	69	212	2	0.985714	0.00943396	T|0.935;C|0.065	0.065	strong	.	ADAMTS7	142	.	NM_014272	exon19	c.A3285G	p.T1095T	TGGGGGTGTCCGG	.	PASS	Atlas-SNP
STARD8	9754	hgsc.bcm.edu	37	X	67938392	67938392	+	Missense_Mutation	SNP	C	C	T	rs58255923	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	75	156	0	0.510204	0	C|0.955;T|0.045	0.045	strong	.	STARD8	282	.	NM_001142503	exon6	c.C1636T	p.P546S	GCGGGGCCCCTGG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971023	45971023	+	Missense_Mutation	SNP	G	G	T	rs478967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	317	125	216	0	0.394322	0	G|0.811;T|0.189	0.189	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C319A	p.P107T	ACACAGGCTTGCA	.	PASS	Atlas-SNP
CS	1431	hgsc.bcm.edu	37	12	56676233	56676233	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	265	18	305	0	0.0679245	0	.	.	none	CS,NS,adenoma,+1,1	CS	44	1	NM_004077	exon6	c.C559T	p.Q187X	TACCCTGTGCATA	.	scavenged	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84492984	84492984	+	Silent	SNP	G	G	A	rs7187624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	49	122	0	0.418803	0	G|0.981;A|0.019	0.019	strong	.	ATP2C2	75	.	NM_014861	exon23	c.G2325A	p.P775P	GCCACCGGCGCAG	.	PASS	Atlas-SNP
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	99	214	0	0.540984	0	C|0.483;G|0.517	0.517	strong	MAT2A,NS,carcinoma,0,1	MAT2A	23	1	NM_005911	exon7	c.C792G	p.R264R	TGGACGCAAAATC	.	PASS	Atlas-SNP
ALG1	56052	hgsc.bcm.edu	37	16	5129756	5129756	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	402	26	344	9	0.0646766	0.0261628	.	.	none	ALG1,NS,carcinoma,0,3	ALG1	35	3	NM_019109	exon9	c.A909G	p.E303E	GTTTGAACAACTG	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149526071	149526071	+	Missense_Mutation	SNP	G	G	A	rs142321773	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	56	129	0	0.491228	0	G|0.997;A|0.003	0.003	strong	.	.	.	.	NM_198455	exon107	c.G15125A	p.R5042H	CTTGCCGCAGGGA	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	37	14	36191030	36191030	+	Silent	SNP	A	A	G	rs2296168	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	49	119	0	0.453704	0	A|0.890;G|0.110	0.110	strong	.	RALGAPA1	289	.	NM_194301	exon16	c.T2130C	p.V710V	AACTGAAACTTTC	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85435742	85435742	+	Silent	SNP	C	C	T	rs146372321	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	47	117	0	0.401709	0	C|0.995;T|0.005	0.005	strong	.	SYTL2	231	.	NM_206927	exon1	c.G1758A	p.K586K	CTCGGCCTTTTCT	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71347060	71347060	+	Missense_Mutation	SNP	A	A	C	rs74904873	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	552	12	501	9	0.0217391	0.0179641	A|0.500;C|0.500	0.500	strong	MUC7,pharynx,carcinoma,0,1	MUC7	91	1	NM_001145007	exon4	c.A599C	p.Q200P	CTACACAAGCTCC	.	scavenged	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18368748	18368748	+	Missense_Mutation	SNP	C	C	T	rs61740685	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	40	99	0	0.47619	0	C|0.999;T|0.001	0.001	strong	.	KIAA1683	190	.	NM_001145304	exon4	c.G3346A	p.A1116T	TCACTGCGAGGAT	.	PASS	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37028762	37028762	+	Missense_Mutation	SNP	C	C	G	rs61730910	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	80	123	0	0.533333	0	C|0.993;G|0.007	0.007	strong	.	FAM47C	267	.	NM_001013736	exon1	c.C2279G	p.S760C	GCGTATCTCATCT	.	PASS	Atlas-SNP
CAP1	10487	hgsc.bcm.edu	37	1	40535945	40535945	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	82	128	0	0.532468	0	.	.	none	.	CAP1	38	.	NM_006367	exon10	c.A1108G	p.I370V	AACTCCATTACAG	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133474286	133474286	+	Silent	SNP	A	A	G	rs8177226	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	77	99	0	0.596899	0	A|0.988;G|0.012	0.012	strong	.	TF	116	.	NM_001063	exon5	c.A582G	p.P194P	GTGTCCAGGGTGT	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249532	71249532	+	Missense_Mutation	SNP	C	C	G	rs11234084		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	9	158	0	0.0405405	0	.	.	weak	.	KRTAP5-8	28	.	NM_021046	exon1	c.C431G	p.S144C	GCTGTTCCCAGTC	.	PASS	Atlas-SNP
PROM1	8842	hgsc.bcm.edu	37	4	16020162	16020162	+	Silent	SNP	C	C	T	rs2286455	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	90	215	0	0.45	0	C|0.873;T|0.127	0.127	strong	.	PROM1	91	.	NM_006017	exon8	c.G786A	p.A262A	CTTGATCGCTATG	.	PASS	Atlas-SNP
SLA2	84174	hgsc.bcm.edu	37	20	35242745	35242745	+	Missense_Mutation	SNP	C	C	T	rs34834764	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	105	176	0	0.512195	0	C|0.968;T|0.032	0.032	strong	.	SLA2	12	.	NM_032214	exon7	c.G628A	p.V210M	TCTGCACAGTCAC	.	PASS	Atlas-SNP
ACP5	54	hgsc.bcm.edu	37	19	11685948	11685948	+	Silent	SNP	A	A	G	rs77911902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	80	163	0	0.506329	0	A|0.967;G|0.033	0.033	strong	.	ACP5	30	.	NM_001111034	exon6	c.T855C	p.T285T	GTCTTCAGTCCCA	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10445427	10445427	+	Silent	SNP	A	A	T	rs7694496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	56	106	0	0.54902	0	A|0.901;T|0.099	0.099	strong	ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	NM_053042	exon3	c.T2526A	p.P842P	CCGCAGAGGTGTC	.	PASS	Atlas-SNP
KHDC1	80759	hgsc.bcm.edu	37	6	74019338	74019338	+	Nonsense_Mutation	SNP	G	G	A	rs16883571	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	39	87	0	0.4875	0	G|0.934;A|0.066	0.066	strong	.	KHDC1	10	.	NM_001251874	exon1	c.C100T	p.Q34X	GGGTCTGGAGAAA	.	PASS	Atlas-SNP
HBEGF	1839	hgsc.bcm.edu	37	5	139722345	139722345	+	Silent	SNP	G	G	A	rs2074611	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	126	258	0	0.461538	0	T|0.002;G|0.881;C|0.008;A|0.110	0.110	strong	HBEGF,NS,carcinoma,0,1	HBEGF	12	1	NM_001945	exon3	c.C273T	p.H91H	TTTCCCGTGCTCC	.	PASS	Atlas-SNP
TSPEAR	54084	hgsc.bcm.edu	37	21	45929192	45929192	+	Silent	SNP	G	G	A	rs115847549	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	97	133	0	0.527174	0	G|0.988;A|0.012	0.012	strong	.	TSPEAR	110	.	NM_144991	exon10	c.C1644T	p.Y548Y	CACATCGTAGCTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48317708	48317708	+	Missense_Mutation	SNP	A	A	C	rs78334925	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	26	66	0	0.382353	0	A|0.900;C|0.100	0.100	strong	.	ABCA13	1192	.	NM_152701	exon18	c.A6917C	p.K2306T	AAGATAAAATTCT	.	PASS	Atlas-SNP
WNT9A	7483	hgsc.bcm.edu	37	1	228109696	228109696	+	Silent	SNP	G	G	A	rs112703157	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	30	69	0	0.357143	0	G|0.977;A|0.023	0.023	strong	.	WNT9A	39	.	NM_003395	exon4	c.C621T	p.I207I	AGCCTTGATCACC	.	PASS	Atlas-SNP
MAST4	375449	hgsc.bcm.edu	37	5	66461583	66461583	+	Silent	SNP	C	C	T	rs56201012	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	40	75	0	0.449438	0	C|0.990;T|0.010	0.010	strong	.	MAST4	218	.	NM_001164664	exon29	c.C6576T	p.H2192H	CAGCCACAAGCCC	.	PASS	Atlas-SNP
METRNL	284207	hgsc.bcm.edu	37	17	81043175	81043175	+	Missense_Mutation	SNP	G	G	T	rs72854240	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	79	179	0	0.470238	0	G|0.934;T|0.066	0.066	strong	METRNL,NS,carcinoma,0,2	METRNL	29	2	NM_001004431	exon2	c.G532T	p.A178S	CACAGGGCGTCGG	.	PASS	Atlas-SNP
PCDHA1	56147	hgsc.bcm.edu	37	5	140167520	140167520	+	Missense_Mutation	SNP	G	G	A	rs61743799	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	60	81	0	0.5	0	G|0.961;A|0.039	0.039	strong	.	PCDHA1	387	.	NM_031410	exon1	c.G1645A	p.V549M	AGCAACGTGACGC	.	PASS	Atlas-SNP
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329793	24329793	+	Missense_Mutation	SNP	C	C	T	rs139232512	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	223	129	194	0	0.578475	0	C|0.963;T|0.037	0.037	strong	.	.	.	.	NM_001136233	exon1	c.G1640A	p.R547H	GGACGGCGCCTGC	.	PASS	Atlas-SNP
PCDH8	5100	hgsc.bcm.edu	37	13	53419765	53419765	+	Silent	SNP	G	G	A	rs5030686	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	48	101	0	0.510638	0	G|0.945;A|0.055	0.055	strong	.	PCDH8	95	.	NM_002590	exon2	c.C2634T	p.P878P	ACCGTAGGGCTGC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	72	114	0	0.672897	0	T|0.445;C|0.555	0.555	strong	.	.	.	.	NM_020893	exon19	c.T2520C	p.C840C	GCATTGTAGGAAG	.	PASS	Atlas-SNP
KXD1	79036	hgsc.bcm.edu	37	19	18679351	18679351	+	Silent	SNP	C	C	T	rs11086117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	39	72	0	0.443182	0	A|0.000;C|0.852;G|0.000;T|0.148	0.148	strong	.	.	.	.	NM_001171948	exon6	c.C441T	p.P147P	GAGCCCCGGCTTC	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6709704	6709704	+	Silent	SNP	C	C	T	rs2230205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	136	149	0	0.978417	0	C|0.836;T|0.164	0.164	strong	.	C3	192	.	NM_000064	exon14	c.G1836A	p.T612T	ACTCTGCGTCAGT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74288422	74288422	+	Missense_Mutation	SNP	T	T	C	rs6501879	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	56	144	0	0.383562	0	T|0.675;C|0.325	0.325	strong	.	QRICH2	143	.	NM_032134	exon4	c.A1888G	p.I630V	GAACTATACCAGG	.	PASS	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156621251	156621251	+	Missense_Mutation	SNP	C	C	T	rs12065791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	26	35	0	0.52	0	C|0.949;T|0.051	0.051	strong	.	BCAN	174	.	NM_198427	exon7	c.C1067T	p.S356L	CAGACTCGGCCCA	.	PASS	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76753588	76753588	+	Missense_Mutation	SNP	A	A	G	rs7240860	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	4	1	0	0.363636	0	A|0.251;G|0.749	0.749	strong	SALL3,NS,carcinoma,0,1	SALL3	162	1	NM_171999	exon2	c.A1597G	p.T533A	CCGCCCACTGTCC	.	scavenged	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116224452	116224452	+	Missense_Mutation	SNP	G	G	A	rs16933949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	72	95	0	0.685714	0	G|0.957;A|0.043	0.043	strong	.	RGS3	251	.	NM_144488	exon4	c.G386A	p.R129K	GGAAGAGGATCAC	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	45	90	0	0.523256	0	C|0.734;T|0.266	0.266	strong	ATP10A,colon,carcinoma,0,1	ATP10A	270	1	NM_024490	exon18	c.G3535A	p.A1179T	GGAAGGCGGCGTC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	705844	705844	+	Silent	SNP	T	T	C	rs8051645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	28	69	0	0.482759	0	T|0.367;C|0.633	0.633	strong	.	WDR90	107	.	NM_145294	exon17	c.T1921C	p.L641L	GGCTTCTTGCGGC	.	PASS	Atlas-SNP
SYCP2	10388	hgsc.bcm.edu	37	20	58475307	58475307	+	Silent	SNP	G	G	A	rs6027185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	37	50	0	0.486842	0	G|0.919;A|0.081	0.081	strong	.	SYCP2	204	.	NM_014258	exon17	c.C1290T	p.V430V	TTCTCCGACTGGT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	2182	80	1912	36	0.0366636	0.0188285	.	.	none	MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	NM_005961	exon31	c.A5950G	p.M1984V	CAGTCATAGGACC	.	scavenged	Atlas-SNP
RBM33	155435	hgsc.bcm.edu	37	7	155530954	155530954	+	Silent	SNP	T	T	C	rs2178428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	197	146	1	1	0.00684932	T|0.707;C|0.293	0.293	strong	.	RBM33	157	.	NM_053043	exon11	c.T1594C	p.L532L	CCAGCCTTGCAGC	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	28	95	0	0.325581	0	C|0.684;T|0.316	0.316	strong	.	FGD3	116	.	NM_001083536	exon13	c.C1455T	p.F485F	CGCCTTCAGCCAG	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737419	248737419	+	Missense_Mutation	SNP	T	T	C	rs145854970		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	17	307	0	0.0825243	0	.	.	weak	OR2T34,NS,carcinoma,+1,2	OR2T34	72	2	NM_001001821	exon1	c.A640G	p.T214A	TGGGGGTGAGAAG	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539186	110539186	+	Missense_Mutation	SNP	G	G	A	rs1783174	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	92	165	0	0.46	0	G|0.742;A|0.258	0.258	strong	.	PKHD1L1	522	.	NM_177531	exon77	c.G12658A	p.V4220I	TGTCTGGTTGGAA	.	PASS	Atlas-SNP
MATN3	4148	hgsc.bcm.edu	37	2	20205848	20205848	+	Silent	SNP	G	G	A	rs28598872	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	75	127	0	0.539568	0	G|0.508;A|0.492	0.492	strong	.	MATN3	28	.	NM_002381	exon2	c.C447T	p.A149A	ACCCACGGCCTGC	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	51	154	0	0.398438	0	C|0.883;T|0.117	0.117	strong	ATR,NS,carcinoma,0,1	ATR	285	1	NM_001184	exon43	c.G7274A	p.R2425Q	AATTCTCGGAATA	.	PASS	Atlas-SNP
EEF1A2	1917	hgsc.bcm.edu	37	20	62119717	62119717	+	Silent	SNP	C	C	T	rs1042796	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	6	30	0	0.222222	0	C|0.966;T|0.034	0.034	strong	.	EEF1A2	60	.	NM_001958	exon8	c.G1326A	p.E442E	CTTCTTCTCCACG	.	PASS	Atlas-SNP
UBE4B	10277	hgsc.bcm.edu	37	1	10218439	10218439	+	Silent	SNP	T	T	C	rs2273299	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	119	124	0	1	0	T|0.658;C|0.342	0.342	strong	UBE4B,NS,carcinoma,0,1	UBE4B	233	1	NM_001105562	exon22	c.T2952C	p.S984S	CACCAGTGAGTTT	.	PASS	Atlas-SNP
UIMC1	51720	hgsc.bcm.edu	37	5	176370402	176370402	+	Missense_Mutation	SNP	A	A	G	rs13360277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	59	139	0	0.508621	0	A|0.846;G|0.154	0.154	strong	.	UIMC1	55	.	NM_016290	exon10	c.T1531C	p.C511R	GAAAGCATTGGTC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116958283	116958283	+	Silent	SNP	G	G	A	rs10982098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	27	78	0	0.350649	0	G|0.993;A|0.007	0.007	strong	.	COL27A1	200	.	NM_032888	exon7	c.G2115A	p.P705P	ACCTCCGGGACGA	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145740622	145740622	+	Silent	SNP	C	C	T	rs34948955	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	49	111	1	0.426087	0.00900901	C|0.997;T|0.003	0.003	strong	RECQL4,brain,glioma,0,2	RECQL4	75	2	NM_004260	exon8	c.G1395A	p.T465T	AGCCGGCGTCTCT	.	scavenged	Atlas-SNP
HPGD	3248	hgsc.bcm.edu	37	4	175443156	175443156	+	Silent	SNP	C	C	T	rs1050145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	38	91	0	0.550725	0	C|0.628;T|0.372	0.372	strong	HPGD,NS,carcinoma,0,1	HPGD	19	1	NM_000860	exon2	c.G156A	p.Q52Q	TTCAAACTGCTCA	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011415	46011415	+	Silent	SNP	G	G	A	rs145570198	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	261	58	358	0	0.222222	0	G|0.976;A|0.024	0.024	strong	.	KRTAP10-6	57	.	NM_198688	exon1	c.C951T	p.C317C	GGGCACGCAGCAG	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610504	38610504	+	Silent	SNP	G	G	A	rs59185302	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	21	27	0	0.552632	0	G|0.866;A|0.134	0.134	strong	.	SIPA1L3	150	.	NM_015073	exon9	c.G2850A	p.E950E	AAGGGAGATAGTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678421	100678421	+	Missense_Mutation	SNP	T	T	A	rs10265276	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	83	105	0	0.557047	0	T|0.819;A|0.181	0.181	strong	MUC17,NS,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.T3724A	p.S1242T	TCAACATCTCCCG	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782173	54782173	+	Missense_Mutation	SNP	A	A	C	rs4993130	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	77	199	0	0.447674	0	A|1.000;C|0.000	0.000	weak	.	LILRB2	94	.	NM_005874	exon7	c.T1199G	p.L400R	GAGTTGAGTGAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507684	195507684	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	203	0	0.470588	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.C10767T	p.D3589D	GGAAGCGTCGGTG	.	scavenged	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8238151	8238151	+	Silent	SNP	C	C	T	rs11603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	130	291	0	0.503876	0	C|0.684;T|0.316	0.316	strong	.	SH3TC1	105	.	NM_018986	exon16	c.C3552T	p.T1184T	CATCACCCTGGGT	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518422	161518422	+	Missense_Mutation	SNP	C	C	G	rs403016	bycluster;bysubmitter;by2hit2allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	408	27	325	7	0.0661765	0.0215385	G|1.000;|0.000	1.000	weak	FCGR3A,NS,carcinoma,-1,1	FCGR3A	38	1	NM_000569	exon3	c.G216C	p.R72S	GAGCACCCTGTAC	.	scavenged	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552060	32552060	+	Missense_Mutation	SNP	A	A	T	rs16822820	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	28	44	0	0.341463	0	T|0.164;C|0.002;A|0.834	0.164	strong	.	HLA-DRB1	41	.	NM_002124	exon2	c.T196A	p.S66T	GCACGGACTCCTC	.	PASS	Atlas-SNP
CEACAM4	1089	hgsc.bcm.edu	37	19	42125709	42125709	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	54	100	0	0.473684	0	.	.	none	CEACAM4,NS,neuroblastoma,0,1	CEACAM4	42	1	NM_001817	exon7	c.C729T	p.V243V	CTAAGAGACCACA	.	PASS	Atlas-SNP
GAS2	2620	hgsc.bcm.edu	37	11	22770669	22770669	+	Silent	SNP	T	T	C	rs7122835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	56	116	0	0.46281	0	T|0.988;C|0.012	0.012	strong	.	GAS2	46	.	NM_177553	exon6	c.T477C	p.Y159Y	AAGGTATGGTGTG	.	PASS	Atlas-SNP
SLC24A1	9187	hgsc.bcm.edu	37	15	65917349	65917349	+	Missense_Mutation	SNP	G	G	C	rs34363823	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	17	39	0	0.435897	0	G|0.990;C|0.010	0.010	strong	.	SLC24A1	58	.	NM_004727	exon2	c.G931C	p.V311L	GGAACAGTCCTGT	.	PASS	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	37	22	31533967	31533967	+	Silent	SNP	G	G	A	rs2074739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	21	49	0	0.4375	0	G|0.488;N|0.000	.	strong	.	PLA2G3	85	.	NM_015715	exon4	c.C795T	p.Y265Y	TGTGCCGTACATC	.	PASS	Atlas-SNP
MID2	11043	hgsc.bcm.edu	37	X	107159291	107159291	+	Missense_Mutation	SNP	C	C	A	rs12849510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	59	106	0	0.567308	0	C|0.965;A|0.035	0.035	strong	.	MID2	122	.	NM_012216	exon6	c.C1133A	p.A378D	ATGATGCCTTTGA	.	PASS	Atlas-SNP
BRAP	8315	hgsc.bcm.edu	37	12	112121090	112121090	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	3	241	0	0.0128755	0	.	.	none	BRAP,NS,carcinoma,+1,1	BRAP	42	1	NM_006768	exon2	c.A104G	p.E35G	TTTATCTCCTCAT	.	scavenged	Atlas-SNP
SLC2A11	66035	hgsc.bcm.edu	37	22	24199704	24199704	+	Missense_Mutation	SNP	C	C	T	rs16986337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	18	27	0	0.486486	0	C|0.885;T|0.115	0.115	strong	.	SLC2A11	32	.	NM_030807	exon2	c.C28T	p.R10W	TCCTTACGGCCTC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628138	33628138	+	Missense_Mutation	SNP	T	T	G	rs9536314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	34	96	0	0.414634	0	T|0.846;G|0.154	0.154	strong	.	KL	106	.	NM_004795	exon2	c.T1054G	p.F352V	CCTGATTTTACTG	.	PASS	Atlas-SNP
ASB18	401036	hgsc.bcm.edu	37	2	237103548	237103548	+	Silent	SNP	G	G	A	rs10177825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	136	121	1	1	0.00826446	G|0.807;A|0.193	0.193	strong	.	ASB18	34	.	NM_212556	exon6	c.C1368T	p.Y456Y	AAGTAGGTAATTC	.	PASS	Atlas-SNP
DENND5B	160518	hgsc.bcm.edu	37	12	31605044	31605044	+	Missense_Mutation	SNP	G	G	T	rs1056320	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	104	198	0	0.454148	0	G|0.818;T|0.182	0.182	strong	.	DENND5B	114	.	NM_144973	exon5	c.C1459A	p.H487N	CACAATGCAGTTT	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33439187	33439187	+	Missense_Mutation	SNP	G	G	A	rs3764633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	28	66	0	0.474576	0	G|0.806;A|0.194	0.194	strong	.	CEP89	82	.	NM_032816	exon5	c.C580T	p.R194W	GTGTCCGCTGTGG	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	18	420	0	0.163636	0	.	.	none	KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	NM_033187	exon1	c.G188C	p.S63T	CAGCAGCTGGGTT	.	scavenged	Atlas-SNP
FGD2	221472	hgsc.bcm.edu	37	6	36976637	36976637	+	Missense_Mutation	SNP	G	G	C	rs831510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	177	87	167	0	0.491525	0	G|0.699;C|0.301	0.301	strong	FGD2,NS,carcinoma,0,1	FGD2	65	1	NM_173558	exon2	c.G96C	p.Q32H	AGGCCAGAGGCTA	.	PASS	Atlas-SNP
GALK2	2585	hgsc.bcm.edu	37	15	49574223	49574223	+	Missense_Mutation	SNP	A	A	G	rs35507772	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	75	133	0	0.559702	0	A|0.992;G|0.008	0.008	strong	.	GALK2	78	.	NM_002044	exon6	c.A544G	p.I182V	CGTTACATTGGCA	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	280	121	293	0	0.432143	0	G|0.784;C|0.216	0.216	strong	STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	NM_153700	exon26	c.C4878G	p.L1626L	GCACTGGAGATGC	.	PASS	Atlas-SNP
NADK	65220	hgsc.bcm.edu	37	1	1688719	1688719	+	Silent	SNP	C	C	A	rs78921781	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	39	71	0	0.534247	0	C|0.995;A|0.005	0.005	strong	.	NADK	79	.	NM_001198994	exon6	c.G606T	p.L202L	CCACGTCAGCCGC	.	PASS	Atlas-SNP
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39191003	39191003	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	18	234	2	0.0762712	0.00854701	.	.	none	KRTAP1-3,NS,carcinoma,0,1	KRTAP1-3	18	1	NM_030966	exon1	c.G71C	p.C24S	TGGCAGCAGCTGG	.	scavenged	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327117	43327117	+	Silent	SNP	C	C	T	rs2277795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	49	105	0	0.49	0	C|0.714;T|0.286	0.286	strong	.	C2CD2	47	.	NM_015500	exon10	c.G1302A	p.A434A	CGGGGACGCCCTC	.	PASS	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	37	11	51411817	51411817	+	Silent	SNP	G	G	A	rs144502772	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	58	88	0	0.552381	0	G|0.993;A|0.007	0.007	strong	.	OR4A5	116	.	NM_001005272	exon1	c.C579T	p.G193G	AGTGAGGCCTATA	.	PASS	Atlas-SNP
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	182	247	0	0.556575	0	C|0.495;T|0.505	0.505	strong	.	ZNF280D	82	.	NM_017661	exon15	c.G1702A	p.V568I	ATTTGACTGTATT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417777	105417777	+	Silent	SNP	C	C	T	rs1960092	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	254	374	0	0.996078	0	C|0.959;T|0.041	0.041	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G4011A	p.S1337S	CCCGAACGACGGC	.	PASS	Atlas-SNP
OR10K1	391109	hgsc.bcm.edu	37	1	158435572	158435572	+	Missense_Mutation	SNP	C	C	T	rs78779179	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	474	204	490	0	0.43038	0	C|0.966;T|0.034	0.034	strong	.	OR10K1	80	.	NM_001004473	exon1	c.C221T	p.T74I	GCTATACCTTTGT	.	PASS	Atlas-SNP
PAH	5053	hgsc.bcm.edu	37	12	103248924	103248924	+	Silent	SNP	C	C	T	rs1126758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	128	153	1	1	0.00653595	C|0.415;T|0.585	0.585	strong	.	PAH	77	.	NM_000277	exon6	c.G696A	p.Q232Q	CAGGAACTGAGAA	.	PASS	Atlas-SNP
OTUD7B	56957	hgsc.bcm.edu	37	1	149916584	149916584	+	Silent	SNP	C	C	G	rs200362140	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	39	63	0	0.557143	0	C|0.999;G|0.001	0.001	strong	.	OTUD7B	76	.	NM_020205	exon12	c.G1704C	p.G568G	CCCATCCCCAGCT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	89	0	1	0	T|0.714;C|0.286	0.286	strong	DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	NM_001369	exon60	c.A10140G	p.E3380E	CAAAAATTCTATC	.	PASS	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	30	48	0	1	0	A|0.826;G|0.174	0.174	strong	.	PRKAR1B	32	.	NM_001164760	exon11	c.T1014C	p.T338T	CACGACAGTGGCC	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9317784	9317784	+	Missense_Mutation	SNP	A	A	G	rs2277413	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	179	170	0	1	0	A|0.677;G|0.323	0.323	strong	.	PZP	422	.	NM_002864	exon19	c.T2438C	p.V813A	GTGAAGACCTCTC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149506195	149506195	+	Missense_Mutation	SNP	C	C	T	rs73727627	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	292	154	259	1	0.527397	0.003861	C|0.978;T|0.022	0.022	strong	.	.	.	.	NM_198455	exon63	c.C9187T	p.R3063C	AGGAACCGCACCC	.	PASS	Atlas-SNP
KRT79	338785	hgsc.bcm.edu	37	12	53227803	53227803	+	Missense_Mutation	SNP	A	A	G	rs2638497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	106	75	0	0.990654	0	A|0.331;G|0.669	0.669	strong	KRT79,NS,carcinoma,+1,1	KRT79	78	1	NM_175834	exon1	c.T242C	p.L81S	CGCCCCAACAAGG	.	PASS	Atlas-SNP
TSEN2	80746	hgsc.bcm.edu	37	3	12531461	12531461	+	Silent	SNP	G	G	A	rs78685815	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	37	74	0	0.513889	0	A|0.060;G|0.940	0.060	strong	TSEN2,NS,carcinoma,+1,2	TSEN2	46	2	NM_001145394	exon2	c.G162A	p.A54A	GAATGCGGAGGAC	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108380609	108380609	+	Silent	SNP	C	C	T	rs115867994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	74	150	0	0.471338	0	C|0.986;T|0.014	0.014	strong	.	EXPH5	193	.	NM_015065	exon6	c.G5625A	p.R1875R	TGCAGACCTGGGA	.	PASS	Atlas-SNP
ANKRD2	26287	hgsc.bcm.edu	37	10	99337572	99337572	+	Missense_Mutation	SNP	G	G	A	rs7094973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	18	45	0	0.375	0	G|0.516;A|0.484	0.484	strong	ANKRD2,NS,carcinoma,0,1	ANKRD2	27	1	NM_001129981	exon2	c.G184A	p.A62T	GGAGACGCACGCC	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79616520	79616520	+	Silent	SNP	G	G	C	rs12243930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	95	206	0	0.479798	0	G|0.857;C|0.143	0.143	strong	.	DLG5	154	.	NM_004747	exon3	c.C504G	p.A168A	AGCAAAGGCCAGG	.	PASS	Atlas-SNP
CEP250	11190	hgsc.bcm.edu	37	20	34091624	34091624	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	41	57	0	0.482353	0	.	.	none	.	CEP250	141	.	NM_007186	exon30	c.G5427A	p.Q1809Q	GGCCCAGAGAGCC	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	102016044	102016044	+	Missense_Mutation	SNP	C	C	T	rs2270962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	82	163	0	0.465909	0	C|0.775;T|0.225	0.225	strong	CWF19L1,NS,carcinoma,0,1	CWF19L1	39	1	NM_018294	exon5	c.G479A	p.C160Y	CCCACACACTTGG	.	PASS	Atlas-SNP
B3GNT2	10678	hgsc.bcm.edu	37	2	62449664	62449664	+	Silent	SNP	G	G	A	rs72893877	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	76	106	0	0.575758	0	G|0.996;A|0.004	0.004	strong	.	B3GNT2	34	.	NM_006577	exon2	c.G309A	p.T103T	GGTCACGTCGGTG	.	PASS	Atlas-SNP
ENAM	10117	hgsc.bcm.edu	37	4	71510368	71510368	+	Silent	SNP	C	C	T	rs61737041	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	266	127	254	0	0.477444	0	C|0.993;T|0.007	0.007	strong	.	ENAM	140	.	NM_031889	exon9	c.C3225T	p.S1075S	ATCTAGCGATGGA	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263643	263643	+	Missense_Mutation	SNP	C	C	A	rs199668575	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	310	14	321	8	0.0451613	0.0249221	C|0.981;A|0.019	0.019	strong	C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	NM_001013672	exon2	c.C1009A	p.P337T	TTCCACCCCGACC	.	scavenged	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002488	36002488	+	Missense_Mutation	SNP	C	C	A	rs57760262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	40	82	0	0.526316	0	C|0.967;A|0.033	0.033	strong	DMKN,NS,carcinoma,+1,1	DMKN	116	1	NM_001126058	exon5	c.G743T	p.S248I	GAGCCGCTGCCTC	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109961032	109961032	+	Missense_Mutation	SNP	C	C	T	rs61730863	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	89	153	0	0.529762	0	C|0.975;T|0.025	0.025	strong	.	TMEM232	57	.	NM_001039763	exon7	c.G704A	p.R235H	TCAGAACGGAGTT	.	PASS	Atlas-SNP
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316870	39316870	+	Missense_Mutation	SNP	T	T	C	rs385055	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	188	1	1	0.00531915	T|0.890;C|0.110	0.110	strong	KRTAP4-4,NS,carcinoma,-1,1	KRTAP4-4	21	1	NM_032524	exon1	c.A74G	p.Y25C	TGGCAGTAGCTGG	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73717103	73717103	+	Missense_Mutation	SNP	G	G	C	rs2017116	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	72	150	0	0.55814	0	G|0.852;C|0.148	0.148	strong	.	ALMS1	384	.	NM_015120	exon10	c.G8014C	p.D2672H	CCATTCGATGAAA	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125315778	125315778	+	Silent	SNP	G	G	C	rs1411271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	64	182	0	0.367816	0	G|0.468;C|0.532	0.532	strong	.	OR1N2	51	.	NM_001004457	exon1	c.G330C	p.S110S	CATCTCGTATTCT	.	PASS	Atlas-SNP
SLC26A10	65012	hgsc.bcm.edu	37	12	58019388	58019388	+	Missense_Mutation	SNP	C	C	T	rs114079678	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	35	81	0	0.426829	0	C|0.999;T|0.001	0.001	strong	.	SLC26A10	89	.	NM_133489	exon14	c.C1552T	p.R518W	CTGACCCGGGTAG	.	PASS	Atlas-SNP
ITPKC	80271	hgsc.bcm.edu	37	19	41223387	41223387	+	Missense_Mutation	SNP	A	A	T	rs145275994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	44	53	0	0.463158	0	A|0.997;T|0.003	0.003	strong	.	ITPKC	36	.	NM_025194	exon1	c.A347T	p.D116V	AGCCAGACAGGTC	.	PASS	Atlas-SNP
SCLY	51540	hgsc.bcm.edu	37	2	239006879	239006879	+	Silent	SNP	C	C	T	rs12993309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	87	0	1	0	C|0.785;T|0.215	0.215	strong	SCLY,NS,carcinoma,0,2	SCLY	51	2	NM_016510	exon12	c.C1245T	p.F415F	CCCCTTCGACGTG	.	PASS	Atlas-SNP
FRMD6	122786	hgsc.bcm.edu	37	14	52182081	52182081	+	Silent	SNP	T	T	A	rs731715	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	35	66	0	0.448718	0	T|0.309;A|0.691	0.691	strong	FRMD6,NS,carcinoma,+1,1	FRMD6	100	1	NM_001267046	exon10	c.T888A	p.S296S	GCCTTCTGCCCGG	.	PASS	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19549250	19549250	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	105	191	0	0.527638	0	.	.	none	.	.	.	.	NM_015047	exon20	c.G2455A	p.A819T	CGGTGGCGTTGTA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412009	105412009	+	Missense_Mutation	SNP	A	A	G	rs28714612	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	324	69	246	0	0.212963	0	A|0.454;G|0.546	0.546	strong	AHNAK2_ENST00000333244,NS,neuroblastoma,0,2	AHNAK2	719	2	NM_138420	exon7	c.T9779C	p.M3260T	ACATCCATCTTCG	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007992	6007992	+	Silent	SNP	A	A	G	rs115266467	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	74	135	0	0.453988	0	A|0.989;G|0.011	0.011	strong	.	OR52L1	100	.	NM_001005173	exon1	c.T169C	p.L57L	CCACTAAAGCAAG	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563550	140563550	+	Silent	SNP	C	C	T	rs56237941	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	70	93	0	0.614035	0	C|0.992;T|0.008	0.008	strong	PCDHB16,NS,carcinoma,0,1	PCDHB16	159	1	NM_020957	exon1	c.C1416T	p.S472S	CGGCAGCGTCAGC	.	PASS	Atlas-SNP
SLC25A42	284439	hgsc.bcm.edu	37	19	19217081	19217081	+	Silent	SNP	C	C	A	rs61740506	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	43	113	0	0.472527	0	C|0.976;A|0.024	0.024	strong	.	SLC25A42	18	.	NM_178526	exon6	c.C384A	p.A128A	CAGAGCCCTGCCC	.	PASS	Atlas-SNP
ZBTB38	253461	hgsc.bcm.edu	37	3	141163705	141163705	+	Silent	SNP	G	G	A	rs3732868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	53	127	0	0.445378	0	G|0.980;A|0.020	0.020	strong	.	ZBTB38	92	.	NM_001080412	exon8	c.G2475A	p.P825P	TCTGCCGGGAACC	.	PASS	Atlas-SNP
PI4KA	5297	hgsc.bcm.edu	37	22	21064203	21064203	+	Missense_Mutation	SNP	G	G	A	rs1801982		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	757	10	742	6	0.01321	0.00808625	.	.	weak	PI4KA_ENST00000255882,trunk,malignant_melanoma,0,4	PI4KA	313	4	NM_058004	exon53	c.C6166T	p.L2056F	TCAAGAGCTTGAT	.	scavenged	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74524724	74524724	+	Silent	SNP	G	G	A	rs59555720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	36	67	0	0.545455	0	G|0.971;A|0.029	0.029	strong	.	CD109	170	.	NM_133493	exon30	c.G3789A	p.V1263V	TAATGTGAAGGCT	.	PASS	Atlas-SNP
LMNB2	84823	hgsc.bcm.edu	37	19	2432450	2432450	+	Silent	SNP	C	C	G	rs11882908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	34	104	1	0.43038	0.00961538	C|0.960;G|0.040	0.040	strong	LMNB2,NS,carcinoma,0,2	LMNB2	40	2	NM_032737	exon9	c.G1554C	p.T518T	CTTGGGCGTGAAC	.	scavenged	Atlas-SNP
NFIA	4774	hgsc.bcm.edu	37	1	61869783	61869783	+	Silent	SNP	G	G	A	rs2236059	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	289	142	254	1	0.491349	0.00393701	G|0.699;A|0.301	0.301	strong	.	NFIA	76	.	NM_001145512	exon9	c.G1218A	p.P406P	AAGTCCGCATGCA	.	PASS	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	37	4	77288833	77288833	+	Missense_Mutation	SNP	C	C	T	rs17001824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	58	98	0	0.456693	0	C|0.981;T|0.019	0.019	strong	.	CCDC158	114	.	NM_001042784	exon11	c.G1444A	p.E482K	ACTCTTCTACTAC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553919	140553919	+	Silent	SNP	C	C	A	rs17844456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	273	116	255	0	0.424908	0	C|0.826;A|0.174	0.174	strong	.	PCDHB7	231	.	NM_018940	exon1	c.C1503A	p.A501A	CCTCGCCTCCCTG	.	PASS	Atlas-SNP
KIAA0020	9933	hgsc.bcm.edu	37	9	2837218	2837218	+	Missense_Mutation	SNP	T	T	C	rs112185565	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	110	196	0	0.447154	0	T|0.999;C|0.001	0.001	strong	.	KIAA0020	56	.	NM_014878	exon3	c.A266G	p.N89S	TTCTTGTTGAATT	.	PASS	Atlas-SNP
ACTA1	58	hgsc.bcm.edu	37	1	229567384	229567384	+	Silent	SNP	G	G	T	rs74897770	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	43	119	0	0.434343	0	G|0.982;T|0.018	0.018	strong	.	ACTA1	65	.	NM_001100	exon7	c.C996A	p.I332I	CGGGGCGATGATC	.	PASS	Atlas-SNP
SPCS2	9789	hgsc.bcm.edu	37	11	74688086	74688086	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	378	4	365	0	0.010582	0	.	.	none	SPCS2_ENST00000263672,colon,carcinoma,-2,1	SPCS2	17	1	NM_014752	exon5	c.T679C	p.X227Q	ATAAAGTAGCCAA	.	scavenged	Atlas-SNP
ETAA1	54465	hgsc.bcm.edu	37	2	67631541	67631541	+	Missense_Mutation	SNP	T	T	C	rs145096592	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	56	106	0	0.518519	0	T|0.999;C|0.001	0.001	strong	.	ETAA1	88	.	NM_019002	exon5	c.T1727C	p.F576S	GTTCTTTCTTTGA	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42644235	42644235	+	Silent	SNP	A	A	G	rs145163630	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	85	141	0	0.442708	0	A|0.999;G|0.001	0.001	strong	.	GANC	57	.	NM_198141	exon24	c.A2643G	p.K881K	TGGTAAAGATCAG	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3428160	3428160	+	Silent	SNP	T	T	G	rs2820999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	39	100	0	0.458824	0	T|0.574;G|0.426	0.426	strong	.	MEGF6	91	.	NM_001409	exon9	c.A1068C	p.T356T	GGGACATGTGCAC	.	PASS	Atlas-SNP
KLHL20	27252	hgsc.bcm.edu	37	1	173725101	173725101	+	Silent	SNP	G	G	A	rs16846395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	60	125	0	0.504202	0	G|0.899;A|0.101	0.101	strong	.	KLHL20	54	.	NM_014458	exon6	c.G891A	p.P297P	ATTGCCGCAAGAA	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121877739	121877739	+	Silent	SNP	G	G	A	rs35674891	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	54	105	0	0.442623	0	G|0.990;A|0.010	0.010	strong	.	KDM2B	218	.	NM_032590	exon22	c.C3750T	p.H1250H	GGTGACGTGGTTA	.	PASS	Atlas-SNP
RDH5	5959	hgsc.bcm.edu	37	12	56117700	56117700	+	Silent	SNP	C	C	G	rs13193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	32	16	40	0	0.5	0	C|0.876;G|0.124	0.124	strong	RDH5,NS,carcinoma,0,1	RDH5	25	1	NM_001199771	exon4	c.C600G	p.V200V	ACGAGTCTCCATC	.	PASS	Atlas-SNP
DACT1	51339	hgsc.bcm.edu	37	14	59113430	59113430	+	Missense_Mutation	SNP	G	G	A	rs698025	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	23	24	0	0.657143	0	G|0.747;T|0.005	.	strong	.	DACT1	119	.	NM_016651	exon4	c.G2089A	p.G697S	CGGCGCGGTCGCC	.	PASS	Atlas-SNP
XPR1	9213	hgsc.bcm.edu	37	1	180772708	180772708	+	Silent	SNP	T	T	C	rs12078050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	36	70	0	0.529412	0	T|0.942;C|0.058	0.058	strong	.	XPR1	76	.	NM_004736	exon4	c.T408C	p.S136S	CTTCAGTGAGTTC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186026366	186026366	+	Missense_Mutation	SNP	C	C	T	rs140744695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	74	0	0.450549	0	C|0.999;T|0.001	0.001	strong	.	HMCN1	797	.	NM_031935	exon46	c.C7145T	p.A2382V	TTACAGCTCCTCC	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209797061	209797061	+	Missense_Mutation	SNP	C	C	T	rs114174766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	101	0	0.493333	0	C|0.998;T|0.002	0.002	strong	.	LAMB3	136	.	NM_000228	exon16	c.G2147A	p.R716Q	AGCATCCGGAAGG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144873983	144873983	+	Silent	SNP	T	T	C	rs148165371	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	418	111	355	0	0.26555	0	T|0.999;C|0.001	0.001	strong	.	PDE4DIP	817	.	NM_014644	exon31	c.A4974G	p.P1658P	TGATGATGGTTTA	.	PASS	Atlas-SNP
PIGT	51604	hgsc.bcm.edu	37	20	44054349	44054349	+	Silent	SNP	T	T	C	rs707577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	113	0	1	0	T|0.259;C|0.741	0.741	strong	PIGT_ENST00000279036,NS,carcinoma,0,2	PIGT	85	2	NM_015937	exon12	c.T1620C	p.Y540Y	GTGCTATGGCTCC	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2555005	2555005	+	Silent	SNP	C	C	T	rs61730027	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	40	77	0	0.481928	0	C|0.895;T|0.105	0.105	strong	.	METTL4	40	.	NM_022840	exon4	c.G492A	p.Q164Q	GATCAACTGTAAA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678405	100678405	+	Silent	SNP	T	T	C	rs4729648	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	27	106	0	0.174194	0	T|0.936;C|0.064	0.064	strong	MUC17,caecum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.T3708C	p.A1236A	TGAGGCTAGCACC	.	PASS	Atlas-SNP
VSTM4	196740	hgsc.bcm.edu	37	10	50315893	50315893	+	Missense_Mutation	SNP	A	A	G	rs13088	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	61	112	0	0.465649	0	A|0.518;G|0.482	0.482	strong	.	VSTM4	83	.	NM_144984	exon2	c.T203C	p.F68S	GAGTCGAAGGAGT	.	PASS	Atlas-SNP
AK8	158067	hgsc.bcm.edu	37	9	135753629	135753629	+	Missense_Mutation	SNP	A	A	G	rs2231400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	95	0	1	0	A|0.871;G|0.129	0.129	strong	.	AK8	45	.	NM_152572	exon1	c.T14C	p.I5T	GGGGCGATAGTGG	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45316804	45316804	+	Silent	SNP	C	C	T	rs3810141	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	64	82	0	0.551724	0	T|0.064;C|0.936	0.064	strong	.	BCAM	53	.	NM_001013257	exon6	c.C711T	p.C237C	CCACTGCGCCGCC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116930194	116930194	+	Missense_Mutation	SNP	A	A	G	rs2567706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	45	62	0	0.714286	0	A|0.748;G|0.252	0.252	strong	.	COL27A1	200	.	NM_032888	exon3	c.A359G	p.Q120R	GCAGCCAGAAACG	.	PASS	Atlas-SNP
SYTL2	54843	hgsc.bcm.edu	37	11	85456703	85456703	+	Silent	SNP	T	T	C	rs647912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	134	127	0	1	0	T|0.426;C|0.574	0.574	strong	.	SYTL2	231	.	NM_032943	exon4	c.A366G	p.E122E	TGCATCTTCTTCT	.	PASS	Atlas-SNP
SNX18	112574	hgsc.bcm.edu	37	5	53814736	53814736	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	15	143	0	0.108696	0	.	.	none	.	SNX18	102	.	NM_052870	exon1	c.G954C	p.W318C	CGACTGGCTGTAC	.	PASS	Atlas-SNP
DPPA4	55211	hgsc.bcm.edu	37	3	109049507	109049507	+	Silent	SNP	A	A	G	rs16834356	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	204	207	1	1	0.00483092	A|0.991;G|0.009	0.009	strong	.	DPPA4	56	.	NM_018189	exon5	c.T543C	p.N181N	AGTGGAATTTTCC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46805007	46805007	+	Silent	SNP	G	G	A	rs35717986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	80	0	0.460674	0	G|0.882;A|0.118	0.118	strong	.	CELSR1	242	.	NM_014246	exon9	c.C5112T	p.D1704D	GTTCAGGTCACTC	.	PASS	Atlas-SNP
KCNA6	3742	hgsc.bcm.edu	37	12	4919267	4919267	+	Silent	SNP	A	A	G	rs758534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	39	40	0	0.975	0	A|0.580;G|0.420	0.420	strong	.	KCNA6	122	.	NM_002235	exon1	c.A60G	p.G20G	GGAGGGAGAGCAA	.	PASS	Atlas-SNP
ARHGAP4	393	hgsc.bcm.edu	37	X	153176284	153176284	+	Silent	SNP	C	C	T	rs62620965	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	45	70	0	0.576923	0	C|0.957;T|0.043	0.043	strong	.	ARHGAP4	103	.	NM_001164741	exon16	c.G1806A	p.E602E	TGGGTCCTCCCCT	.	PASS	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116049199	116049199	+	Silent	SNP	C	C	T	rs148020287	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	93	139	0	0.574074	0	C|0.994;T|0.006	0.006	strong	VWA2,caecum,carcinoma,0,1	VWA2	64	1	NM_001272046	exon12	c.C2073T	p.Y691Y	AGCTTACGCCGAC	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	50	50	0	0.980392	0	T|0.355;G|0.645	0.645	strong	.	OR51G1	74	.	NM_001005237	exon1	c.A374C	p.Y125S	GCCACGTAGCGGT	.	PASS	Atlas-SNP
NMT2	9397	hgsc.bcm.edu	37	10	15170387	15170387	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	149	6	97	0	0.0402685	0	.	.	none	.	NMT2	44	.	NM_004808	exon8	c.A961G	p.T321A	GTAAAGTCATATT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92534829	92534829	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	2	136	0	0.017094	0	.	.	none	FAT3_ENST00000409404,extremity,malignant_melanoma,0,1	FAT3	1822	1	NM_001008781	exon9	c.G8650A	p.E2884K	GATCACGAGACAG	.	scavenged	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52774158	52774158	+	Silent	SNP	G	G	A	rs951772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	124	131	0	0.992	0	G|0.688;A|0.312	0.312	strong	.	KRT84	61	.	NM_033045	exon7	c.C1413T	p.G471G	CTCCTCGCCCTCC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54115904	54115904	+	Silent	SNP	A	A	G	rs805400	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	63	105	0	0.492188	0	A|0.711;G|0.289	0.289	strong	.	PSME4	247	.	NM_014614	exon38	c.T4342C	p.L1448L	ATTCCAACAGCAG	.	PASS	Atlas-SNP
TBC1D10C	374403	hgsc.bcm.edu	37	11	67171736	67171736	+	Silent	SNP	C	C	T	rs2514256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	76	79	1	0.987013	0.0126582	C|0.683;T|0.317	0.317	strong	TBC1D10C,NS,carcinoma,0,1	TBC1D10C	42	1	NM_001256508	exon2	c.C63T	p.S21S	CAGCTCCTTGGGG	.	scavenged	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113741590	113741590	+	Silent	SNP	G	G	A	rs9604022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	59	109	0	0.491667	0	G|0.832;A|0.168	0.168	strong	.	MCF2L	182	.	NM_001112732	exon22	c.G2415A	p.S805S	GGGCTCGTTCAGC	.	PASS	Atlas-SNP
SLC30A4	7782	hgsc.bcm.edu	37	15	45779810	45779810	+	Silent	SNP	G	G	A	rs2453531	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	59	60	0	1	0	G|0.240;A|0.760	0.760	strong	.	SLC30A4	25	.	NM_013309	exon6	c.C915T	p.D305D	GATGGGGTCAGCA	.	PASS	Atlas-SNP
TBC1D10C	374403	hgsc.bcm.edu	37	11	67172911	67172911	+	Silent	SNP	C	C	T	rs61734600	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	77	128	0	0.631148	0	C|0.948;T|0.052	0.052	strong	.	TBC1D10C	42	.	NM_001256508	exon4	c.C294T	p.R98R	CCTGCGCGCCCGA	.	PASS	Atlas-SNP
ECI2	10455	hgsc.bcm.edu	37	6	4119492	4119492	+	Silent	SNP	T	T	C	rs10708	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	27	80	0	0.482143	0	T|0.962;C|0.038	0.038	strong	.	ECI2	59	.	NM_206836	exon8	c.A813G	p.P271P	ACTAAATGGTGTA	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133201327	133201327	+	Missense_Mutation	SNP	T	T	A	rs73481453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	72	169	0	0.467532	0	T|0.995;A|0.005	0.005	strong	.	POLE	416	.	NM_006231	exon49	c.A6817T	p.T2273S	CCAGGGTCTCCAG	.	PASS	Atlas-SNP
GPRASP1	9737	hgsc.bcm.edu	37	X	101912118	101912118	+	Missense_Mutation	SNP	C	C	T	rs2235804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	145	225	0	0.591837	0	C|0.895;T|0.105	0.105	strong	.	GPRASP1	140	.	NM_001099411	exon3	c.C3277T	p.P1093S	CTTAGCCCAGAAG	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11706693	11706693	+	Missense_Mutation	SNP	T	T	C	rs4669751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	149	1	0.992754	0.00671141	T|0.700;C|0.300	0.300	strong	.	GREB1	308	.	NM_148903	exon4	c.T365C	p.V122A	TGGGGGTCAAGTC	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	47	0	0.490909	0	A|0.706;G|0.294	0.294	strong	.	PDXDC1	59	.	NM_015027	exon23	c.A2205G	p.L735L	GCGCCTATCCAGT	.	PASS	Atlas-SNP
JMY	133746	hgsc.bcm.edu	37	5	78596044	78596044	+	Silent	SNP	T	T	C	rs10514159	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	75	92	0	0.986842	0	T|0.348;C|0.652	0.652	strong	JMY_ENST00000396137,NS,carcinoma,+2,4	JMY	82	4	NM_152405	exon5	c.T1596C	p.D532D	TTATGATCTGCAA	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10944728	10944728	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	345	5	368	1	0.0144928	0.00271739	.	.	none	TPTE_ENST00000361285,NS,carcinoma,-1,2	TPTE	513	2	NM_199261	exon11	c.T506C	p.L169P	AGCAGAAGAATCA	.	scavenged	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134108546	134108546	+	Missense_Mutation	SNP	T	T	C	rs2069569	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	143	143	0	1	0	C|0.598;N|0.002	0.598	strong	.	TG	416	.	NM_003235	exon43	c.T7501C	p.W2501R	TCTTTATGGGTAG	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	37	9	20978439	20978439	+	Missense_Mutation	SNP	A	A	C	rs149031092	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	80	138	0	0.526316	0	A|1.000;C|0.000	0.000	strong	.	.	.	.	NM_017794	exon39	c.A4363C	p.I1455L	CCACTGATCCACA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721839	101721839	+	Missense_Mutation	SNP	C	C	A	rs202074479	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	294	88	177	0	0.29932	0	.	.	weak	.	PABPC1	76	.	NM_002568	exon8	c.G1093T	p.V365L	AAGCTACATACAA	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117103900	117103900	+	Missense_Mutation	SNP	T	T	C	rs2787344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	40	103	0	0.31746	0	T|0.919;C|0.081	0.081	strong	.	AKNA	119	.	NM_030767	exon21	c.A3980G	p.Y1327C	GCCAGATACCACA	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595343	140595343	+	Missense_Mutation	SNP	G	G	C	rs56309578	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	84	157	0	0.54902	0	G|0.921;C|0.079	0.079	strong	.	PCDHB13	142	.	NM_018933	exon1	c.G1648C	p.V550L	CGCGTGGTGGTGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179613962	179613962	+	Missense_Mutation	SNP	C	C	T	rs72648903	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	28	74	0	0.337349	0	C|0.980;T|0.020	0.020	strong	TTN_ENST00000360870,rectum,carcinoma,+1,1	TTN	18412	1	NM_133379	exon46	c.G13165A	p.V4389I	TAGTGACATCACT	.	PASS	Atlas-SNP
JMY	133746	hgsc.bcm.edu	37	5	78610174	78610174	+	Missense_Mutation	SNP	A	A	G	rs16876657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	54	128	0	0.45	0	A|0.926;G|0.074	0.074	strong	.	JMY	82	.	NM_152405	exon9	c.A2159G	p.H720R	AGGATCATTGTGA	.	PASS	Atlas-SNP
NQO1	1728	hgsc.bcm.edu	37	16	69745145	69745145	+	Missense_Mutation	SNP	G	G	A	rs1800566	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	55	125	0	0.478261	0	G|0.761;A|0.239	0.239	strong	NQO1,NS,carcinoma,0,1	NQO1	21	1	NM_000903	exon6	c.C559T	p.P187S	GTTGAGGTTCTAA	.	PASS	Atlas-SNP
SSTR3	6753	hgsc.bcm.edu	37	22	37603744	37603744	+	Silent	SNP	C	C	T	rs86583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	64	110	0	0.496124	0	C|0.664;T|0.336	0.336	strong	SSTR3,NS,carcinoma,-1,1	SSTR3	42	1	NM_001051	exon2	c.G99A	p.A33A	TGGGCCCGCCGAC	.	PASS	Atlas-SNP
ZNHIT1	10467	hgsc.bcm.edu	37	7	100866015	100866015	+	Silent	SNP	C	C	T	rs142012618	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	84	152	0	0.485549	0	C|0.999;T|0.001	0.001	strong	.	ZNHIT1	21	.	NM_006349	exon2	c.C153T	p.L51L	TCAGCTCGGCAAG	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167142979	167142979	+	Missense_Mutation	SNP	C	C	T	rs58022607	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	181	168	0	1	0	C|0.964;T|0.036	0.036	strong	.	SCN9A	296	.	NM_002977	exon11	c.G1469A	p.S490N	TCTCCACTGGAGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417286	105417286	+	Missense_Mutation	SNP	G	G	A	rs149840830	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	355	337	370	0	0.949296	0	G|0.966;A|0.034	0.034	strong	AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C4502T	p.P1501L	AACGACGGCATCT	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16337538	16337538	+	Silent	SNP	G	G	A	rs28587162	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	69	127	0	0.482517	0	G|0.979;A|0.021	0.021	strong	.	NRIP1	103	.	NM_003489	exon4	c.C2976T	p.S992S	GCAACTGCTGGGC	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2439767	2439767	+	Missense_Mutation	SNP	T	T	C	rs886277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	190	220	0	1	0	T|0.506;C|0.494	0.494	strong	.	TRPM5	86	.	NM_014555	exon5	c.A704G	p.N235S	AAGGTGTTGGGAT	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32962004	32962004	+	Silent	SNP	C	C	T	rs73988752	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	40	75	0	0.470588	0	C|0.929;T|0.071	0.071	strong	.	TMEM132E	122	.	NM_207313	exon8	c.C1605T	p.T535T	GGTCACCGACCTA	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22155434	22155434	+	Missense_Mutation	SNP	T	T	C	rs139351235	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	16	21	0	0.615385	0	T|0.972;C|0.028	0.028	strong	.	ZNF208	817	.	NM_007153	exon4	c.A2402G	p.D801G	TTCTCATCAGTAT	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117329597	117329597	+	Silent	SNP	G	G	C	rs115831160	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	48	100	0	0.40678	0	G|0.999;C|0.001	0.001	strong	.	DSCAML1	286	.	NM_020693	exon19	c.C3621G	p.T1207T	CCGCGTGGTGGTG	.	PASS	Atlas-SNP
GCOM1	145781	hgsc.bcm.edu	37	15	57925873	57925873	+	Missense_Mutation	SNP	G	G	C	rs148672365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	79	170	0	0.487654	0	G|0.994;C|0.006	0.006	strong	.	GCOM1	66	.	NM_001018090	exon8	c.G867C	p.E289D	AGCAGAGATCAGC	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160019901	160019901	+	Missense_Mutation	SNP	C	C	T	rs55929944	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	278	165	280	0	0.593525	0	C|0.971;T|0.029	0.029	strong	.	TANC1	157	.	NM_033394	exon8	c.C790T	p.R264C	CATGACCGCAGGG	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117078702	117078702	+	Silent	SNP	A	A	C	rs596314	bysubmitter	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	750	335	923	221	0.446667	0.239437	.	.	weak	PCSK7,NS,carcinoma,0,1	PCSK7	59	1	NM_004716	exon14	c.T1770G	p.L590L	GATGACAAGCCTG	.	scavenged	Atlas-SNP
MAP3K9	4293	hgsc.bcm.edu	37	14	71204973	71204973	+	Silent	SNP	C	C	T	rs7153601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	89	187	0	0.463542	0	C|0.823;T|0.177	0.177	strong	.	MAP3K9	109	.	NM_033141	exon8	c.G1833A	p.S611S	ATCTCCCGAGGCA	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93154540	93154540	+	Silent	SNP	C	C	T	rs71461983	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	12	3	0	0.8	0	C|0.974;T|0.026	0.026	strong	.	RIN3	81	.	NM_024832	exon10	c.C2901T	p.G967G	TGGTGGCGGCGGC	.	PASS	Atlas-SNP
MTSS1	9788	hgsc.bcm.edu	37	8	125575047	125575047	+	Silent	SNP	G	G	T	rs16899702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	50	88	0	0.537634	0	G|0.936;T|0.064	0.064	strong	.	MTSS1	79	.	NM_014751	exon10	c.C1011A	p.P337P	CGGCATGGGGGAT	.	PASS	Atlas-SNP
BTBD3	22903	hgsc.bcm.edu	37	20	11903654	11903654	+	Silent	SNP	G	G	A	rs35364034	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	87	165	1	0.55414	0.00606061	G|0.944;A|0.056	0.056	strong	BTBD3,caecum,carcinoma,+1,4	BTBD3	92	4	NM_014962	exon4	c.G909A	p.A303A	TCTGGCGTTGAGC	.	scavenged	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	79	149	0	0.572464	0	A|0.846;G|0.154	0.154	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.A674G	p.Y225C	AGCTTTATTGTTA	.	PASS	Atlas-SNP
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	75	134	0	0.551471	0	G|0.824;A|0.176	0.176	strong	ADH4,NS,carcinoma,0,1	ADH4	35	1	NM_000670	exon8	c.C1051T	p.L351L	TCACCAGTGCATC	.	PASS	Atlas-SNP
MED26	9441	hgsc.bcm.edu	37	19	16687870	16687870	+	Silent	SNP	G	G	A	rs61734286	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	106	0	0.460674	0	G|0.967;A|0.033	0.033	strong	.	MED26	25	.	NM_004831	exon3	c.C771T	p.D257D	AGTCTCGTCCACC	.	PASS	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140256275	140256275	+	Silent	SNP	G	G	A	rs73793508	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	312	151	307	1	0.483974	0.00325733	G|0.990;A|0.010	0.010	strong	PCDHA12,NS,carcinoma,+1,1	PCDHA12	196	1	NM_018903	exon1	c.G1218A	p.S406S	CTACTCGTTGGTG	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43176799	43176799	+	Silent	SNP	T	T	G	rs13049286	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	45	100	0	0.463918	0	T|0.869;G|0.131	0.131	strong	.	RIPK4	151	.	NM_020639	exon2	c.A360C	p.R120R	GATGATTCGGAAC	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43689004	43689004	+	Silent	SNP	G	G	A	rs2302112	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	271	110	149	1	0.405904	0.00671141	G|0.795;A|0.205	0.205	strong	PSG5,NS,carcinoma,0,1	PSG5	58	1	NM_002781	exon2	c.C360T	p.Y120Y	TAAGGTGTAGGAT	.	scavenged	Atlas-SNP
SLC7A1	6541	hgsc.bcm.edu	37	13	30107067	30107067	+	Silent	SNP	G	G	C	rs2277451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	60	145	0	0.382166	0	G|0.860;C|0.140	0.140	strong	SLC7A1,NS,carcinoma,0,1	SLC7A1	64	1	NM_003045	exon4	c.C423G	p.G141G	GGGTCTGCCTATC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281290	152281290	+	Silent	SNP	A	A	G	rs80353812	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	505	246	246	0	0.487129	0	A|0.974;G|0.026	0.026	strong	.	FLG	900	.	NM_002016	exon3	c.T6072C	p.H2024H	TTGTCCATGCCCA	.	PASS	Atlas-SNP
SEZ6	124925	hgsc.bcm.edu	37	17	27286851	27286851	+	Missense_Mutation	SNP	T	T	C	rs1976165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	25	63	0	0.438596	0	T|0.664;C|0.336	0.336	strong	.	SEZ6	61	.	NM_001098635	exon8	c.A1636G	p.T546A	TGGGTGTGCTGCT	.	PASS	Atlas-SNP
PDHX	8050	hgsc.bcm.edu	37	11	34938269	34938269	+	Missense_Mutation	SNP	C	C	T	rs1049306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	89	0	1	0	C|0.802;T|0.198	0.198	strong	.	PDHX	40	.	NM_003477	exon1	c.C67T	p.R23C	CCCGGCCGCCGAA	.	PASS	Atlas-SNP
SSTR5	6755	hgsc.bcm.edu	37	16	1129023	1129023	+	Missense_Mutation	SNP	C	C	T	rs4988484	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	10	25	0	0.4	0	C|0.930;T|0.070	0.070	strong	.	SSTR5	36	.	NM_001172560	exon2	c.C155T	p.A52V	TGTGTGCGGCCGG	.	PASS	Atlas-SNP
C12orf50	160419	hgsc.bcm.edu	37	12	88380094	88380094	+	Missense_Mutation	SNP	T	T	C	rs10777084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	15	27	0	0.428571	0	T|0.704;C|0.296	0.296	strong	.	C12orf50	70	.	NM_152589	exon10	c.A917G	p.Q306R	CCTCTCTGCATTC	.	PASS	Atlas-SNP
GNG12	55970	hgsc.bcm.edu	37	1	68171215	68171215	+	Silent	SNP	A	A	G	rs17130202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	42	102	0	0.407767	0	A|0.991;G|0.009	0.009	strong	.	GNG12	11	.	NM_018841	exon4	c.T138C	p.H46H	CCTGGCATGTTCC	.	PASS	Atlas-SNP
PINX1	54984	hgsc.bcm.edu	37	8	10623138	10623138	+	Missense_Mutation	SNP	T	T	A	rs1078543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	111	88	0	0.973684	0	T|0.831;A|0.169	0.169	strong	PINX1,NS,carcinoma,+2,1	PINX1	38	1	NM_017884	exon7	c.A760T	p.S254C	GCGCGCTCTTCTT	.	PASS	Atlas-SNP
OR10G8	219869	hgsc.bcm.edu	37	11	123900968	123900968	+	Missense_Mutation	SNP	A	A	G	rs146815262	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	406	224	437	0	0.551724	0	A|0.999;G|0.001	0.001	strong	.	OR10G8	132	.	NM_001004464	exon1	c.A639G	p.I213M	CCTGATAGTGCTG	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46761135	46761135	+	Silent	SNP	G	G	T	rs9627424	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	75	0	0.509091	0	G|0.911;T|0.089	0.089	strong	.	CELSR1	242	.	NM_014246	exon32	c.C8547A	p.T2849T	TTTGGGGGTGCTG	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29843833	29843833	+	Silent	SNP	C	C	T	rs1547169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	63	113	0	0.567568	0	C|0.740;T|0.260	0.260	strong	.	SVIL	226	.	NM_003174	exon7	c.G39A	p.G13G	TTCAATCCCTTCC	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18737095	18737095	+	Missense_Mutation	SNP	C	C	T	rs4424652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	179	178	0	1	0	C|0.231;N|0.000	.	strong	.	IGSF22	211	.	NM_173588	exon11	c.G1415A	p.R472Q	TCTGCTCGCTTGC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919963	12919963	+	Missense_Mutation	SNP	T	T	G	rs72472699	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	103	179	0	0.602339	0	T|0.756;G|0.244	0.244	strong	PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	NM_023014	exon3	c.T703G	p.C235G	ACTCTTTGCAAAC	.	PASS	Atlas-SNP
OR7D4	125958	hgsc.bcm.edu	37	19	9324863	9324863	+	Silent	SNP	G	G	A	rs8109935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	93	85	0	0.989362	0	G|0.833;A|0.167	0.167	strong	OR7D4,NS,malignant_melanoma,-1,2	OR7D4	66	2	NM_001005191	exon1	c.C651T	p.S217S	AGAGTAGGAGAAG	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16354394	16354394	+	Missense_Mutation	SNP	C	C	T	rs34188929	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	708	399	702	85	0.563559	0.121083	C|0.240;T|0.760	0.760	strong	CLCNKA,NS,carcinoma,+1,1	CLCNKA	56	1	NM_004070	exon9	c.C860T	p.A287V	TTGTGGCGCTGGG	.	scavenged	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68650913	68650913	+	Silent	SNP	G	G	A	rs61729771	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	74	74	0	0.986667	0	G|0.956;A|0.044	0.044	strong	.	ITGA11	110	.	NM_001004439	exon6	c.C483T	p.T161T	CATGTAGGTCTGG	.	PASS	Atlas-SNP
GBP7	388646	hgsc.bcm.edu	37	1	89615023	89615023	+	Missense_Mutation	SNP	C	C	G	rs74098339	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	235	120	202	1	0.510638	0.00495049	C|0.988;G|0.012	0.012	strong	.	GBP7	57	.	NM_207398	exon7	c.G1104C	p.M368I	GTACTCCATGAAG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7017322	7017322	+	Silent	SNP	A	A	G	rs539713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	110	99	0	1	0	A|0.392;G|0.608	0.608	strong	.	LAMA1	458	.	NM_005559	exon20	c.T2763C	p.C921C	GCAGTCACAGAGC	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1811603	1811603	+	Missense_Mutation	SNP	C	C	T	rs7250872	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	70	0	1	0	C|0.614;T|0.386	0.386	strong	.	ATP8B3	108	.	NM_138813	exon2	c.G133A	p.G45R	CACCTCCGCGGAT	.	PASS	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90784862	90784862	+	Missense_Mutation	SNP	G	G	A	rs75296384	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	18	48	0	0.36	0	G|0.962;A|0.038	0.038	strong	.	.	.	.	NM_001013657	exon4	c.G722A	p.G241E	ACCCTGGAGGCCA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129899543	129899543	+	Silent	SNP	C	C	T	rs10082504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	73	123	1	0.453416	0.00813008	C|0.913;T|0.087	0.087	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon14	c.G9684A	p.R3228R	TGCACACCTCTTG	.	scavenged	Atlas-SNP
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	80	125	0	0.454545	0	A|0.881;G|0.119	0.119	strong	.	VTN	45	.	NM_000638	exon8	c.T1344C	p.N448N	GCGAAGATTGACT	.	PASS	Atlas-SNP
NPTN	27020	hgsc.bcm.edu	37	15	73862606	73862606	+	Silent	SNP	C	C	T	rs35100473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	103	160	0	0.550802	0	C|0.988;G|0.000;T|0.012	0.012	strong	.	NPTN	35	.	NM_001161363	exon6	c.G999A	p.V333V	GCTCCGCACCCTG	.	PASS	Atlas-SNP
CCDC160	347475	hgsc.bcm.edu	37	X	133378851	133378851	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	91	149	0	0.623288	0	.	.	none	.	CCDC160	38	.	NM_001101357	exon2	c.C21T	p.H7H	AAAACACTGGAAG	.	PASS	Atlas-SNP
ZNF439	90594	hgsc.bcm.edu	37	19	11976987	11976987	+	Missense_Mutation	SNP	C	C	T	rs10421552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	61	88	0	0.592233	0	C|0.975;T|0.025	0.025	strong	.	ZNF439	67	.	NM_152262	exon1	c.C16T	p.P6S	CTCTCACCCATCC	.	PASS	Atlas-SNP
TPSD1	23430	hgsc.bcm.edu	37	16	1306680	1306680	+	Silent	SNP	C	C	T	rs1969653	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	77	166	0	0.411765	0	C|0.850;T|0.150	0.150	strong	.	TPSD1	47	.	NM_012217	exon2	c.C246T	p.C82C	GCACTGCGTGGAA	.	PASS	Atlas-SNP
ZNF442	79973	hgsc.bcm.edu	37	19	12462873	12462873	+	Nonsense_Mutation	SNP	C	C	A	rs73507958	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	61	133	0	0.516949	0	C|0.993;A|0.007	0.007	strong	.	ZNF442	102	.	NM_030824	exon5	c.G217T	p.E73X	TGTCTTCCCATTT	.	PASS	Atlas-SNP
ATP8A1	10396	hgsc.bcm.edu	37	4	42457545	42457545	+	Silent	SNP	G	G	A	rs61735691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	90	196	0	0.483871	0	G|0.866;A|0.134	0.134	strong	.	ATP8A1	206	.	NM_006095	exon28	c.C2691T	p.N897N	TACCACGTTATAG	.	PASS	Atlas-SNP
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	61	29	55	0	0.47541	0	A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong	.	.	.	.	NM_012192	exon1	c.C34A	p.R12R	CAACTGCGAAACG	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	94562	94562	+	Silent	SNP	G	G	A	rs145350711	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	62	107	0	0.558559	0	G|0.999;A|0.001	0.001	strong	.	TUBB8	62	.	NM_177987	exon3	c.C270T	p.F90F	GAAGATGAAGTTG	.	PASS	Atlas-SNP
HSPBAP1	79663	hgsc.bcm.edu	37	3	122496628	122496628	+	Missense_Mutation	SNP	A	A	C	rs16833517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	346	191	275	0	0.552023	0	A|0.951;C|0.049	0.049	strong	HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	NM_024610	exon2	c.T190G	p.S64A	CCTGCGAAAGGTA	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153418524	153418524	+	Missense_Mutation	SNP	C	C	T	rs731613	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	1010	311	439	0	0.307921	0	C|0.830;T|0.170	0.170	strong	.	OPN1LW	87	.	NM_020061	exon3	c.C521T	p.A174V	GCATTGCCTTCTC	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011544	46011544	+	Silent	SNP	G	G	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	33	257	0	0.100917	0	.	.	none	.	KRTAP10-6	57	.	NM_198688	exon1	c.C822G	p.V274V	AGAGCAGACGGGC	.	PASS	Atlas-SNP
GOLPH3	64083	hgsc.bcm.edu	37	5	32126441	32126441	+	Silent	SNP	G	G	A	rs34212503	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	65	136	0	0.460993	0	G|0.966;A|0.034	0.034	strong	.	GOLPH3	25	.	NM_022130	exon4	c.C774T	p.D258D	CTGCTCGTCCAGA	.	PASS	Atlas-SNP
PRPF4	9128	hgsc.bcm.edu	37	9	116041316	116041316	+	Silent	SNP	T	T	C	rs146246780	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	57	76	0	0.587629	0	T|0.999;C|0.001	0.001	strong	.	PRPF4	56	.	NM_004697	exon3	c.T300C	p.N100N	GATCAATGTTTCC	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30043486	30043486	+	Silent	SNP	T	T	C	rs11758516	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	77	159	0	0.475309	0	T|0.897;C|0.103	0.103	strong	.	RNF39	27	.	NM_025236	exon1	c.A81G	p.K27K	ATTAACTTTTGCC	.	PASS	Atlas-SNP
OMP	4975	hgsc.bcm.edu	37	11	76814110	76814110	+	Silent	SNP	G	G	A	rs2233549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	75	118	0	0.551471	0	G|0.790;A|0.210	0.210	strong	OMP,NS,carcinoma,+2,1	OMP	14	1	NM_006189	exon1	c.G225A	p.P75P	CAAGCCGGGCAAG	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41827757	41827757	+	Missense_Mutation	SNP	T	T	A	rs2297382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	53	101	0	0.490741	0	T|0.855;A|0.145	0.145	strong	.	RPAP1	111	.	NM_015540	exon5	c.A494T	p.K165M	GGGCCCTTGGCTT	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	100226900	100226900	+	Silent	SNP	G	G	A	rs34539243	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	56	115	0	0.595745	0	G|0.988;A|0.012	0.012	strong	.	CNTN5	324	.	NM_001243270	exon24	c.G3252A	p.S1084S	ATCTTCGTCATCA	.	PASS	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226074436	226074436	+	Silent	SNP	G	G	C	rs35684337	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	109	182	0	0.550505	0	G|0.963;C|0.037	0.037	strong	.	LEFTY1	30	.	NM_020997	exon4	c.C1092G	p.L364L	TGGCTGGAGCCTC	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38770198	38770198	+	Missense_Mutation	SNP	T	T	G	rs146028829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	347	160	324	0	0.461095	0	T|0.999;G|0.001	0.001	strong	SCN10A,NS,carcinoma,0,2	SCN10A	359	2	NM_006514	exon15	c.A2475C	p.E825D	CCAGTCTTCATGG	.	PASS	Atlas-SNP
MTFR2	113115	hgsc.bcm.edu	37	6	136560948	136560948	+	Silent	SNP	G	G	A	rs10484485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	37	56	0	0.493333	0	G|0.939;A|0.061	0.061	strong	.	.	.	.	NM_138419	exon6	c.C525T	p.G175G	ACTCAAGCCAAAG	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113662508	113662508	+	Silent	SNP	A	A	G	rs7839690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	90	225	0	0.410959	0	A|0.972;G|0.028	0.028	strong	CSMD3_ENST00000343508,colon,carcinoma,-2,2	CSMD3	2325	2	NM_198123	exon19	c.T3075C	p.D1025D	GGAGAAATCATGA	.	PASS	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35450229	35450229	+	Missense_Mutation	SNP	C	C	T	rs2651079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	330	327	296	0	0.990909	0	C|0.367;T|0.633	0.633	strong	.	ZNF792	46	.	NM_175872	exon4	c.G530A	p.R177Q	TGTTTCCGGGGAA	.	PASS	Atlas-SNP
SLC35E4	339665	hgsc.bcm.edu	37	22	31032881	31032881	+	Silent	SNP	G	G	A	rs8136373	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	38	46	0	0.974359	0	G|0.900;A|0.100	0.100	strong	.	SLC35E4	22	.	NM_001001479	exon1	c.G444A	p.L148L	CACCCTGGCCCTG	.	PASS	Atlas-SNP
CAPN9	10753	hgsc.bcm.edu	37	1	230916057	230916057	+	Missense_Mutation	SNP	T	T	G	rs79844715	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	71	136	0	0.47973	0	T|0.998;G|0.002	0.002	strong	.	CAPN9	116	.	NM_006615	exon10	c.T1247G	p.L416R	ATGTGCTGACAAT	.	PASS	Atlas-SNP
ZNF678	339500	hgsc.bcm.edu	37	1	227842516	227842516	+	Missense_Mutation	SNP	G	G	C	rs61744724	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	30	56	0	0.5	0	G|0.987;C|0.013	0.013	strong	.	ZNF678	137	.	NM_178549	exon4	c.G730C	p.V244L	GACAAAGTTTTTA	.	PASS	Atlas-SNP
ZNF10	7556	hgsc.bcm.edu	37	12	133732512	133732512	+	Missense_Mutation	SNP	A	A	G	rs11147259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	50	113	0	0.413223	0	A|0.918;G|0.082	0.082	strong	ZNF10,bladder,carcinoma,+1,1	ZNF10	58	1	NM_015394	exon5	c.A680G	p.Q227R	TTATTCAGTTTGC	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662732	7662732	+	Silent	SNP	C	C	T	rs4643071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	74	149	0	0.573643	0	C|0.307;T|0.693	0.693	strong	PPFIBP2,NS,carcinoma,+1,1	PPFIBP2	87	1	NM_003621	exon16	c.C1398T	p.D466D	CTGGGACGACACT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410827	105410827	+	Missense_Mutation	SNP	C	C	T	rs28380382	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	272	272	262	0	1	0	C|0.468;T|0.532	0.532	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G10961A	p.G3654E	GACTTCCCTGGGG	.	PASS	Atlas-SNP
SNAP91	9892	hgsc.bcm.edu	37	6	84303273	84303273	+	Silent	SNP	G	G	A	rs181491904	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	57	96	0	0.542857	0	G|0.995;A|0.005	0.005	strong	.	SNAP91	199	.	NM_001242792	exon17	c.C1620T	p.T540T	AGCGGCGGTGGCA	.	PASS	Atlas-SNP
OR10AG1	282770	hgsc.bcm.edu	37	11	55735343	55735343	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	226	3	168	1	0.0132743	0.00595238	.	.	none	OR10AG1,NS,carcinoma,0,1	OR10AG1	100	1	NM_001005491	exon1	c.G597A	p.T199T	TGGCACCGTGATA	.	scavenged	Atlas-SNP
AFAP1L2	84632	hgsc.bcm.edu	37	10	116056779	116056779	+	Silent	SNP	C	C	T	rs62641713	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	337	337	297	1	1	0.003367	C|0.953;T|0.047	0.047	strong	.	AFAP1L2	90	.	NM_001001936	exon18	c.G2388A	p.S796S	CACGACCGAGAGA	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123725971	123725971	+	Silent	SNP	C	C	T	rs12237774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	279	101	271	0	0.362007	0	C|0.914;T|0.086	0.086	strong	.	C5	124	.	NM_001735	exon34	c.G4266A	p.A1422A	CATCACCGCATGA	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11289073	11289073	+	Missense_Mutation	SNP	C	C	T	rs115473443	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	45	81	0	0.441176	0	C|0.985;T|0.015	0.015	strong	.	KANK2	47	.	NM_015493	exon4	c.G1492A	p.A498T	GGTCTGCAACCTC	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29416750	29416750	+	Silent	SNP	A	A	G	rs55772745	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	78	146	0	0.586466	0	A|0.979;G|0.021	0.021	strong	.	ALK	533	.	NM_004304	exon29	c.T4203C	p.Y1401Y	TGGACCATATTCT	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49951232	49951232	+	Silent	SNP	T	T	C	rs2241418	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	99	109	1	0.99	0.00917431	T|0.792;C|0.208	0.208	strong	.	KCNH3	88	.	NM_012284	exon15	c.T2748C	p.G916G	GGAGGGTCCGTGC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78938186	78938186	+	Missense_Mutation	SNP	G	G	C	rs2803429	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	66	112	0	0.589286	0	G|0.675;C|0.325	0.325	strong	.	PCSK5	329	.	NM_001190482	exon31	c.G4240C	p.E1414Q	GAAAAGGAGACTA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2162810	2162810	+	Missense_Mutation	SNP	G	G	A	rs147910505	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	11	27	0	0.423077	0	G|0.999;A|0.001	0.001	strong	.	PKD1	184	.	NM_000296	exon13	c.C3140T	p.S1047L	ACGGCCGAGTCCA	.	PASS	Atlas-SNP
CRELD1	78987	hgsc.bcm.edu	37	3	9984855	9984855	+	Silent	SNP	C	C	T	rs79223485	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	43	107	0	0.421569	0	C|0.975;T|0.025	0.025	strong	.	CRELD1	48	.	NM_001077415	exon9	c.C912T	p.L304L	GTGTCTCGGTGAG	.	PASS	Atlas-SNP
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227172	99227172	+	Silent	SNP	A	A	G	rs1859690	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	80	70	0	1	0	A|0.737;G|0.263	0.263	strong	.	.	.	.	NM_145115	exon8	c.A1164G	p.E388E	GAGAGAATACCTG	.	PASS	Atlas-SNP
ANKRD36B	57730	hgsc.bcm.edu	37	2	98197010	98197010	+	Missense_Mutation	SNP	G	G	A	rs2922614	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	517	223	533	0	0.431335	0	G|0.984;A|0.016	0.016	strong	.	.	.	.	NM_025190	exon4	c.C472T	p.L158F	CAGCAAGTAACAG	.	PASS	Atlas-SNP
ARVCF	421	hgsc.bcm.edu	37	22	19968971	19968971	+	Missense_Mutation	SNP	G	G	A	rs2073748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	7	9	0	0.5	0	G|0.654;T|0.005	.	strong	.	ARVCF	54	.	NM_001670	exon5	c.C659T	p.P220L	GGGCCTGGGCCAA	.	PASS	Atlas-SNP
OTUD1	220213	hgsc.bcm.edu	37	10	23729361	23729361	+	Silent	SNP	C	C	G	rs141182498	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	90	42	84	0	0.466667	0	C|0.989;G|0.011	0.011	strong	.	OTUD1	9	.	NM_001145373	exon1	c.C975G	p.V325V	AGCTGTCAGCAAG	.	PASS	Atlas-SNP
EPM2AIP1	9852	hgsc.bcm.edu	37	3	37033348	37033348	+	Silent	SNP	A	A	G	rs200289425	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	65	144	0	0.481481	0	A|0.999;G|0.001	0.001	strong	.	EPM2AIP1	47	.	NM_014805	exon1	c.T1221C	p.A407A	AAAGGCAGCAGCA	.	PASS	Atlas-SNP
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988193	50988193	+	Missense_Mutation	SNP	A	A	G	rs131779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	31	43	0	1	0	A|0.413;G|0.587	0.587	strong	KLHDC7B,NS,carcinoma,0,1	KLHDC7B	39	1	NM_138433	exon1	c.A1598G	p.H533R	CACTGCACTGCAC	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444693	61444693	+	Missense_Mutation	SNP	G	G	A	rs35813009	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	13	8	8	0	0.615385	0	G|0.780;A|0.220	0.220	strong	OGFR,rectum,carcinoma,0,2	OGFR	63	2	NM_007346	exon7	c.G1726A	p.E576K	CCAGCCGAGAGCC	.	scavenged	Atlas-SNP
CNTROB	116840	hgsc.bcm.edu	37	17	7849087	7849087	+	Silent	SNP	C	C	G	rs4462665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	47	69	0	0.516484	0	C|0.474;G|0.526	0.526	strong	CNTROB,colon,carcinoma,0,1	CNTROB	61	1	NM_001037144	exon13	c.C1776G	p.P592P	GGAGCCCGAGAAG	.	PASS	Atlas-SNP
NET1	10276	hgsc.bcm.edu	37	10	5498102	5498102	+	Missense_Mutation	SNP	C	C	T	rs34658946	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	20	65	0	0.363636	0	C|0.984;T|0.016	0.016	strong	.	NET1	82	.	NM_001047160	exon11	c.C1250T	p.T417I	CCGTCACACGGAA	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	37	4	119952589	119952589	+	Missense_Mutation	SNP	G	G	A	rs115012720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	42	53	0	0.506024	0	G|0.993;A|0.007	0.007	strong	.	SYNPO2	353	.	NM_001128934	exon4	c.G2659A	p.V887M	AAGTATGTGGTCG	.	PASS	Atlas-SNP
LUZP1	7798	hgsc.bcm.edu	37	1	23419914	23419914	+	Missense_Mutation	SNP	G	G	A	rs142425004	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	313	147	341	0	0.469649	0	G|0.999;A|0.001	0.001	strong	LUZP1,NS,carcinoma,+1,1	LUZP1	83	1	NM_033631	exon4	c.C841T	p.R281C	GATTGCGGTTCTT	.	PASS	Atlas-SNP
C16orf89	146556	hgsc.bcm.edu	37	16	5115811	5115811	+	Silent	SNP	G	G	A	rs35751409	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	61	127	0	0.426573	0	G|0.990;A|0.010	0.010	strong	.	C16orf89	64	.	NM_001098514	exon1	c.C99T	p.A33A	AATGGTGGCTTTA	.	PASS	Atlas-SNP
CDK2AP1	8099	hgsc.bcm.edu	37	12	123749834	123749834	+	Silent	SNP	G	G	A	rs76783415	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	77	147	0	0.52027	0	G|0.970;A|0.030	0.030	strong	.	CDK2AP1	8	.	NM_004642	exon3	c.C189T	p.Y63Y	CTCCGCGTATTTG	.	PASS	Atlas-SNP
C7orf71	285941	hgsc.bcm.edu	37	7	26678856	26678856	+	Silent	SNP	A	A	G	rs57000259	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	31	40	0	1	0	A|0.601;G|0.399	0.399	strong	.	C7orf71	6	.	NM_001145531	exon2	c.A93G	p.R31R	GACAAGACACATG	.	PASS	Atlas-SNP
GPR97	222487	hgsc.bcm.edu	37	16	57722328	57722328	+	Silent	SNP	C	C	T	rs12444859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	65	115	0	0.477941	0	C|0.646;T|0.354	0.354	strong	.	GPR97	74	.	NM_170776	exon12	c.C1605T	p.S535S	CTCCTCCTCTACT	.	PASS	Atlas-SNP
TATDN2	9797	hgsc.bcm.edu	37	3	10311939	10311939	+	Missense_Mutation	SNP	C	C	T	rs2075352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	71	67	0	0.591667	0	C|0.833;N|0.000	.	strong	.	TATDN2	59	.	NM_014760	exon4	c.C1073T	p.P358L	CCGTTCCGGAGCC	.	PASS	Atlas-SNP
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	38	72	0	0.542857	0	T|0.702;C|0.298	0.298	strong	.	CBY1	10	.	NM_001002880	exon6	c.T450C	p.A150A	CACTGCTGAATCC	.	PASS	Atlas-SNP
HPSE2	60495	hgsc.bcm.edu	37	10	100219374	100219374	+	Missense_Mutation	SNP	T	T	A	rs10883100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	48	108	0	0.466019	0	A|0.539;N|0.000	0.539	strong	HPSE2,NS,carcinoma,0,1	HPSE2	203	1	NM_021828	exon12	c.A1736T	p.Y579F	ACCACATAAAAGC	.	PASS	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116131916	116131916	+	Missense_Mutation	SNP	G	G	A	rs377189582	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	50	59	0	0.746269	0	.	.	alt	.	BSPRY	21	.	NM_017688	exon6	c.G703A	p.D235N	CGGATCGATGAGA	.	PASS	Atlas-SNP
TNIP2	79155	hgsc.bcm.edu	37	4	2747194	2747194	+	Silent	SNP	C	C	T	rs61734614	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	77	104	0	0.534722	0	C|0.984;T|0.016	0.016	strong	.	TNIP2	28	.	NM_024309	exon3	c.G636A	p.L212L	TTTTAACAGTCGA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46652737	46652737	+	Silent	SNP	G	G	A	rs6008362	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	67	112	0	0.553719	0	G|0.737;A|0.263	0.263	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C6483T	p.C2161C	CAAGACGCAGATC	.	PASS	Atlas-SNP
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	52	71	0	0.525253	0	G|0.541;A|0.459	0.459	strong	TRIT1,NS,carcinoma,0,2	TRIT1	40	2	NM_017646	exon1	c.C33T	p.P11P	GCCCACGGGAACT	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43524188	43524188	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	7	49	0	0.148936	0	.	.	none	.	UMODL1	186	.	NM_173568	exon9	c.C1510T	p.R504C	GGGACACGCGTGC	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150214	11150214	+	Silent	SNP	G	G	A	rs11054142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	40	98	0	0.373832	0	G|0.672;A|0.328	0.328	strong	.	TAS2R20	17	.	NM_176889	exon1	c.C261T	p.A87A	TGCCCAGGCATTA	.	PASS	Atlas-SNP
SNAI1	6615	hgsc.bcm.edu	37	20	48600809	48600809	+	Silent	SNP	G	G	A	rs1063210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	182	171	1	0.994536	0.00584795	G|0.726;A|0.274	0.274	strong	.	SNAI1	28	.	NM_005985	exon2	c.G531A	p.T177T	CCACACGCTGCCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416010	105416010	+	Silent	SNP	T	T	C	rs2582511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	267	266	272	1	0.996255	0.00367647	T|0.428;C|0.572	0.572	strong	AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.A5778G	p.T1926T	AACATCTGTCTGG	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95921722	95921722	+	Missense_Mutation	SNP	G	G	A	rs74079986	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	45	79	0	0.6	0	G|0.988;A|0.012	0.012	strong	.	SYNE3	130	.	NM_152592	exon5	c.C1129T	p.R377C	AGTAGCGTCTCCA	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28712639	28712639	+	Silent	SNP	T	T	C	rs16961338	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	50	144	0	0.480769	0	T|0.959;C|0.041	0.041	strong	.	DSC1	240	.	NM_004948	exon14	c.A2130G	p.T710T	GAAACATGTAAAC	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33457328	33457328	+	Silent	SNP	C	C	T	rs150504912		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	50	75	1	0.531915	0.0133333	C|1.000;T|0.000	0.000	weak	CEP89,caecum,carcinoma,0,1	CEP89	82	1	NM_032816	exon2	c.G84A	p.P28P	TGCCTTCGGAGCA	.	scavenged	Atlas-SNP
KIAA1456	57604	hgsc.bcm.edu	37	8	12878755	12878755	+	Silent	SNP	C	C	T	rs61736893	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	37	97	0	0.393617	0	C|0.978;T|0.022	0.022	strong	.	KIAA1456	20	.	NM_020844	exon5	c.C567T	p.P189P	CCATCCCTACCAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512768	195512768	+	Missense_Mutation	SNP	T	T	A	rs2688553	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	287	177	370	1	0.616725	0.0027027	T|0.934;A|0.066	0.066	strong	.	MUC4	1505	.	NM_018406	exon2	c.A5683T	p.N1895Y	CTGAGTTAGTGTC	.	PASS	Atlas-SNP
ACOX3	8310	hgsc.bcm.edu	37	4	8390948	8390948	+	Missense_Mutation	SNP	C	C	T	rs13434465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	47	86	0	0.51087	0	C|0.954;T|0.046	0.046	strong	.	ACOX3	70	.	NM_001101667	exon13	c.G1489A	p.D497N	TCTGGTCAAGGAT	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125298690	125298690	+	Silent	SNP	G	G	A	rs3761552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	388	387	310	1	0.997423	0.00322581	G|0.437;A|0.563	0.563	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.C1218T	p.C406C	TCTGCCGCAGGCA	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21078693	21078693	+	Silent	SNP	T	T	A	rs861424	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	54	104	0	0.509434	0	G|0.438;T|0.562	.	strong	.	DNAH3	1142	.	NM_017539	exon24	c.A3429T	p.A1143A	CTTCTCTGCCATC	.	PASS	Atlas-SNP
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24331328	24331328	+	Silent	SNP	A	A	G	rs150934306	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	562	221	524	2	0.393238	0.00381679	A|0.947;G|0.053	0.053	strong	.	.	.	.	NM_001136233	exon1	c.T105C	p.T35T	CTGCAGAGTTTTT	.	PASS	Atlas-SNP
KCNQ2	3785	hgsc.bcm.edu	37	20	62078184	62078184	+	Silent	SNP	G	G	C	rs145415996	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	39	114	0	0.428571	0	G|0.998;C|0.002	0.002	strong	.	KCNQ2	201	.	NM_172106	exon2	c.C303G	p.L101L	AACCAGGAGGAAC	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111854859	111854859	+	Missense_Mutation	SNP	C	C	T	rs61752461	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	92	188	0	0.467005	0	C|0.988;T|0.012	0.012	strong	CHIA_ENST00000369740,NS,carcinoma,-2,1	CHIA	115	1	NM_201653	exon4	c.C103T	p.R35W	CAGTACCGGCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512455	195512455	+	Missense_Mutation	SNP	G	G	T	rs202241172	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	109	390	0	0.521531	0	G|0.993;T|0.007	0.007	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5996A	p.T1999N	AGAGGGGTGGCAT	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56369668	56369668	+	Silent	SNP	C	C	T	rs112565033	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	143	78	174	0	0.545455	0	C|0.994;T|0.006	0.006	strong	.	NLRP4	331	.	NM_134444	exon3	c.C909T	p.N303N	ATTCAACGAGAGT	.	PASS	Atlas-SNP
CCDC151	115948	hgsc.bcm.edu	37	19	11537006	11537006	+	Silent	SNP	G	G	A	rs61739937	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	19	52	0	0.44186	0	G|0.986;A|0.014	0.014	strong	.	CCDC151	44	.	NM_145045	exon7	c.C921T	p.R307R	CTCGGCGCGCTTC	.	PASS	Atlas-SNP
TMEM132D	121256	hgsc.bcm.edu	37	12	129559086	129559086	+	Missense_Mutation	SNP	C	C	A	rs555131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	72	124	0	0.510638	0	C|0.938;A|0.062	0.062	strong	.	TMEM132D	299	.	NM_133448	exon9	c.G2634T	p.L878F	GGTCTGCAAGTGG	.	PASS	Atlas-SNP
EDIL3	10085	hgsc.bcm.edu	37	5	83433087	83433087	+	Silent	SNP	G	G	A	rs58219060	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	59	0	0.522388	0	G|0.965;A|0.035	0.035	strong	.	EDIL3	94	.	NM_005711	exon5	c.C441T	p.G147G	AAATTCGCCTGGG	.	PASS	Atlas-SNP
TPMT	7172	hgsc.bcm.edu	37	6	18139214	18139214	+	Silent	SNP	G	G	A	rs56622291	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	132	203	0	0.503817	0	G|0.250;A|0.750	0.750	strong	.	TPMT	17	.	NM_000367	exon6	c.C474T	p.I158I	TGGATTGATGGCA	.	PASS	Atlas-SNP
XPA	7507	hgsc.bcm.edu	37	9	100449436	100449436	+	Missense_Mutation	SNP	A	A	G	rs143374902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	55	76	0	0.774648	0	A|0.996;G|0.004	0.004	strong	.	XPA	21	.	NM_000380	exon4	c.T497C	p.V166A	TTCTTCACAATAA	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56388238	56388238	+	Missense_Mutation	SNP	C	C	G	rs2680704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	124	118	1	0.992	0.00847458	C|0.730;G|0.270	0.270	strong	BZRAP1_ENST00000355701,NS,carcinoma,0,4	BZRAP1	287	4	NM_004758	exon19	c.G3418C	p.A1140P	CTTTTGCCATCTC	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	37001761	37001761	+	Missense_Mutation	SNP	T	T	C	rs2232618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	34	73	0	0.414634	0	T|0.884;C|0.116	0.116	strong	.	LBP	60	.	NM_004139	exon13	c.T1306C	p.F436L	AACACCTTCTACC	.	PASS	Atlas-SNP
CCDC83	220047	hgsc.bcm.edu	37	11	85627108	85627108	+	Silent	SNP	T	T	C	rs7927222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	78	188	0	0.453488	0	T|0.812;C|0.188	0.188	strong	.	CCDC83	48	.	NM_173556	exon11	c.T1005C	p.S335S	AGAAAGTAGAGAC	.	PASS	Atlas-SNP
IFLTD1	160492	hgsc.bcm.edu	37	12	25672877	25672877	+	Missense_Mutation	SNP	C	C	T	rs34074522	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	50	159	0	0.420168	0	C|0.980;T|0.020	0.020	strong	IFLTD1_ENST00000458174,NS,carcinoma,+1,2	IFLTD1	121	2	NM_001145728	exon7	c.G931A	p.A311T	TTGTAGCTGTAGA	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909637	123909637	+	Silent	SNP	G	G	T	rs78602645		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	114	412	0	0.5	0	.	.	weak	OR10G7,NS,carcinoma,0,1	OR10G7	103	1	NM_001004463	exon1	c.C72A	p.P24P	AAAGAGGGGGGCG	.	PASS	Atlas-SNP
OR1N1	138883	hgsc.bcm.edu	37	9	125288893	125288893	+	Missense_Mutation	SNP	C	C	T	rs58226717	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	31	95	0	0.303922	0	C|0.949;T|0.051	0.051	strong	OR1N1,NS,carcinoma,-1,2	OR1N1	38	2	NM_012363	exon1	c.G680A	p.R227Q	CGGGTTCGGACCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195514969	195514969	+	Missense_Mutation	SNP	G	G	A	rs192133475	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	354	163	128	1	0.460452	0.0078125	G|0.855;A|0.145	0.145	strong	MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	NM_018406	exon2	c.C3482T	p.A1161V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183616884	183616884	+	Missense_Mutation	SNP	C	C	T	rs10911390	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	68	125	0	0.453333	0	C|0.929;T|0.071	0.071	strong	.	APOBEC4	45	.	NM_203454	exon2	c.G1033A	p.V345M	TTTCCACTATCTC	.	PASS	Atlas-SNP
MORN4	118812	hgsc.bcm.edu	37	10	99376152	99376152	+	Silent	SNP	A	A	G	rs3814556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	37	58	0	0.4625	0	A|0.673;G|0.327	0.327	strong	MORN4_ENST00000307450,NS,carcinoma,0,2	MORN4	24	2	NM_001098831	exon5	c.T309C	p.P103P	ACCATCAGGGAAA	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	37	15	77407516	77407516	+	Missense_Mutation	SNP	G	G	T	rs56079860	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	76	184	0	0.444444	0	G|0.984;T|0.016	0.016	strong	.	.	.	.	NM_024776	exon8	c.C4223A	p.P1408Q	TCATCTGGATCCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124288212	124288212	+	Silent	SNP	C	C	T	rs80041527	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	14	58	0	0.378378	0	C|0.827;T|0.173	0.173	strong	.	DNAH10	888	.	NM_207437	exon16	c.C2265T	p.I755I	AGGTATCGGTGAC	.	PASS	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	101	105	1	0.990196	0.00952381	C|0.764;T|0.236	0.236	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.G492A	p.E164E	GTCTTCCTCTTCG	.	PASS	Atlas-SNP
SLC5A2	6524	hgsc.bcm.edu	37	16	31501642	31501642	+	Missense_Mutation	SNP	C	C	T	rs61746400	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	31	84	0	0.413333	0	C|0.992;T|0.008	0.008	strong	.	SLC5A2	58	.	NM_003041	exon14	c.C1805T	p.P602L	AGGCCCCGGCACC	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31112737	31112737	+	Missense_Mutation	SNP	C	C	A	rs130079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	18	46	0	0.529412	0	C|0.801;A|0.199	0.199	strong	.	CCHCR1	68	.	NM_001105564	exon14	c.G1990T	p.G664C	GCTGGCCCTGGCG	.	PASS	Atlas-SNP
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	85	128	0	0.505952	0	C|0.690;T|0.310	0.310	strong	.	ILK	41	.	NM_001014794	exon4	c.C297T	p.H99H	TGAACACGGGAAT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361038	107361038	+	Silent	SNP	C	C	T	rs75872480	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	134	173	0	0.632075	0	C|0.998;T|0.002	0.002	strong	OR13C5,NS,haematopoietic_neoplasm,-1,1	OR13C5	60	1	NM_001004482	exon1	c.G657A	p.T219T	GATTAACGTGTAA	.	PASS	Atlas-SNP
EDEM2	55741	hgsc.bcm.edu	37	20	33706509	33706509	+	Silent	SNP	G	G	A	rs3192415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	100	95	0	0.990099	0	G|0.886;A|0.114	0.114	strong	.	EDEM2	46	.	NM_018217	exon10	c.C1128T	p.S376S	CATTGCGCTTTCA	.	PASS	Atlas-SNP
DCAF4L2	138009	hgsc.bcm.edu	37	8	88886059	88886059	+	Silent	SNP	G	G	A	rs142584363	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	283	3	275	1	0.0106007	0.00363636	G|0.998;A|0.002	0.002	strong	DCAF4L2,NS,carcinoma,-1,2	DCAF4L2	187	2	NM_152418	exon1	c.C141T	p.R47R	CAGCTCGCGAGCT	.	scavenged	Atlas-SNP
CARD17	440068	hgsc.bcm.edu	37	11	104971257	104971257	+	Missense_Mutation	SNP	G	G	A	rs12806837	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	66	200	0	0.314286	0	G|0.903;A|0.097	0.097	strong	.	CARD17	15	.	NM_001007232	exon2	c.C257T	p.T86M	CCCAGCGTCCCTG	.	PASS	Atlas-SNP
AGRN	375790	hgsc.bcm.edu	37	1	979748	979748	+	Missense_Mutation	SNP	A	A	T	rs113288277	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	84	109	0	0.512195	0	A|0.975;T|0.025	0.025	strong	.	AGRN	110	.	NM_198576	exon12	c.A2183T	p.E728V	GCACCGAGTGTGA	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56001665	56001665	+	Missense_Mutation	SNP	C	C	T	rs114976626	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	58	113	0	0.471545	0	C|0.956;T|0.044	0.044	strong	.	SSC5D	65	.	NM_001195267	exon5	c.C476T	p.A159V	TCCCAGCCCCCCG	.	PASS	Atlas-SNP
EPHB2	2048	hgsc.bcm.edu	37	1	23222008	23222008	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	59	103	0	0.513043	0	.	.	none	.	EPHB2	257	.	NM_004442	exon8	c.C1635T	p.I545I	CATCATCGGCTCC	.	PASS	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	25	53	0	0.568182	0	T|0.004;G|0.002	.	strong	.	C20orf111	28	.	NM_016470	exon4	c.T221G	p.V74G	GTTCTCACTGCTC	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76853783	76853783	+	Missense_Mutation	SNP	T	T	C	rs1052030	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	129	142	0	0.992308	0	T|0.491;C|0.509	0.509	strong	.	MYO7A	164	.	NM_001127179	exon3	c.T47C	p.L16S	TGAGATTGGGGCA	.	PASS	Atlas-SNP
UAP1	6675	hgsc.bcm.edu	37	1	162560209	162560209	+	Silent	SNP	G	G	A	rs61743694	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	88	167	0	0.54321	0	G|0.969;A|0.031	0.031	strong	.	UAP1	47	.	NM_003115	exon8	c.G1266A	p.R422R	TGCAAGGCATGCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940540	144940540	+	Silent	SNP	G	G	A	rs56034452	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	12	42	1	0.255319	0.0238095	G|0.500;A|0.500	0.500	weak	EPPK1,NS,carcinoma,0,3	EPPK1	199	3	NM_031308	exon1	c.C6882T	p.G2294G	GATCTCGCCGCCC	.	scavenged	Atlas-SNP
CHAF1B	8208	hgsc.bcm.edu	37	21	37787615	37787615	+	Missense_Mutation	SNP	A	A	C	rs74900401	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	20	38	0	0.4	0	A|0.984;C|0.016;T|0.000	0.016	strong	.	CHAF1B	47	.	NM_005441	exon13	c.A1516C	p.K506Q	CCCTTAAAGACGG	.	PASS	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	37	1	38184470	38184470	+	Silent	SNP	C	C	G	rs610213	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	224	101	191	0	0.450893	0	C|0.889;G|0.111	0.111	strong	.	EPHA10	120	.	NM_001099439	exon16	c.G2775C	p.A925A	ACGGTCCGCTAGT	.	PASS	Atlas-SNP
TMEM254	80195	hgsc.bcm.edu	37	10	81838864	81838864	+	Missense_Mutation	SNP	A	A	G	rs61748824	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	232	120	193	0	0.517241	0	A|0.988;G|0.012	0.012	strong	.	TMEM254	1	.	NM_001270368	exon1	c.A83G	p.N28S	CCAGCAATGCGGC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8171068	8171068	+	Silent	SNP	G	G	A	rs7258713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	42	69	0	0.512195	0	G|0.925;A|0.075	0.075	strong	.	FBN3	300	.	NM_032447	exon37	c.C4737T	p.C1579C	GTTGACGCAGTCA	.	PASS	Atlas-SNP
ADAM33	80332	hgsc.bcm.edu	37	20	3651742	3651742	+	Silent	SNP	C	C	G	rs528557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	173	187	1	0.994253	0.00534759	C|0.599;G|0.401	0.401	strong	.	ADAM33	76	.	NM_025220	exon19	c.G2151C	p.G717G	GCCGGCCCCTGGG	.	PASS	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40512906	40512906	+	Silent	SNP	A	A	G	rs35611758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	137	73	151	0	0.532847	0	A|0.915;G|0.085	0.085	strong	.	BUB1B	71	.	NM_001211	exon23	c.A3099G	p.K1033K	GAACAAAGCCTTA	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179285781	179285781	+	Missense_Mutation	SNP	G	G	A	rs199537217	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	27	59	0	0.54	0	G|0.999;A|0.001	0.001	strong	.	C5orf45	23	.	NM_016175	exon1	c.C16T	p.R6C	GAGAACGCTGAAG	.	PASS	Atlas-SNP
OR6F1	343169	hgsc.bcm.edu	37	1	247875415	247875415	+	Missense_Mutation	SNP	A	A	G	rs2282316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	55	76	0	0.544554	0	A|0.635;G|0.365	0.365	strong	OR6F1,NS,carcinoma,0,1	OR6F1	88	1	NM_001005286	exon1	c.T643C	p.F215L	AGACAAAGGTGAT	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	20	44	0	0.526316	0	C|0.631;T|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.G1701A	p.P567P	AGCCAGCGGTGAC	.	PASS	Atlas-SNP
ATP6V1G3	127124	hgsc.bcm.edu	37	1	198498234	198498234	+	Missense_Mutation	SNP	C	C	G	rs16843254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	58	66	0	0.58	0	C|0.959;G|0.041	0.041	strong	.	ATP6V1G3	26	.	NM_133262	exon3	c.G160C	p.E54Q	GAAACTCTTTATC	.	PASS	Atlas-SNP
POLE4	56655	hgsc.bcm.edu	37	2	75185856	75185856	+	Missense_Mutation	SNP	G	G	T	rs12366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	30	45	0	0.545455	0	G|0.638;T|0.362	0.362	strong	.	POLE4	2	.	NM_019896	exon1	c.G50T	p.G17V	AGGAGGGACCTGC	.	PASS	Atlas-SNP
UBALD2	283991	hgsc.bcm.edu	37	17	74266322	74266322	+	Silent	SNP	T	T	C	rs712833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	67	135	0	0.471831	0	T|0.888;C|0.112	0.112	strong	.	.	.	.	NM_182565	exon3	c.T231C	p.D77D	CCCCGATGCGCTG	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53294381	53294381	+	Silent	SNP	T	T	C	rs8608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	33	60	0	0.458333	0	T|0.483;C|0.517	0.517	strong	.	KRT8	41	.	NM_001256282	exon5	c.A765G	p.L255L	TTCATATAGCTGC	.	PASS	Atlas-SNP
APOL5	80831	hgsc.bcm.edu	37	22	36122930	36122930	+	Missense_Mutation	SNP	C	C	T	rs2076671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	135	143	1	1	0.00699301	C|0.663;T|0.337	0.337	strong	.	APOL5	45	.	NM_030642	exon3	c.C815T	p.T272M	TCTGGACGGCTAG	.	PASS	Atlas-SNP
CXXC11	285093	hgsc.bcm.edu	37	2	242814778	242814778	+	Silent	SNP	C	C	T	rs7597435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	88	182	0	0.444444	0	C|0.963;T|0.037	0.037	strong	.	.	.	.	NM_173821	exon2	c.C1071T	p.T357T	GCCCACCGATGGC	.	PASS	Atlas-SNP
REG4	83998	hgsc.bcm.edu	37	1	120341193	120341193	+	Missense_Mutation	SNP	C	C	T	rs75358916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	225	120	203	1	0.533333	0.00492611	C|0.991;T|0.009	0.009	strong	.	REG4	36	.	NM_032044	exon5	c.G336A	p.M112I	CAGATACATGGCC	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51096974	51096974	+	Missense_Mutation	SNP	C	C	T	rs2240090	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	257	210	0	0.992278	0	C|0.360;T|0.640	0.640	strong	.	COBL	167	.	NM_015198	exon10	c.G1819A	p.V607I	TTCCGACGTCATG	.	PASS	Atlas-SNP
C19orf45	374877	hgsc.bcm.edu	37	19	7573225	7573225	+	Missense_Mutation	SNP	C	C	T	rs141790796	bycluster;alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	10	124	0	0.0719424	0	C|1.000;A|0.000	.	alt	.	C19orf45	36	.	NM_198534	exon9	c.C1427T	p.P476L	TCGTGCCCCTGGG	.	PASS	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	37035934	37035934	+	Missense_Mutation	SNP	A	A	G	rs2072526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	178	92	170	0	0.516854	0	G|0.137;N|0.000	0.137	strong	.	VIT	138	.	NM_053276	exon15	c.A1709G	p.K570R	GCAGCAAGCCTGA	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37182940	37182940	+	Silent	SNP	T	T	A	rs73750949	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	41	79	0	0.525641	0	T|0.973;A|0.027	0.027	strong	.	C5orf42	422	.	NM_023073	exon26	c.A5343T	p.T1781T	GGCAGCTGTAGAG	.	PASS	Atlas-SNP
TXK	7294	hgsc.bcm.edu	37	4	48096101	48096101	+	Silent	SNP	A	A	G	rs73151620	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	92	87	0	1	0	A|0.959;G|0.041	0.041	strong	.	TXK	58	.	NM_003328	exon8	c.T702C	p.N234N	GGCTGCATTGTGC	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169529973	169529973	+	Silent	SNP	C	C	T	rs6029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	80	151	0	0.5	0	C|0.653;T|0.347	0.347	strong	.	F5	301	.	NM_000130	exon4	c.G405A	p.A135A	CTTCTCCGCAGGG	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150319	11150319	+	Silent	SNP	T	T	C	rs11054143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	262	121	252	0	0.461832	0	T|0.678;C|0.322	0.322	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A156G	p.A52A	GGAGACTGCCAGA	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89655120	89655120	+	Missense_Mutation	SNP	G	G	A	rs28568523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	41	66	0	0.706897	0	G|0.992;A|0.008	0.008	strong	.	CPNE7	56	.	NM_014427	exon12	c.G1190A	p.R397Q	ACCCGCGGAACAG	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36856579	36856579	+	Silent	SNP	G	G	A	rs74723843	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	27	12	37	0	0.444444	0	G|0.974;A|0.026	0.026	strong	.	KIAA1755	145	.	NM_001029864	exon6	c.C1935T	p.P645P	CAGACCGGGCTGT	.	PASS	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475958	140475958	+	Silent	SNP	G	G	T	rs371176940	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	10	209	0	0.0487805	0	.	.	alt	.	PCDHB2	163	.	NM_018936	exon1	c.G1584T	p.A528A	GCAGGCGTTCGAG	.	PASS	Atlas-SNP
TRIM15	89870	hgsc.bcm.edu	37	6	30131515	30131515	+	Silent	SNP	C	C	A	rs2523733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	133	61	121	0	0.458647	0	C|0.820;A|0.180	0.180	strong	.	TRIM15	34	.	NM_033229	exon1	c.C54A	p.L18L	TACCCTCTGTGCG	.	PASS	Atlas-SNP
CC2D2B	387707	hgsc.bcm.edu	37	10	97779510	97779510	+	Missense_Mutation	SNP	T	T	C	rs9943393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	288	127	271	0	0.440972	0	T|0.988;C|0.012	0.012	strong	.	CC2D2B	46	.	NM_001001732	exon8	c.T709C	p.Y237H	TTTGACTATTCAA	.	PASS	Atlas-SNP
GLIS1	148979	hgsc.bcm.edu	37	1	54060107	54060107	+	Missense_Mutation	SNP	A	A	G	rs34961060	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	31	68	0	0.492063	0	A|0.968;G|0.032	0.032	strong	.	GLIS1	52	.	NM_147193	exon3	c.T469C	p.F157L	GCCCAAAGAGCTC	.	PASS	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	37	19	44740602	44740602	+	Silent	SNP	G	G	A	rs3810137	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	65	0	1	0	G|0.861;A|0.139	0.139	strong	ZNF227,NS,carcinoma,+1,2	ZNF227	62	2	NM_182490	exon6	c.G2019A	p.S673S	CAGTTCGCAGTTT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46786315	46786315	+	Missense_Mutation	SNP	T	T	C	rs4044210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	29	72	0	0.491525	0	T|0.693;C|0.307	0.307	strong	.	CELSR1	242	.	NM_014246	exon17	c.A6319G	p.I2107V	AGGAGATGGTGGT	.	PASS	Atlas-SNP
PRRG2	5639	hgsc.bcm.edu	37	19	50091798	50091798	+	Missense_Mutation	SNP	G	G	T	rs2288920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	127	94	0	1	0	G|0.723;T|0.277	0.277	strong	.	PRRG2	13	.	NM_000951	exon5	c.G346T	p.G116C	CTGACAGGTGGCA	.	PASS	Atlas-SNP
DNAJC17	55192	hgsc.bcm.edu	37	15	41068409	41068409	+	Missense_Mutation	SNP	C	C	T	rs73398528	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	46	88	0	0.446602	0	C|0.947;T|0.053	0.053	strong	.	DNAJC17	18	.	NM_018163	exon6	c.G463A	p.D155N	TCTGGTCACGCTC	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200945910	200945910	+	Silent	SNP	G	G	A	rs61740477	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	44	96	0	0.407407	0	G|0.958;A|0.042	0.042	strong	.	KIF21B	208	.	NM_001252102	exon32	c.C4437T	p.Y1479Y	CTTAACGTAGTGG	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22155520	22155520	+	Silent	SNP	A	A	G	rs7258270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	6	22	0	0.352941	0	A|0.814;G|0.186	0.186	strong	ZNF208_ENST00000428290,NS,carcinoma,-1,3	ZNF208	817	3	NM_007153	exon4	c.T2316C	p.T772T	CTCTACAGTATGA	.	PASS	Atlas-SNP
OR4B1	119765	hgsc.bcm.edu	37	11	48239071	48239071	+	Missense_Mutation	SNP	C	C	A	rs12292056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	125	226	0	0.510204	0	C|0.890;A|0.110	0.110	strong	OR4B1,NS,carcinoma,0,1	OR4B1	52	1	NM_001005470	exon1	c.C710A	p.T237N	TCTCCACCTGTGC	.	PASS	Atlas-SNP
LNP1	348801	hgsc.bcm.edu	37	3	100170600	100170600	+	Missense_Mutation	SNP	A	A	T	rs76354691	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	12	143	0	0.0888889	0	A|0.818;T|0.182	0.182	strong	.	LNP1	26	.	NM_001085451	exon3	c.A194T	p.H65L	ACTGCCATCCTAG	.	PASS	Atlas-SNP
SMYD2	56950	hgsc.bcm.edu	37	1	214507580	214507580	+	Missense_Mutation	SNP	A	A	G	rs34259050	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	86	133	0	0.480447	0	A|0.983;G|0.017	0.017	strong	.	SMYD2	40	.	NM_020197	exon11	c.A1150G	p.M384V	GCCTCCATGTGGT	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	717544	717544	+	Silent	SNP	G	G	C	rs3752492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	39	66	0	0.506494	0	G|0.777;C|0.223;A|0.001	0.223	strong	.	WDR90	107	.	NM_145294	exon41	c.G5202C	p.T1734T	CTTCACGGCCGCC	.	PASS	Atlas-SNP
CIC	23152	hgsc.bcm.edu	37	19	42795554	42795554	+	Silent	SNP	T	T	C	rs10410185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	71	115	0	0.537879	0	T|0.924;C|0.076	0.076	strong	.	CIC	249	.	NM_015125	exon10	c.T2634C	p.A878A	CCTGGCTGCCACT	.	PASS	Atlas-SNP
COL1A1	1277	hgsc.bcm.edu	37	17	48263786	48263786	+	Silent	SNP	G	G	A	rs34940368	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	63	134	1	0.446809	0.00746269	G|0.994;A|0.006	0.006	strong	COL1A1,rectum,carcinoma,0,1	COL1A1	158	1	NM_000088	exon49	c.C3897T	p.C1299C	GTACACGCAGGTC	.	scavenged	Atlas-SNP
EPC2	26122	hgsc.bcm.edu	37	2	149528738	149528738	+	Missense_Mutation	SNP	A	A	G	rs34444151	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	96	216	0	0.530387	0	A|0.992;G|0.008	0.008	strong	.	EPC2	57	.	NM_015630	exon10	c.A1502G	p.N501S	GGACCAATGCTTC	.	PASS	Atlas-SNP
TRIM72	493829	hgsc.bcm.edu	37	16	31235548	31235548	+	Silent	SNP	G	G	C	rs58585879	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	10	25	0	0.30303	0	G|0.966;C|0.034	0.034	strong	.	TRIM72	32	.	NM_001008274	exon7	c.G906C	p.L302L	GAGCCTGGTGGTG	.	PASS	Atlas-SNP
KCNQ1	3784	hgsc.bcm.edu	37	11	2683252	2683252	+	Silent	SNP	C	C	T	rs17215465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	83	133	0	0.553333	0	C|0.983;T|0.017	0.017	strong	.	KCNQ1	60	.	NM_000218	exon11	c.C1455T	p.F485F	CAGCTTCGCCGAG	.	PASS	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	37	15	52350879	52350879	+	Silent	SNP	T	T	C	rs2306793	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	41	75	0	0.5	0	T|0.921;C|0.079	0.079	strong	.	MAPK6	70	.	NM_002748	exon4	c.T750C	p.V250V	TCCTGTTGTACAT	.	PASS	Atlas-SNP
TEX11	56159	hgsc.bcm.edu	37	X	69772000	69772000	+	Silent	SNP	A	A	G	rs16991177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	203	90	229	0	0.44335	0	A|0.896;0|0.017	.	strong	.	TEX11	132	.	NM_001003811	exon29	c.T2541C	p.D847D	CAGAGCATCTTCA	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56085002	56085002	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	507	7	482	5	0.0138067	0.0103734	.	.	none	PSPH,NS,carcinoma,0,2	PSPH	23	2	NM_004577	exon6	c.G346A	p.V116I	GCTCTACAATACT	.	scavenged	Atlas-SNP
ZNF708	7562	hgsc.bcm.edu	37	19	21476912	21476912	+	Missense_Mutation	SNP	C	C	T	rs112819776	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	23	9	31	0	0.391304	0	C|0.994;T|0.006	0.006	strong	ZNF708,NS,carcinoma,0,1	ZNF708	66	1	NM_021269	exon4	c.G856A	p.G286S	CTTTGCCACATTC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225393828	225393828	+	Missense_Mutation	SNP	A	A	G	rs143058170	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	19	62	0	0.395833	0	A|0.993;G|0.007	0.007	strong	.	DNAH14	300	.	NM_001373	exon39	c.A6067G	p.N2023D	GTGGACAATCTCT	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113352899	113352899	+	Missense_Mutation	SNP	G	G	A	rs2074379	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	88	0	1	0	G|0.353;A|0.647	0.647	strong	.	ALPK1	125	.	NM_001102406	exon11	c.G2196A	p.M732I	GAATATGGGCACA	.	PASS	Atlas-SNP
ZNF614	80110	hgsc.bcm.edu	37	19	52520518	52520518	+	Silent	SNP	T	T	C	rs73934728	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	87	121	0	0.58	0	T|0.949;C|0.051	0.051	strong	.	ZNF614	58	.	NM_025040	exon5	c.A333G	p.R111R	AATATTTCTAAGT	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7963976	7963976	+	Missense_Mutation	SNP	T	T	C	rs2115108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	26	54	0	0.45614	0	T|0.676;C|0.324	0.324	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.T569C	p.M190T	TGGCCATGGCAGG	.	PASS	Atlas-SNP
C13orf35	400165	hgsc.bcm.edu	37	13	113333809	113333809	+	Missense_Mutation	SNP	G	G	A	rs114091399	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	51	94	0	0.472222	0	G|0.985;A|0.015	0.015	strong	.	C13orf35	13	.	NM_207440	exon2	c.G116A	p.G39D	CGGCAGGTCTGGA	.	PASS	Atlas-SNP
MYLIP	29116	hgsc.bcm.edu	37	6	16145325	16145325	+	Missense_Mutation	SNP	A	A	G	rs9370867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	117	0	1	0	A|0.313;G|0.687	0.687	strong	.	MYLIP	44	.	NM_013262	exon6	c.A1025G	p.N342S	CAAGAAACAACCA	.	PASS	Atlas-SNP
FOSB	2354	hgsc.bcm.edu	37	19	45971961	45971961	+	Silent	SNP	C	C	G	rs2282695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	54	55	0	0.981818	0	C|0.632;G|0.368	0.368	strong	.	FOSB	29	.	NM_001114171	exon1	c.C117G	p.A39A	CGCCGCCGCCTCC	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39227889	39227889	+	Silent	SNP	C	C	T	rs202082771	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	20	28	0	0.571429	0	.	.	weak	.	CAPN12	43	.	NM_144691	exon10	c.G1269A	p.K423K	CGTGCACTTGGGC	.	PASS	Atlas-SNP
BHLHB9	80823	hgsc.bcm.edu	37	X	102005371	102005371	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	429	59	438	0	0.137529	0	.	.	none	.	BHLHB9	60	.	NM_001142530	exon2	c.A1448T	p.N483I	TGATCAATATGAA	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124135143	124135143	+	Missense_Mutation	SNP	G	G	A	rs200012972	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	127	332	0	0.492248	0	.	.	weak	.	.	.	.	NM_001005198	exon1	c.G421A	p.V141I	TTCCTCGTTTTTG	.	PASS	Atlas-SNP
POTEB	339010	hgsc.bcm.edu	37	15	21071492	21071492	+	Missense_Mutation	SNP	G	G	T	rs2664992		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	465	145	325	101	0.311828	0.310769	.	.	weak	ENSG00000230031,NS,carcinoid-endocrine_tumour,0,1	POTEB	22	1	NM_207355	exon1	c.C119A	p.T40K	TTGCTCGTGCCGC	.	scavenged	Atlas-SNP
NDUFV2	4729	hgsc.bcm.edu	37	18	9117899	9117899	+	Missense_Mutation	SNP	G	G	A	rs75362221	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	52	126	0	0.422764	0	G|0.996;A|0.004	0.004	strong	.	NDUFV2	17	.	NM_021074	exon2	c.G118A	p.V40M	TTATTTGTGGTAA	.	PASS	Atlas-SNP
GOLGA1	2800	hgsc.bcm.edu	37	9	127661645	127661645	+	Missense_Mutation	SNP	G	G	A	rs634710	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	46	63	0	0.666667	0	G|0.595;T|0.005	.	strong	.	GOLGA1	60	.	NM_002077	exon14	c.C1274T	p.T425M	GCCCGCGTTCTCT	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	81	80	74	0	0.987654	0	C|0.706;T|0.294	0.294	strong	SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	NM_004174	exon13	c.G2031A	p.A677A	CTTGGCCGCCTTC	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52992812	52992812	+	Missense_Mutation	SNP	T	T	C	rs11170187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	218	116	229	0	0.53211	0	T|0.649;C|0.351	0.351	strong	.	KRT72	70	.	NM_001146225	exon2	c.A511G	p.N171D	CCAGGTTCTTCCT	.	PASS	Atlas-SNP
ZFP28	140612	hgsc.bcm.edu	37	19	57066013	57066013	+	Missense_Mutation	SNP	C	C	T	rs10409531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	131	121	0	0.992424	0	C|0.594;T|0.406	0.406	strong	ZFP28,NS,carcinoma,0,1	ZFP28	99	1	NM_020828	exon8	c.C1859T	p.A620V	AATGTGCGGAGTG	.	PASS	Atlas-SNP
NFATC3	4775	hgsc.bcm.edu	37	16	68225197	68225197	+	Silent	SNP	C	C	T	rs140991156	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	251	125	243	1	0.498008	0.00411523	C|1.000;T|0.000	0.000	strong	.	NFATC3	190	.	NM_173163	exon9	c.C2625T	p.T875T	GCATACCCTGCCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100683067	100683067	+	Silent	SNP	C	C	T	rs112360991		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	181	21	108	0	0.116022	0	C|0.500;T|0.500	0.500	weak	.	MUC17	804	.	NM_001040105	exon3	c.C8370T	p.S2790S	CAGTTCCTCTCCT	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	37	X	39932907	39932907	+	Silent	SNP	T	T	C	rs6520618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	83	0	1	0	0|0.003;C|0.438	0.438	strong	.	BCOR	351	.	NM_001123385	exon4	c.A1692G	p.A564A	GCGGCCTGCACTC	.	PASS	Atlas-SNP
CEACAM8	1088	hgsc.bcm.edu	37	19	43087428	43087428	+	Missense_Mutation	SNP	A	A	C	rs8103051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	318	157	323	0	0.493711	0	A|0.937;C|0.063	0.063	strong	.	CEACAM8	44	.	NM_001816	exon5	c.T1020G	p.I340M	TACTCCAATCATG	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26374571	26374571	+	Silent	SNP	G	G	A	rs115820857	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	216	96	215	0	0.444444	0	G|0.988;A|0.012	0.012	strong	.	BTN3A2	44	.	NM_001197246	exon7	c.G981A	p.S327S	GTCTTCGTCCGAT	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	95169	95169	+	Missense_Mutation	SNP	T	T	G	rs199817418	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	10	130	0	0.0675676	0	T|0.980;G|0.020	0.020	strong	TUBB8,colon,carcinoma,0,2	TUBB8	62	2	NM_177987	exon1	c.A10C	p.I4L	GCACGATCTCCCT	.	scavenged	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103371	53103371	+	Missense_Mutation	SNP	G	G	T	rs72598684	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	42	53	0	0.6	0	G|0.715;T|0.285	0.285	strong	.	POM121L12	146	.	NM_182595	exon1	c.G7T	p.A3S	ATGGGCGCTGCAG	.	PASS	Atlas-SNP
PRUNE	58497	hgsc.bcm.edu	37	1	150997155	150997155	+	Missense_Mutation	SNP	G	G	A	rs56805474	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	33	106	0	0.33	0	G|0.965;A|0.035	0.035	strong	.	PRUNE	40	.	NM_021222	exon4	c.G404A	p.C135Y	AACACTGCCCTCC	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18907029	18907029	+	Missense_Mutation	SNP	A	A	G	rs2074283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	20	52	0	0.408163	0	A|0.778;G|0.222	0.222	strong	.	FAM83G	51	.	NM_001039999	exon2	c.T326C	p.I109T	GCCTCGATGGGGA	.	PASS	Atlas-SNP
TMEM8B	51754	hgsc.bcm.edu	37	9	35845998	35845998	+	Silent	SNP	G	G	C	rs34807292	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	50	24	65	0	0.48	0	G|0.969;C|0.031	0.031	strong	.	TMEM8B	53	.	NM_001042590	exon7	c.G306C	p.T102T	CGTGACGGTGTTT	.	PASS	Atlas-SNP
DPYS	1807	hgsc.bcm.edu	37	8	105478933	105478933	+	Silent	SNP	G	G	A	rs2298840	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	19	13	16	0	0.684211	0	G|0.763;A|0.237	0.237	strong	.	DPYS	107	.	NM_001385	exon1	c.C216T	p.F72F	GAAGGGGAACTGC	.	PASS	Atlas-SNP
ASNSD1	54529	hgsc.bcm.edu	37	2	190531615	190531615	+	Silent	SNP	T	T	C	rs3828267	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	43	75	0	0.551282	0	T|0.870;C|0.130	0.130	strong	.	ASNSD1	63	.	NM_019048	exon4	c.T757C	p.L253L	GCTGCATTGGAGA	.	PASS	Atlas-SNP
DNAI2	64446	hgsc.bcm.edu	37	17	72278080	72278080	+	Missense_Mutation	SNP	G	G	A	rs151176313	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	75	144	0	0.493421	0	G|0.996;A|0.004	0.004	strong	.	DNAI2	102	.	NM_001172810	exon2	c.G124A	p.V42M	CAGTTCGTGGAGC	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60909316	60909316	+	Missense_Mutation	SNP	C	C	T	rs6062223	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	182	210	1	0.994536	0.0047619	C|0.902;T|0.098	0.098	strong	.	LAMA5	268	.	NM_005560	exon22	c.G2665A	p.V889M	AGCGCACGGCGTG	.	PASS	Atlas-SNP
FAM111B	374393	hgsc.bcm.edu	37	11	58892558	58892558	+	Silent	SNP	C	C	T	rs35732637	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	38	74	0	0.550725	0	C|0.940;T|0.060	0.060	strong	.	FAM111B	84	.	NM_198947	exon4	c.C988T	p.L330L	CAGGATCTAAGCC	.	PASS	Atlas-SNP
ZNF843	283933	hgsc.bcm.edu	37	16	31448168	31448168	+	Missense_Mutation	SNP	C	C	T	rs150789330	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	37	55	0	0.578125	0	C|0.999;T|0.001	0.001	strong	.	ZNF843	14	.	NM_001136509	exon2	c.G3A	p.M1I	GCTTCTCATGAGC	.	PASS	Atlas-SNP
FAM212A	389119	hgsc.bcm.edu	37	3	49840843	49840843	+	Silent	SNP	T	T	C	rs115355405	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	87	153	0	0.58	0	T|0.984;C|0.016	0.016	strong	.	.	.	.	NM_203370	exon1	c.T24C	p.L8L	TCGGCTTGACAGC	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192372	102192372	+	Silent	SNP	G	G	A	rs61745023	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	455	145	507	0	0.318681	0	G|0.981;A|0.019	0.019	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.G126A	p.P42P	GTCCCCGTACAGT	.	PASS	Atlas-SNP
KRT4	3851	hgsc.bcm.edu	37	12	53205757	53205757	+	Missense_Mutation	SNP	T	T	C	rs7959052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	141	310	1	0.501779	0.00322581	C|0.245;N|0.000	0.245	strong	.	KRT4	110	.	NM_002272	exon2	c.A467G	p.Q156R	AAGAACTGCACCT	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124418879	124418879	+	Silent	SNP	T	T	C	rs56047676	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	33	81	0	0.55	0	T|0.879;C|0.121	0.121	strong	.	KALRN	556	.	NM_001024660	exon56	c.T7995C	p.Y2665Y	AGAATATGGTGAG	.	PASS	Atlas-SNP
TRABD2A	129293	hgsc.bcm.edu	37	2	85059205	85059205	+	Silent	SNP	G	G	A	rs60429698	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	104	0	1	0	G|0.982;A|0.018	0.018	strong	.	.	.	.	NM_001080824	exon4	c.C909T	p.A303A	AGGGGCGTGTTCT	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80788465	80788465	+	Silent	SNP	T	T	C	rs12938126	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	83	130	0	0.515528	0	T|0.600;C|0.400	0.400	strong	.	ZNF750	60	.	NM_024702	exon3	c.A1725G	p.A575A	AGGTTCTGCAGCT	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55105743	55105743	+	Missense_Mutation	SNP	A	A	G	rs1974982	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	109	218	0	1	0	A|0.864;G|0.136	0.136	strong	.	LILRA1	105	.	NM_006863	exon2	c.A34G	p.R12G	TGTCTCAGTGAGA	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242046785	242046785	+	Missense_Mutation	SNP	A	A	C	rs1131293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	76	130	0	0.5	0	C|0.280;N|0.000	0.280	strong	.	PASK	230	.	NM_001252119	exon17	c.T3818G	p.F1273C	ACTCGAAACACCT	.	PASS	Atlas-SNP
PHYHIP	9796	hgsc.bcm.edu	37	8	22084503	22084503	+	Silent	SNP	C	C	T	rs11547656	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	15	51	0	0.306122	0	T|0.357;G|0.000;C|0.642	0.357	strong	.	PHYHIP	24	.	NM_014759	exon3	c.G201A	p.P67P	GGGCAGCGGCACT	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179342	55179342	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	378	11	340	0	0.0291005	0	.	.	none	LILRB4,NS,carcinoma,0,1	LILRB4	86	1	NM_006847	exon12	c.C1219T	p.P407S	GAAGCCCCCCAGG	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093228	1093228	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	13	60	0	0.19697	0	.	.	none	.	MUC2	614	.	NM_002457	exon30	c.A5047G	p.T1683A	ACCACTACGGTGA	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871058	170871058	+	Silent	SNP	G	G	A	rs113440919		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	18	77	0	0.257143	0	G|0.500;A|0.500	0.500	weak	TBP,caecum,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.G234A	p.Q78Q	GCAGCAGCAGCAG	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2253641	2253641	+	Silent	SNP	G	G	T	rs200918439	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	24	15	31	0	0.625	0	G|0.996;T|0.004	0.004	strong	.	JSRP1	18	.	NM_144616	exon5	c.C414A	p.G138G	AGCCGAGCCCAGC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82837631	82837631	+	Missense_Mutation	SNP	G	G	T	rs160277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	37	78	0	0.397849	0	G|0.618;T|0.382	0.382	strong	.	VCAN	498	.	NM_004385	exon8	c.G8809T	p.D2937Y	AAAACCGATGGTC	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242051777	242051777	+	Silent	SNP	G	G	A	rs2074824	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	64	128	0	0.551724	0	G|0.727;A|0.273	0.273	strong	.	PASK	230	.	NM_001252119	exon15	c.C3432T	p.A1144A	GTCCTCGGCGATC	.	PASS	Atlas-SNP
SPANXN1	494118	hgsc.bcm.edu	37	X	144337286	144337286	+	Silent	SNP	G	G	A	rs75090998	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	365	363	374	0	0.994521	0	G|0.919;A|0.081	0.081	strong	.	SPANXN1	23	.	NM_001009614	exon2	c.G171A	p.R57R	CTACAGGAAAGCT	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6189780	6189780	+	Silent	SNP	T	T	C	rs3764814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	42	56	0	0.583333	0	T|0.728;C|0.272	0.272	strong	.	USP42	138	.	NM_032172	exon13	c.T1953C	p.L651L	CGAGCTTCAAGAA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158631106	158631106	+	Missense_Mutation	SNP	G	G	C	rs35121052	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	338	165	311	0	0.488166	0	G|0.933;C|0.067	0.067	strong	.	SPTA1	720	.	NM_003126	exon18	c.C2558G	p.T853R	CTTTCTGTTATCT	.	PASS	Atlas-SNP
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	60	22	100	0	0.366667	0	A|0.552;G|0.446	0.446	strong	SHD,NS,carcinoma,0,3	SHD	33	3	NM_020209	exon5	c.A809G	p.N270S	AGACCAACCCCCA	.	PASS	Atlas-SNP
MLXIP	22877	hgsc.bcm.edu	37	12	122618417	122618417	+	Missense_Mutation	SNP	G	G	T	rs34702867	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	14	55	0	0.368421	0	G|0.973;T|0.027	0.027	strong	.	MLXIP	46	.	NM_014938	exon9	c.G1615T	p.V539L	ACTTTTGTGCACC	.	PASS	Atlas-SNP
ZNF610	162963	hgsc.bcm.edu	37	19	52869022	52869022	+	Missense_Mutation	SNP	G	G	T	rs2241586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	99	0	1	0	G|0.164;T|0.836	0.836	strong	.	ZNF610	84	.	NM_001161426	exon6	c.G391T	p.A131S	CTTGAGGCACATC	.	PASS	Atlas-SNP
GPC1	2817	hgsc.bcm.edu	37	2	241404914	241404914	+	Silent	SNP	C	C	T	rs2228329	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	115	54	117	0	0.469565	0	C|0.991;T|0.009	0.009	strong	.	GPC1	32	.	NM_002081	exon8	c.C1293T	p.D431D	GGGTGACGGCCTG	.	PASS	Atlas-SNP
NPR2	4882	hgsc.bcm.edu	37	9	35792423	35792423	+	Silent	SNP	T	T	C	rs2228580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	121	121	82	0	1	0	T|0.691;C|0.309	0.309	strong	.	NPR2	162	.	NM_003995	exon1	c.T18C	p.L6L	ATCACTTCTGCTG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	53	87	0	0.464912	0	C|0.836;G|0.164	0.164	strong	.	DNHD1	198	.	NM_173589	exon8	c.C1678G	p.Q560E	TCATCACAGCTGG	.	PASS	Atlas-SNP
MYL2	4633	hgsc.bcm.edu	37	12	111353556	111353556	+	Silent	SNP	A	A	G	rs2301610	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	319	147	284	0	0.460815	0	A|0.911;G|0.089	0.089	strong	.	MYL2	31	.	NM_000432	exon3	c.T132C	p.I44I	CTTGTCAATGAAG	.	PASS	Atlas-SNP
CPT1A	1374	hgsc.bcm.edu	37	11	68529027	68529027	+	Silent	SNP	A	A	G	rs2228503	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	51	119	0	0.459459	0	A|0.991;G|0.009	0.009	strong	CPT1A,colon,carcinoma,0,1	CPT1A	89	1	NM_001876	exon16	c.T2004C	p.A668A	CTCCACAGCGAGA	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	37	17	39081713	39081713	+	Silent	SNP	A	A	G	rs8037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	258	258	305	0	1	0	A|0.501;G|0.499	0.499	strong	.	KRT23	59	.	NM_015515	exon7	c.T1035C	p.H345H	CAGTTCATGGCGT	.	PASS	Atlas-SNP
VPS52	6293	hgsc.bcm.edu	37	6	33235755	33235755	+	Silent	SNP	G	G	A	rs213199	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	86	0	1	0	G|0.576;A|0.424	0.424	strong	.	VPS52	56	.	NM_022553	exon9	c.C820T	p.L274L	TGCCCAGCAGAAA	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242065624	242065624	+	Silent	SNP	A	A	G	rs2240541	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	64	128	0	0.470588	0	A|0.812;G|0.188	0.188	strong	.	PASK	230	.	NM_015148	exon10	c.T2706C	p.D902D	TAAGCCATCTCGA	.	PASS	Atlas-SNP
MKL1	57591	hgsc.bcm.edu	37	22	40814594	40814594	+	Silent	SNP	C	C	T	rs56211152	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	30	56	0	0.508475	0	C|0.833;T|0.167	0.167	strong	.	MKL1	69	.	NM_020831	exon12	c.G1848A	p.P616P	GGGCCCCGGGGCC	.	PASS	Atlas-SNP
SYT2	127833	hgsc.bcm.edu	37	1	202569555	202569555	+	Silent	SNP	C	C	T	rs907699	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	55	87	0	0.518868	0	C|0.917;T|0.083	0.083	strong	.	SYT2	51	.	NM_177402	exon7	c.G849A	p.T283T	CCCGGCCGTGGGC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40399385	40399385	+	Missense_Mutation	SNP	C	C	T	rs78608182	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	50	243	0	0.198413	0	C|0.500;T|0.500	0.500	strong	FCGBP,NS,carcinoma,0,2	FCGBP	416	2	NM_003890	exon13	c.G6310A	p.G2104R	GTGGTCCGTGGCA	.	scavenged	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150664183	150664183	+	Silent	SNP	G	G	C	rs17111902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	59	119	0	0.468254	0	G|0.895;C|0.105	0.105	strong	.	SLC36A3	54	.	NM_001145017	exon8	c.C921G	p.G307G	ACCGACGCCTTCA	.	PASS	Atlas-SNP
SLC25A23	79085	hgsc.bcm.edu	37	19	6454651	6454651	+	Silent	SNP	T	T	C	rs8103745	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	42	60	0	0.545455	0	T|0.820;C|0.180	0.180	strong	.	SLC25A23	43	.	NM_024103	exon5	c.A561G	p.K187K	CAGCTGTTTCCAC	.	PASS	Atlas-SNP
SNAI1	6615	hgsc.bcm.edu	37	20	48600557	48600557	+	Silent	SNP	T	T	C	rs4647959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	62	64	0	1	0	T|0.712;C|0.288	0.288	strong	.	SNAI1	28	.	NM_005985	exon2	c.T279C	p.D93D	GTCAGATGAGGAC	.	PASS	Atlas-SNP
CXorf36	79742	hgsc.bcm.edu	37	X	45011018	45011018	+	Missense_Mutation	SNP	C	C	A	rs143817529	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	108	121	0	0.990826	0	C|0.970;A|0.030	0.030	strong	.	CXorf36	53	.	NM_176819	exon5	c.G1181T	p.R394L	TCTGGGCGGATGC	.	PASS	Atlas-SNP
WBSCR27	155368	hgsc.bcm.edu	37	7	73254871	73254871	+	Silent	SNP	A	A	G	rs61741292	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	111	0	1	0	A|0.974;G|0.026	0.026	strong	.	WBSCR27	21	.	NM_152559	exon4	c.T261C	p.A87A	GCCTGGAGCCCGC	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671742	25671742	+	Missense_Mutation	SNP	G	G	A	rs140135080	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	6	98	0	0.05	0	G|0.919;A|0.081	0.081	strong	PABPC3,NS,carcinoma,+1,1	PABPC3	129	1	NM_030979	exon1	c.G1406A	p.R469Q	TTCCACGAGTCAT	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	47	19	57	0	0.404255	0	A|0.731;G|0.269	0.269	strong	RNF213_ENST00000456466,NS,carcinoma,0,3	RNF213	766	3	NM_001256071	exon4	c.A453G	p.P151P	GCCCCCAGGCACA	.	PASS	Atlas-SNP
TRPM8	79054	hgsc.bcm.edu	37	2	234915540	234915540	+	Silent	SNP	C	C	G	rs11563071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	58	75	0	0.651685	0	C|0.880;G|0.120	0.120	strong	.	TRPM8	146	.	NM_024080	exon23	c.C3174G	p.V1058V	GGGTGTCATGAAG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118634297	118634297	+	Missense_Mutation	SNP	A	A	C	rs150596428	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	145	59	145	0	0.406897	0	A|0.997;C|0.003	0.003	strong	.	SPAG17	263	.	NM_206996	exon10	c.T1291G	p.Y431D	GCAAATAATTGTA	.	PASS	Atlas-SNP
FTSJ2	29960	hgsc.bcm.edu	37	7	2275177	2275177	+	Silent	SNP	G	G	A	rs11547272	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	29	35	0	0.690476	0	G|0.982;C|0.000;A|0.018	0.018	strong	.	FTSJ2	22	.	NM_013393	exon3	c.C321T	p.F107F	AAGCACGAAGCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678610	100678610	+	Missense_Mutation	SNP	A	A	T	rs78010183	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	21	112	0	0.166667	0	A|0.943;T|0.057	0.057	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3913T	p.T1305S	GTTGACACTAAAG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149479335	149479335	+	Silent	SNP	G	G	C	rs855680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	16	51	0	0.421053	0	G|0.868;C|0.132	0.132	strong	.	.	.	.	NM_198455	exon14	c.G1848C	p.L616L	CTGCCTGCACGCC	.	PASS	Atlas-SNP
GLRA3	8001	hgsc.bcm.edu	37	4	175598280	175598280	+	Silent	SNP	A	A	G	rs12648678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	86	180	0	0.457447	0	A|0.807;G|0.193	0.193	strong	GLRA3,NS,carcinoma,0,1	GLRA3	76	1	NM_001042543	exon7	c.T876C	p.T292T	TAGCACAGTGGTT	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241831005	241831005	+	Silent	SNP	C	C	T	rs10195453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	44	84	0	0.571429	0	C|0.497;T|0.503	0.503	strong	.	C2orf54	14	.	NM_001085437	exon2	c.G690A	p.R230R	GAGGATCCTTCTC	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80900348	80900348	+	Missense_Mutation	SNP	T	T	G	rs7965277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	28	23	0	1	0	T|0.686;G|0.314	0.314	strong	PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	NM_001145026	exon13	c.T1940G	p.V647G	CTTTAGTACTGAA	.	PASS	Atlas-SNP
CYP3A43	64816	hgsc.bcm.edu	37	7	99447241	99447241	+	Silent	SNP	T	T	C	rs800667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	86	171	0	0.441026	0	T|0.798;G|0.002	.	strong	.	CYP3A43	52	.	NM_057096	exon7	c.T594C	p.N198N	CAACAATCCACAA	.	PASS	Atlas-SNP
SPHK2	56848	hgsc.bcm.edu	37	19	49133020	49133020	+	Missense_Mutation	SNP	G	G	A	rs11881285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	165	150	1	1	0.00666667	G|0.942;A|0.058	0.058	strong	.	SPHK2	62	.	NM_020126	exon7	c.G1955A	p.R652Q	CGGGGCGGGAGCC	.	PASS	Atlas-SNP
DGKA	1606	hgsc.bcm.edu	37	12	56346891	56346891	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	48	123	0	0.444444	0	.	.	none	.	DGKA	70	.	NM_201554	exon22	c.C2010T	p.T670T	CTATACCAAGCTC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	27	331	0	0.127962	0	G|0.689;C|0.311	0.311	strong	SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	NM_001040022	exon3	c.G224C	p.G75A	GACCAGGCCGGGA	.	PASS	Atlas-SNP
KCNJ4	3761	hgsc.bcm.edu	37	22	38822905	38822905	+	Silent	SNP	C	C	T	rs105153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	82	136	0	0.543046	0	C|0.929;T|0.071	0.071	strong	.	KCNJ4	74	.	NM_004981	exon2	c.G1233A	p.A411A	GATGCCCGCCTCC	.	PASS	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55815072	55815072	+	Silent	SNP	C	C	T	rs17851414	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	60	158	0	0.491803	0	C|0.969;T|0.031	0.031	strong	.	BRSK1	192	.	NM_032430	exon12	c.C1164T	p.S388S	GCTGAGCCGTCAC	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473928	18473928	+	Silent	SNP	T	T	C	rs12309666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	245	244	274	1	0.995918	0.00364964	T|0.786;C|0.214	0.214	strong	PIK3C2G,NS,carcinoma,0,1	PIK3C2G	315	1	NM_004570	exon7	c.T1170C	p.N390N	TCTGAATCAACTT	.	PASS	Atlas-SNP
CDH26	60437	hgsc.bcm.edu	37	20	58558073	58558073	+	Silent	SNP	C	C	T	rs6015610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	76	131	0	0.496732	0	C|0.915;T|0.085	0.085	strong	.	CDH26	229	.	NM_177980	exon5	c.C489T	p.P163P	TGCACCCCAGTTT	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81208348	81208348	+	Missense_Mutation	SNP	G	G	T	rs745211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	67	115	0	0.567797	0	G|0.924;T|0.076	0.076	strong	.	PKD1L2	361	.	NM_001076780	exon16	c.C2755A	p.L919M	TGCTCAGTGACTG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512661	4512661	+	Silent	SNP	G	G	A	rs58830758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	32	211	1	0.196319	0.00473934	G|0.927;A|0.073	0.073	strong	PLIN4_ENST00000301286,caecum,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon3	c.C1269T	p.C423C	CCCACTGCAGACG	.	scavenged	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20163529	20163529	+	Silent	SNP	A	A	G	rs2703791	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	69	0	1	0	A|0.284;G|0.716	0.716	strong	.	SPECC1	100	.	NM_001033553	exon12	c.A2862G	p.A954A	TCTGGCAGCCTTG	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214527	45214527	+	Missense_Mutation	SNP	T	T	C	rs62075618	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	6	26	2	0.176471	0.0769231	T|0.500;C|0.500	0.500	strong	CDC27_ENST00000531206,colon,carcinoma,-1,2	CDC27	337	2	NM_001114091	exon14	c.A1922G	p.Y641C	GCATTATAATGTC	.	scavenged	Atlas-SNP
PSMF1	9491	hgsc.bcm.edu	37	20	1106143	1106143	+	Silent	SNP	G	G	A	rs35517343	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	52	90	0	0.490566	0	G|0.995;A|0.005	0.005	strong	.	PSMF1	27	.	NM_006814	exon2	c.G132A	p.P44P	CCAGCCGGGTCCC	.	PASS	Atlas-SNP
TRAF1	7185	hgsc.bcm.edu	37	9	123671613	123671613	+	Silent	SNP	C	C	T	rs112060909	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	48	109	0	0.377953	0	C|0.983;T|0.017	0.017	strong	.	TRAF1	42	.	NM_005658	exon7	c.G927A	p.L309L	CAGGTACAGCCGC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341589	55341589	+	Silent	SNP	C	C	T	rs112943025	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	45	48	0	0.394737	0	C|0.946;T|0.054	0.054	strong	.	KIR3DL1	174	.	NM_013289	exon9	c.C1194T	p.Y398Y	GACATACGCACAG	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	41	41	0	1	0	C|0.192;A|0.808	0.808	strong	.	ESPL1	158	.	NM_012291	exon2	c.C74A	p.A25D	TGCCCGCCTTGAA	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	62	146	1	0.455882	0.00684932	G|0.800;C|0.200	0.200	strong	VILL,NS,carcinoma,0,1	VILL	61	1	NM_015873	exon18	c.G2220C	p.L740F	CAACTTGCGGCTA	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179610619	179610619	+	Missense_Mutation	SNP	C	C	G	rs16866489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	66	91	0	0.559322	0	C|0.992;G|0.008	0.008	strong	.	TTN	18412	.	NM_133379	exon46	c.G16508C	p.S5503T	AAAAAACTGTCTG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184299068	184299068	+	Silent	SNP	G	G	A	rs9881589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	282	150	233	1	0.531915	0.00429185	G|0.834;A|0.166	0.166	strong	.	EPHB3	114	.	NM_004443	exon15	c.G2760A	p.T920T	CCGCACGGTCCCA	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17118687	17118687	+	Missense_Mutation	SNP	T	T	C	rs11604561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	42	84	0	0.538462	0	T|0.898;C|0.102	0.102	strong	.	PIK3C2A	148	.	NM_002645	exon26	c.A4243G	p.T1415A	AGTATGTTTTAGG	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34030767	34030767	+	Silent	SNP	G	G	T	rs115185294	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	25	65	0	0.423729	0	G|0.994;T|0.006	0.006	strong	.	RYR3	760	.	NM_001243996	exon50	c.G7632T	p.G2544G	CTGGGGGATTTTT	.	PASS	Atlas-SNP
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	65	132	0	0.471014	0	C|0.986;T|0.014	0.014	strong	.	RFFL	27	.	NM_001017368	exon3	c.G440A	p.R147H	GAGGCACGAGTCC	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	335373	335373	+	Missense_Mutation	SNP	C	C	T	rs2685127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	78	107	0	0.655462	0	C|0.898;T|0.102	0.102	strong	.	PDIA2	51	.	NM_006849	exon6	c.C857T	p.T286M	ACCAGACGCTGGC	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117849314	117849314	+	Silent	SNP	T	T	C	rs2992147	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	130	140	0	1	0	T|0.532;C|0.468	0.468	strong	.	TNC	282	.	NM_002160	exon3	c.A696G	p.V232V	TCCATTTACGCAC	.	PASS	Atlas-SNP
RALBP1	10928	hgsc.bcm.edu	37	18	9517221	9517221	+	Missense_Mutation	SNP	G	G	A	rs28552921	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	380	179	366	1	0.471053	0.00273224	G|0.996;A|0.004	0.004	strong	.	RALBP1	48	.	NM_006788	exon3	c.G623A	p.R208Q	GCATTCGGCTGCC	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102315	22102315	+	Silent	SNP	A	A	G	rs61753931	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	356	173	375	0	0.485955	0	A|0.983;G|0.017	0.017	strong	.	OR10G2	35	.	NM_001005466	exon1	c.T684C	p.H228H	GATGGCATGGACT	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123886984	123886984	+	Missense_Mutation	SNP	A	A	G	rs4936880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	340	340	363	1	1	0.00275482	A|0.538;G|0.462	0.462	strong	.	OR10G4	77	.	NM_001004462	exon1	c.A703G	p.R235G	AGGCGCAGAGCCT	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	51	87	0	0.495146	0	T|0.773;C|0.227	0.227	strong	IL4R,colon,carcinoma,0,1	IL4R	70	1	NM_000418	exon11	c.T1507C	p.S503P	AGCAACTCCCTGA	.	PASS	Atlas-SNP
ZC3H13	23091	hgsc.bcm.edu	37	13	46584500	46584500	+	Silent	SNP	G	G	A	rs79878411	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	162	70	115	0	0.432099	0	G|0.990;A|0.010	0.010	strong	.	ZC3H13	197	.	NM_015070	exon7	c.C729T	p.P243P	CAACAGGGGAGAA	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45856963	45856963	+	Silent	SNP	T	T	C	rs11910471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	31	45	0	0.574074	0	T|0.901;C|0.099	0.099	strong	.	TRPM2	196	.	NM_003307	exon29	c.T4080C	p.D1360D	CGAGGATGGAGCC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15807305	15807305	+	Silent	SNP	T	T	C	rs688755	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	305	212	172	1	0.695082	0.00581395	T|0.764;C|0.236	0.236	strong	.	CYP4F12	89	.	NM_023944	exon12	c.T1380C	p.P460P	TATTCCTTTCTCC	.	PASS	Atlas-SNP
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221494	67221494	+	Missense_Mutation	SNP	C	C	T	rs79820293	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	30	63	0	0.4	0	C|0.978;T|0.022	0.022	strong	.	EXOC3L1	52	.	NM_178516	exon5	c.G674A	p.R225H	GCCACACGCACAG	.	PASS	Atlas-SNP
ING1	3621	hgsc.bcm.edu	37	13	111368023	111368023	+	Missense_Mutation	SNP	C	C	G	rs56682720	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	86	42	70	0	0.488372	0	C|0.961;G|0.039	0.039	strong	.	ING1	106	.	NM_005537	exon1	c.C233G	p.S78C	GCTCTTCCGCCCT	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377319	49377319	+	Missense_Mutation	SNP	A	A	G	rs610308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	97	109	0	0.989796	0	A|0.546;G|0.454	0.454	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.A829G	p.K277E	GCACACAAAGAAA	.	PASS	Atlas-SNP
SPAG4	6676	hgsc.bcm.edu	37	20	34204168	34204168	+	Silent	SNP	G	G	A	rs115161777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	15	32	0	0.375	0	G|0.980;A|0.020	0.020	strong	.	SPAG4	36	.	NM_003116	exon1	c.G243A	p.A81A	GCCAGCGCCTCGG	.	PASS	Atlas-SNP
SCRN1	9805	hgsc.bcm.edu	37	7	29980471	29980471	+	Missense_Mutation	SNP	C	C	T	rs35960711	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	35	40	0	0.603448	0	C|0.936;T|0.064	0.064	strong	.	SCRN1	85	.	NM_001145514	exon5	c.G626A	p.S209N	AGCTGACTGCAAA	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	37	19	7711221	7711221	+	Silent	SNP	T	T	C	rs10001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	73	159	1	0.480263	0.00628931	T|0.548;C|0.452	0.452	strong	STXBP2,NS,adenoma,0,1	STXBP2	63	1	NM_001272034	exon16	c.T1476C	p.D492D	CAAGGATGTAATG	.	scavenged	Atlas-SNP
ARHGEF39	84904	hgsc.bcm.edu	37	9	35665153	35665153	+	Missense_Mutation	SNP	C	C	A	rs45567235	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	33	44	0	0.445946	0	C|0.927;A|0.073	0.073	strong	.	.	.	.	NM_032818	exon1	c.G14T	p.C5F	CCGGGGCAGGAGA	.	PASS	Atlas-SNP
DCTD	1635	hgsc.bcm.edu	37	4	183814234	183814234	+	Silent	SNP	G	G	A	rs369366826		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	110	215	0	0.472103	0	.	.	weak	.	DCTD	30	.	NM_001012732	exon5	c.C441T	p.D147D	TGCCTCGTCACTA	.	PASS	Atlas-SNP
GIMAP7	168537	hgsc.bcm.edu	37	7	150217089	150217089	+	Silent	SNP	G	G	A	rs7800829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	37	81	0	0.440476	0	G|0.776;A|0.224	0.224	strong	.	GIMAP7	47	.	NM_153236	exon2	c.G27A	p.L9L	CTCCCTGAGGATC	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	43	46	0	1	0	T|0.193;G|0.806;C|0.000	0.193	strong	CIITA_ENST00000324288,NS,lymphoid_neoplasm,0,1	CIITA	92	1	NM_000246	exon11	c.G2421T	p.L807L	GCTGCTGGAGCTG	.	PASS	Atlas-SNP
SGTA	6449	hgsc.bcm.edu	37	19	2762585	2762585	+	Silent	SNP	A	A	C	rs2302491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	45	88	0	0.409091	0	A|0.635;C|0.365	0.365	strong	.	SGTA	19	.	NM_003021	exon7	c.T555G	p.A185A	CTCCAGAGCCTTC	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58575489	58575489	+	Silent	SNP	G	G	A	rs11540994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	152	157	0	1	0	G|0.584;A|0.416	0.416	strong	.	CNOT1	359	.	NM_016284	exon34	c.C4716T	p.Y1572Y	CTCTTCGTAAACA	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	93	162	1	0.494681	0.00617284	A|0.687;G|0.313	0.313	strong	IFT140,NS,carcinoma,0,1	IFT140	128	1	NM_014714	exon19	c.T2253C	p.P751P	CATCTGAGGGATG	.	scavenged	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605257	32605257	+	Missense_Mutation	SNP	C	C	A	rs1047989	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	86	174	0	0.988506	0	C|0.493;A|0.507	0.507	strong	.	HLA-DQA1	52	.	NM_002122	exon1	c.C22A	p.L8M	GCTCTGCTGCTGG	.	PASS	Atlas-SNP
TNIP1	10318	hgsc.bcm.edu	37	5	150436503	150436503	+	Missense_Mutation	SNP	G	G	C	rs2233290	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	52	0	1	0	G|0.885;C|0.115	0.115	strong	TNIP1,NS,lymphoid_neoplasm,0,1	TNIP1	51	1	NM_001252385	exon6	c.C451G	p.P151A	CACGGGGCAGGGG	.	PASS	Atlas-SNP
RIN1	9610	hgsc.bcm.edu	37	11	66099888	66099888	+	Silent	SNP	C	C	T	rs61547186	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	182	181	0	1	0	C|0.969;T|0.031	0.031	strong	.	RIN1	64	.	NM_004292	exon10	c.G2211A	p.G737G	AGCATCCCCATCT	.	PASS	Atlas-SNP
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	66	33	69	0	0.5	0	C|0.719;T|0.281	0.281	strong	.	FAM83F	29	.	NM_138435	exon4	c.C1266T	p.N422N	CCGAAACGGCATG	.	PASS	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86267633	86267633	+	Silent	SNP	C	C	T	rs17211115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	35	88	0	0.522388	0	C|0.784;T|0.216	0.216	strong	.	ME3	70	.	NM_006680	exon4	c.G429A	p.L143L	ACAGGCCAGCCCC	.	PASS	Atlas-SNP
NCR2	9436	hgsc.bcm.edu	37	6	41318578	41318578	+	Silent	SNP	T	T	C	rs115509322	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	19	45	0	0.452381	0	T|0.990;C|0.010	0.010	strong	.	NCR2	44	.	NM_004828	exon5	c.T807C	p.D269D	AAGCGATGATGAT	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43411150	43411150	+	Silent	SNP	G	G	A	rs78024453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	70	199	0	0.409357	0	G|0.976;A|0.024	0.024	strong	.	PSG6	89	.	NM_001031850	exon5	c.C1164T	p.S388S	GAGCCCGCTATGA	.	PASS	Atlas-SNP
COL19A1	1310	hgsc.bcm.edu	37	6	70733547	70733547	+	Missense_Mutation	SNP	C	C	G	rs2273426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	95	95	82	0	1	0	C|0.761;G|0.239	0.239	strong	.	COL19A1	232	.	NM_001858	exon12	c.C1055G	p.A352G	ATCCAGCTCTGGC	.	PASS	Atlas-SNP
KRI1	65095	hgsc.bcm.edu	37	19	10672493	10672493	+	Missense_Mutation	SNP	C	C	T	rs12984043	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	52	144	0	0.460177	0	C|0.715;T|0.285	0.285	strong	KRI1,NS,carcinoma,0,1	KRI1	65	1	NM_023008	exon5	c.G430A	p.G144R	TCTCCCCGTCTGA	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036959	33036959	+	Silent	SNP	G	G	A	rs2308929	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	102	142	0	1	0	G|0.695;A|0.305	0.305	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.C465T	p.N155N	CTCCCCGTTGCAC	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883711	152883711	+	Missense_Mutation	SNP	G	G	C	rs7545520	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	190	189	141	0	0.994737	0	G|0.646;C|0.354	0.354	strong	.	IVL	100	.	NM_005547	exon2	c.G1438C	p.V480L	GGCCAGGTGAAGC	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	37	7	75583325	75583325	+	Silent	SNP	A	A	G	rs10262966	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	46	114	0	0.396552	0	A|0.934;G|0.066	0.066	strong	.	POR	46	.	NM_000941	exon2	c.A15G	p.G5G	CATGGGAGACTCC	.	PASS	Atlas-SNP
OTOP2	92736	hgsc.bcm.edu	37	17	72926879	72926879	+	Silent	SNP	T	T	C	rs16967162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	84	147	0	0.48	0	T|0.925;C|0.075	0.075	strong	.	OTOP2	81	.	NM_178160	exon6	c.T1149C	p.S383S	CATCTCTTACTAC	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12409197	12409197	+	Missense_Mutation	SNP	C	C	G	rs78231473	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	66	166	0	0.478261	0	C|0.986;G|0.014	0.014	strong	VWDE_ENST00000275358,NS,carcinoma,+1,2	VWDE	123	2	NM_001135924	exon12	c.G2735C	p.S912T	TAGGAACTAAAGC	.	PASS	Atlas-SNP
TEX14	56155	hgsc.bcm.edu	37	17	56636908	56636908	+	Silent	SNP	T	T	C	rs9903050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	505	267	497	0	0.528713	0	T|0.759;C|0.241	0.241	strong	.	TEX14	343	.	NM_001201457	exon31	c.A4311G	p.K1437K	TTGATCTTTGATA	.	PASS	Atlas-SNP
SREK1IP1	285672	hgsc.bcm.edu	37	5	64020241	64020241	+	Silent	SNP	T	T	C	rs16879016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	90	179	0	0.5	0	T|0.886;C|0.114	0.114	strong	.	SREK1IP1	28	.	NM_173829	exon5	c.A438G	p.T146T	ATTAGGTGTAGAA	.	PASS	Atlas-SNP
LARP6	55323	hgsc.bcm.edu	37	15	71128691	71128691	+	Silent	SNP	G	G	A	rs78188777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	93	250	0	0.451456	0	G|0.984;A|0.016	0.016	strong	.	LARP6	43	.	NM_018357	exon2	c.C354T	p.H118H	CCTCACGTGTTTT	.	PASS	Atlas-SNP
MOGAT2	80168	hgsc.bcm.edu	37	11	75431049	75431049	+	Missense_Mutation	SNP	C	C	T	rs35828061	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	31	58	0	0.449275	0	C|0.974;T|0.026	0.026	strong	MOGAT2,NS,carcinoma,+1,1	MOGAT2	49	1	NM_025098	exon2	c.C104T	p.T35I	TCTGCACTGTGGG	.	PASS	Atlas-SNP
ACOT7	11332	hgsc.bcm.edu	37	1	6324747	6324747	+	Silent	SNP	G	G	A	rs61739537	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	34	47	0	0.435897	0	G|0.972;A|0.028	0.028	strong	ACOT7,NS,carcinoma,0,1	ACOT7	71	1	NM_181864	exon9	c.C1053T	p.T351T	GTCCTCGGTCTCG	.	PASS	Atlas-SNP
CD3G	917	hgsc.bcm.edu	37	11	118221350	118221350	+	Missense_Mutation	SNP	G	G	T	rs3753058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	195	102	235	1	0.523077	0.00425532	G|0.828;T|0.172	0.172	strong	.	CD3G	31	.	NM_000073	exon4	c.G391T	p.V131F	CTTGCTGTTGGGG	.	PASS	Atlas-SNP
SUV39H2	79723	hgsc.bcm.edu	37	10	14939067	14939067	+	Silent	SNP	A	A	C	rs45473500	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	43	23	46	0	0.534884	0	A|0.990;C|0.010	0.010	strong	.	SUV39H2	72	.	NM_001193424	exon3	c.A400C	p.R134R	AAACAAAGGATAG	.	PASS	Atlas-SNP
CNTN2	6900	hgsc.bcm.edu	37	1	205033518	205033518	+	Missense_Mutation	SNP	C	C	G	rs79431021	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	82	175	0	0.509317	0	C|0.962;G|0.038	0.038	strong	.	CNTN2	116	.	NM_005076	exon11	c.C1309G	p.L437V	GAGATCCTTATCC	.	PASS	Atlas-SNP
ZNF736	728927	hgsc.bcm.edu	37	7	63808867	63808867	+	Missense_Mutation	SNP	C	C	A	rs76371517	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	10	10	0	0.454545	0	.	.	weak	.	ZNF736	33	.	NM_001170905	exon5	c.C626A	p.A209E	GCAAAGCGTTTAA	.	PASS	Atlas-SNP
PDIA6	10130	hgsc.bcm.edu	37	2	10930903	10930903	+	Missense_Mutation	SNP	T	T	C	rs4807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	77	141	0	0.5	0	T|0.748;C|0.252	0.252	strong	PDIA6,colon,carcinoma,0,1	PDIA6	31	1	NM_005742	exon7	c.A641G	p.K214R	TTCACTTTTCCTT	.	PASS	Atlas-SNP
AP5B1	91056	hgsc.bcm.edu	37	11	65547775	65547775	+	Silent	SNP	C	C	T	rs114368095	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	19	41	0	0.372549	0	C|0.975;T|0.025	0.025	strong	.	AP5B1	40	.	NM_138368	exon2	c.G189A	p.Q63Q	CCACAGCTGCGCA	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744287	31744287	+	Missense_Mutation	SNP	C	C	T	rs113360916	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	182	86	178	0	0.472527	0	C|0.990;T|0.010	0.010	strong	.	KRTAP13-2	29	.	NM_181621	exon1	c.G245A	p.R82H	CTGGGGCGGTAGC	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24175021	24175021	+	Missense_Mutation	SNP	T	T	A	rs9460973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	153	113	0	1	0	T|0.853;A|0.147	0.147	strong	.	DCDC2	53	.	NM_001195610	exon11	c.A1368T	p.K456N	GGTAATTTTTACT	.	PASS	Atlas-SNP
FBXO42	54455	hgsc.bcm.edu	37	1	16577948	16577948	+	Silent	SNP	G	G	A	rs61731119	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	159	87	181	0	0.54717	0	G|0.973;A|0.027	0.027	strong	.	FBXO42	53	.	NM_018994	exon10	c.C1371T	p.D457D	AGGACTGTCCAAA	.	PASS	Atlas-SNP
GPRC5B	51704	hgsc.bcm.edu	37	16	19883364	19883364	+	Silent	SNP	G	G	A	rs61742688	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	44	64	0	0.594595	0	A|0.107;C|0.000;G|0.893	0.107	strong	.	GPRC5B	54	.	NM_016235	exon2	c.C804T	p.N268N	GGGGTCGTTCCAG	.	PASS	Atlas-SNP
KLF12	11278	hgsc.bcm.edu	37	13	74387412	74387412	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	2	159	0	0.0121212	0	.	.	none	KLF12,right_upper_lobe,carcinoma,+1,1	KLF12	42	1	NM_007249	exon5	c.C683T	p.P228L	CCTCGGGGGTCCA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512603	195512603	+	Missense_Mutation	SNP	T	T	C	rs79969373	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	240	60	384	0	0.25	0	T|0.989;C|0.011	0.011	strong	.	MUC4	1505	.	NM_018406	exon2	c.A5848G	p.T1950A	GGGTGGTGTGACC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78319380	78319380	+	Silent	SNP	G	G	C	rs4890012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	151	151	182	0	1	0	G|0.447;C|0.553	0.553	strong	.	RNF213	766	.	NM_001256071	exon29	c.G7245C	p.P2415P	GATCCCGGTTATC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81211496	81211496	+	Missense_Mutation	SNP	C	C	A	rs9935113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	38	69	0	0.550725	0	C|0.823;A|0.177	0.177	strong	.	PKD1L2	361	.	NM_001076780	exon14	c.G2353T	p.G785C	CGGTGCCCTCCTC	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25288632	25288632	+	Silent	SNP	G	G	A	rs6107027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	33	0	1	0	G|0.608;A|0.392	0.392	strong	.	ABHD12	46	.	NM_001042472	exon9	c.C837T	p.R279R	TTCTTCGCGGATA	.	PASS	Atlas-SNP
CSRNP1	64651	hgsc.bcm.edu	37	3	39185077	39185077	+	Silent	SNP	G	G	A	rs1274957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	71	177	0	0.422619	0	G|0.495;A|0.505	0.505	strong	.	CSRNP1	59	.	NM_033027	exon5	c.C1239T	p.S413S	CCCCACGCTCCCT	.	PASS	Atlas-SNP
RNF112	7732	hgsc.bcm.edu	37	17	19319374	19319374	+	Silent	SNP	T	T	C	rs76138388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	34	84	0	0.447368	0	T|0.829;C|0.171	0.171	strong	RNF112,NS,haematopoietic_neoplasm,0,1	RNF112	37	1	NM_007148	exon14	c.T1782C	p.A594A	GGCCGCTGTGGTT	.	PASS	Atlas-SNP
NRN1L	123904	hgsc.bcm.edu	37	16	67919930	67919930	+	Missense_Mutation	SNP	A	A	C	rs73593844	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	34	80	0	0.43038	0	A|0.944;C|0.056	0.056	strong	.	NRN1L	13	.	NM_198443	exon3	c.A266C	p.E89A	GTCCGGAGGAGGC	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83999000	83999000	+	Silent	SNP	C	C	G	rs3743627	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	17	8	12	0	0.470588	0	C|0.896;G|0.104	0.104	strong	.	OSGIN1	33	.	NM_182981	exon6	c.C822G	p.A274A	GGAGGCCGCCACA	.	PASS	Atlas-SNP
SARS2	54938	hgsc.bcm.edu	37	19	39416935	39416935	+	Silent	SNP	C	C	T	rs144229840	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	26	12	39	0	0.461538	0	C|0.995;T|0.005	0.005	strong	SARS2,rectum,carcinoma,0,1	SARS2	33	1	NM_001145901	exon2	c.G273A	p.S91S	CCATGTCGAGATC	.	PASS	Atlas-SNP
EIF2A	83939	hgsc.bcm.edu	37	3	150280445	150280445	+	Missense_Mutation	SNP	C	C	G	rs1132979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	17	53	0	0.485714	0	C|0.635;G|0.365	0.365	strong	EIF2A_ENST00000487799,NS,carcinoma,0,1	EIF2A	59	1	NM_032025	exon4	c.C290G	p.T97S	CTTACACTAGTAA	.	PASS	Atlas-SNP
SPTAN1	6709	hgsc.bcm.edu	37	9	131395568	131395568	+	Silent	SNP	C	C	T	rs2228952	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	52	80	0	0.675325	0	C|0.967;T|0.033	0.033	strong	.	SPTAN1	266	.	NM_001130438	exon57	c.C7389T	p.T2463T	CCCCACCGCGTTC	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2190951	2190951	+	Missense_Mutation	SNP	C	C	T	rs6356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	94	180	0	0.52514	0	C|0.652;T|0.348	0.348	strong	.	TH	43	.	NM_199292	exon3	c.G334A	p.V112M	TTAGCACGGCCTT	.	PASS	Atlas-SNP
C19orf57	79173	hgsc.bcm.edu	37	19	14006300	14006300	+	Missense_Mutation	SNP	C	C	A	rs58722011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	174	79	146	0	0.454023	0	C|0.974;A|0.026	0.026	strong	.	C19orf57	34	.	NM_024323	exon3	c.G91T	p.D31Y	GGGGGTCCCCATA	.	PASS	Atlas-SNP
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387503	46387503	+	Silent	SNP	T	T	C	rs3745926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	44	45	0	1	0	T|0.681;C|0.319	0.319	strong	.	IRF2BP1	23	.	NM_015649	exon1	c.A1530G	p.L510L	GTCTTCTAGCCGC	.	PASS	Atlas-SNP
HTATSF1	27336	hgsc.bcm.edu	37	X	135593167	135593167	+	Silent	SNP	G	G	A	rs1058376	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	252	251	260	0	0.996032	0	0|0.004;A|0.148	0.148	strong	.	HTATSF1	66	.	NM_001163280	exon10	c.G1263A	p.A421A	AATGGCGTTTGAA	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721709	101721709	+	Missense_Mutation	SNP	T	T	A	rs146200489	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	58	203	0	0.206406	0	T|0.899;A|0.101	0.101	strong	PABPC1,NS,carcinoma,0,1	PABPC1	76	1	NM_002568	exon8	c.A1223T	p.Y408F	ATGAAGTAACCTG	.	PASS	Atlas-SNP
HK3	3101	hgsc.bcm.edu	37	5	176315822	176315822	+	Silent	SNP	G	G	T	rs61749652	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	40	111	0	0.481928	0	G|0.979;T|0.021	0.021	strong	HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	NM_002115	exon9	c.C958A	p.R320R	CCAGCCGCACCAG	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	72972771	72972771	+	Missense_Mutation	SNP	C	C	T	rs61757569	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	21	31	0	0.512195	0	C|0.986;T|0.014	0.014	strong	.	UNC5B	123	.	NM_001244889	exon1	c.C29T	p.A10V	GGGGCGCGCTGCT	.	PASS	Atlas-SNP
DCC	1630	hgsc.bcm.edu	37	18	50976898	50976898	+	Silent	SNP	G	G	A	rs35891220	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	127	64	117	1	0.503937	0.00854701	G|0.966;A|0.034	0.034	strong	DCC,colon,carcinoma,0,1	DCC	360	1	NM_005215	exon23	c.G3258A	p.P1086P	CCCCCCGCATGGC	.	scavenged	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55107869	55107869	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	14	200	0	0.0551181	0	.	.	none	LILRA1,NS,carcinoma,0,2	LILRA1	105	2	NM_006863	exon7	c.T1174G	p.S392A	GCCCACTCGGGGA	.	scavenged	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108380213	108380213	+	Silent	SNP	G	G	A	rs4917481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	57	94	0	0.53271	0	G|0.707;A|0.293	0.293	strong	.	SORCS1	534	.	NM_001206572	exon20	c.C2769T	p.Y923Y	CCACACGTAAGTG	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43028207	43028207	+	Silent	SNP	G	G	C	rs143391538	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	166	83	184	0	0.5	0	G|0.998;C|0.002	0.002	strong	.	CDAN1	70	.	NM_138477	exon3	c.C639G	p.T213T	GAAGCAGGTCTTG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036853	33036853	+	Missense_Mutation	SNP	A	A	C	rs1042308	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	167	148	0	0.988166	0	T|0.000;G|0.000;C|0.321;N|0.000;A|0.679	0.321	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.T571G	p.F191V	CATAGAAGTCCTC	.	PASS	Atlas-SNP
RPUSD4	84881	hgsc.bcm.edu	37	11	126074192	126074192	+	Silent	SNP	A	A	G	rs2276312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	39	29	41	0	0.74359	0	A|0.818;G|0.182	0.182	strong	.	RPUSD4	36	.	NM_032795	exon6	c.T828C	p.S276S	TCCAAAAGACAAG	.	PASS	Atlas-SNP
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417682	138417682	+	Silent	SNP	G	G	A	rs143883618	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	63	144	0	0.508065	0	G|0.995;A|0.005	0.005	strong	.	ATP6V0A4	93	.	NM_130841	exon16	c.C1848T	p.F616F	GTTGATGAAGTGG	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100995758	100995758	+	Missense_Mutation	SNP	G	G	T	rs879368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	81	106	0	0.618321	0	G|0.769;T|0.231	0.231	strong	.	TBC1D2	70	.	NM_001267571	exon4	c.C721A	p.P241T	TCTGTGGAGAATC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs55790575		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	27	44	0	0.529412	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.C1758A	p.D586E	ACACACGTCGACC	.	PASS	Atlas-SNP
ERCC1	2067	hgsc.bcm.edu	37	19	45923653	45923653	+	Silent	SNP	A	A	G	rs11615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	59	58	63	0	0.983051	0	A|0.403;G|0.597	0.597	strong	.	ERCC1	46	.	NM_001983	exon4	c.T354C	p.N118N	GGGCACATTGCGC	.	PASS	Atlas-SNP
ADCY3	109	hgsc.bcm.edu	37	2	25141434	25141434	+	Silent	SNP	G	G	A	rs61732745	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	73	147	0	0.431953	0	G|0.885;A|0.115	0.115	strong	.	ADCY3	114	.	NM_004036	exon1	c.C423T	p.Y141Y	CAGCACGTAGGGC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085046	17085046	+	Missense_Mutation	SNP	C	C	G	rs200838083	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	878	78	742	0	0.0888383	0	C|0.994;G|0.006	0.006	strong	Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	NM_001271733	exon11	c.G1429C	p.D477H	GCCGATCCACCCT	.	PASS	Atlas-SNP
KCNV2	169522	hgsc.bcm.edu	37	9	2729705	2729705	+	Missense_Mutation	SNP	T	T	C	rs112673841	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	52	93	0	0.504854	0	T|0.962;C|0.038	0.038	strong	.	KCNV2	72	.	NM_133497	exon2	c.T1616C	p.L539P	CACAGCTCACCCC	.	PASS	Atlas-SNP
ZNF699	374879	hgsc.bcm.edu	37	19	9407468	9407468	+	Silent	SNP	G	G	A	rs189167193	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	153	89	178	0	0.581699	0	G|0.998;A|0.002	0.002	strong	.	ZNF699	67	.	NM_198535	exon5	c.C612T	p.F204F	ATCCACGAAGGCC	.	PASS	Atlas-SNP
PEX14	5195	hgsc.bcm.edu	37	1	10684422	10684422	+	Silent	SNP	C	C	A	rs35046754	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	314	171	311	0	0.544586	0	C|0.986;A|0.014	0.014	strong	.	PEX14	40	.	NM_004565	exon7	c.C513A	p.A171A	CCTCGCCTCCGTC	.	PASS	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75938179	75938179	+	Silent	SNP	G	G	A	rs3775527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	97	206	0	0.60625	0	G|0.698;A|0.302	0.302	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.G588A	p.P196P	GTCCCCGACAGAG	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129286413	129286413	+	Silent	SNP	G	G	C	rs2245285	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	41	91	0	0.450549	0	G|0.549;C|0.451	0.451	strong	.	PLXND1	149	.	NM_015103	exon22	c.C4008G	p.L1336L	CTTGGTGAGATCT	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71844124	71844124	+	Missense_Mutation	SNP	G	G	A	rs41277901	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	70	228	0	0.275591	0	G|0.988;A|0.012	0.012	strong	.	TJP2	120	.	NM_001170416	exon10	c.G1571A	p.R524K	CCCCGAGAACTTT	.	PASS	Atlas-SNP
COG2	22796	hgsc.bcm.edu	37	1	230810756	230810756	+	Missense_Mutation	SNP	T	T	A	rs6681346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	101	49	104	0	0.485149	0	T|0.922;A|0.078	0.078	strong	.	COG2	61	.	NM_007357	exon9	c.T912A	p.N304K	AGGCAATACTGTT	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239025630	239025630	+	Silent	SNP	T	T	C	rs11904159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	65	130	0	0.485075	0	T|0.803;C|0.197	0.197	strong	.	ESPNL	63	.	NM_194312	exon5	c.T942C	p.H314H	GTACCATGGACAC	.	PASS	Atlas-SNP
AHSP	51327	hgsc.bcm.edu	37	16	31539934	31539934	+	Silent	SNP	G	G	T	rs17677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	63	63	73	0	1	0	G|0.755;T|0.245	0.245	strong	.	AHSP	10	.	NM_016633	exon3	c.G231T	p.L77L	CACTCTGGCCAAC	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163128883	163128883	+	Silent	SNP	G	G	A	rs13418718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	188	106	248	0	0.56383	0	G|0.888;A|0.112	0.112	strong	.	IFIH1	102	.	NM_022168	exon13	c.C2469T	p.A823A	AGCTCTGGCTCGA	.	PASS	Atlas-SNP
ITIH3	3699	hgsc.bcm.edu	37	3	52840325	52840325	+	Silent	SNP	C	C	T	rs34397833	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	64	125	0	0.520325	0	C|0.971;T|0.029	0.029	strong	.	ITIH3	132	.	NM_002217	exon18	c.C1959T	p.H653H	TCCCCACTTCATC	.	PASS	Atlas-SNP
VPS33A	65082	hgsc.bcm.edu	37	12	122720423	122720423	+	Silent	SNP	G	G	A	rs34461198	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	253	125	240	0	0.494071	0	G|0.944;A|0.056	0.056	strong	.	VPS33A	61	.	NM_022916	exon11	c.C1350T	p.A450A	CAGGCCGGCCTTC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	rs112233131	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	14	28	1	0.175	0.0357143	C|0.966;T|0.034	0.034	strong	CRIPAK,rectum,carcinoma,0,3	CRIPAK	185	3	NM_175918	exon1	c.C460T	p.R154W	CCCATGCGGAGTG	.	scavenged	Atlas-SNP
SPAM1	6677	hgsc.bcm.edu	37	7	123594206	123594206	+	Silent	SNP	G	G	A	rs2285996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	93	102	0	0.989362	0	G|0.754;T|0.001	.	strong	.	SPAM1	195	.	NM_153189	exon3	c.G582A	p.K194K	TGAAAAGGCAGGG	.	PASS	Atlas-SNP
OR2F1	26211	hgsc.bcm.edu	37	7	143657473	143657473	+	Missense_Mutation	SNP	A	A	G	rs2072165	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	137	269	0	0.498182	0	A|0.807;G|0.193	0.193	strong	.	OR2F1	71	.	NM_012369	exon1	c.A410G	p.H137R	TCATGCATGGAGG	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957721	111957721	+	Missense_Mutation	SNP	C	C	T	rs115512535	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	300	134	298	0	0.446667	0	C|0.997;T|0.003	0.003	strong	.	OVGP1	177	.	NM_002557	exon11	c.G1402A	p.G468R	TCTCTCCTAGAGC	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85492658	85492658	+	Missense_Mutation	SNP	A	A	C	rs139758674	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	94	47	92	1	0.5	0.0108696	A|0.995;C|0.005	0.005	strong	LRRIQ1_ENST00000393217,NS,carcinoma,-1,2	LRRIQ1	512	2	NM_001079910	exon13	c.A3095C	p.E1032A	CCTTGGAGAATCT	.	scavenged	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108026455	108026455	+	Silent	SNP	A	A	G	rs1546960	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	128	1	1	0.0078125	A|0.095;G|0.905	0.905	strong	.	SCML4	65	.	NM_198081	exon8	c.T1194C	p.P398P	CAGTGCAGGTCCC	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43319214	43319214	+	Silent	SNP	C	C	T	rs9985096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	50	90	0	0.454545	0	C|0.938;T|0.062	0.062	strong	.	C2CD2	47	.	NM_015500	exon13	c.G1818A	p.L606L	CTCTGACAGCTCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515027	195515027	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	441	28	138	0	0.0634921	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,4	MUC4	1505	4	NM_018406	exon2	c.A3424G	p.T1142A	AGGAAGTGTCGGT	.	PASS	Atlas-SNP
HS3ST2	9956	hgsc.bcm.edu	37	16	22926511	22926511	+	Silent	SNP	A	A	G	rs35682499	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	68	117	0	0.507463	0	A|0.834;G|0.166	0.166	strong	HS3ST2,NS,NS,0,1	HS3ST2	59	1	NM_006043	exon2	c.A732G	p.S244S	CGTGTCATGGAAC	.	PASS	Atlas-SNP
MRPL53	116540	hgsc.bcm.edu	37	2	74699778	74699778	+	Missense_Mutation	SNP	C	C	A	rs1047911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	111	106	0	1	0	C|0.587;A|0.413	0.413	strong	.	MRPL53	13	.	NM_053050	exon1	c.G10T	p.A4S	CCAAGGCAGCTGC	.	PASS	Atlas-SNP
RERE	473	hgsc.bcm.edu	37	1	8415621	8415621	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	36	43	0	0.62069	0	.	.	none	.	RERE	129	.	NM_012102	exon23	c.C4525T	p.P1509S	TGGGGGGTGGGAT	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104171742	104171742	+	Silent	SNP	C	C	T	rs17034524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	72	135	0	0.455696	0	C|0.815;T|0.185	0.185	strong	NT5DC3,NS,carcinoma,0,1	NT5DC3	113	1	NM_001031701	exon14	c.G1512A	p.L504L	GCAGCTCAGAGAC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634341	32634341	+	Missense_Mutation	SNP	A	A	G	rs3189152	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	15	42	0	1	0	A|0.710;G|0.290	0.290	strong	HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	NM_002123	exon1	c.T44C	p.V15A	GTTGCTACCCGAA	.	scavenged	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	37	12	56822690	56822690	+	Silent	SNP	C	C	T	rs11832580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	54	127	0	0.453782	0	C|0.949;T|0.051	0.051	strong	.	TIMELESS	107	.	NM_003920	exon11	c.G1281A	p.K427K	AGCTTCCTTGCGG	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52823864	52823864	+	Missense_Mutation	SNP	A	A	T	rs61730358	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	29	56	0	0.467742	0	A|0.981;T|0.019	0.019	strong	.	ITIH1	108	.	NM_002215	exon19	c.A2315T	p.Q772L	TGCGGCAGGACGG	.	PASS	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32110163	32110163	+	Missense_Mutation	SNP	G	G	A	rs140078	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	116	57	125	0	0.491379	0	G|0.689;A|0.311	0.311	strong	.	PRR14L	198	.	NM_173566	exon4	c.C3662T	p.S1221L	GACATCGACTCTT	.	PASS	Atlas-SNP
DUPD1	338599	hgsc.bcm.edu	37	10	76803567	76803567	+	Missense_Mutation	SNP	T	T	G	rs16931938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	33	33	25	0	1	0	T|0.742;G|0.258	0.258	strong	.	DUPD1	30	.	NM_001003892	exon2	c.A409C	p.S137R	CGTCGCTTAGCGC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	39	87	0	0.419355	0	A|0.741;G|0.259	0.259	strong	.	MYOM2	251	.	NM_003970	exon37	c.A4296G	p.T1432T	CGTGACAGTGAGC	.	PASS	Atlas-SNP
TNFRSF19	55504	hgsc.bcm.edu	37	13	24242166	24242166	+	Missense_Mutation	SNP	C	C	T	rs35041805	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	79	144	0	0.568345	0	C|0.981;T|0.019	0.019	strong	.	TNFRSF19	52	.	NM_018647	exon8	c.C784T	p.P262S	TGCAGCCCCAACC	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117803271	117803271	+	Missense_Mutation	SNP	C	C	T	rs2274750	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	62	228	0	0.295238	0	C|0.937;T|0.063	0.063	strong	TNC,NS,carcinoma,+2,1	TNC	282	1	NM_002160	exon19	c.G5341A	p.A1781T	TCATGGCGATGAT	.	PASS	Atlas-SNP
SLC39A11	201266	hgsc.bcm.edu	37	17	70645366	70645366	+	Missense_Mutation	SNP	C	C	G	rs115567758	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	95	0	0.431193	0	C|0.999;G|0.001	0.001	strong	.	SLC39A11	32	.	NM_001159770	exon8	c.G734C	p.G245A	GCCAGGCCCTCGG	.	PASS	Atlas-SNP
LSG1	55341	hgsc.bcm.edu	37	3	194371925	194371925	+	Silent	SNP	A	A	G	rs35636619	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	83	182	0	0.451087	0	A|0.999;G|0.001	0.001	strong	.	LSG1	38	.	NM_018385	exon9	c.T1194C	p.G398G	ACTCTTACCAACA	.	PASS	Atlas-SNP
ARNT2	9915	hgsc.bcm.edu	37	15	80843578	80843578	+	Missense_Mutation	SNP	G	G	A	rs150765047	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	23	26	0	0.605263	0	G|0.999;A|0.001	0.001	strong	.	ARNT2	88	.	NM_014862	exon9	c.G916A	p.G306S	GGACAAGGCAGTA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	30	63	0	0.447761	0	A|0.613;G|0.387	0.387	strong	.	ACAN	220	.	NM_013227	exon17	c.A7499G	p.Q2500R	AGCCTCAGATCAC	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730234	61730234	+	Silent	SNP	T	T	C	rs1800009	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	67	98	0	0.531746	0	C|0.406;N|0.000	0.406	strong	.	BEST1	85	.	NM_004183	exon10	c.T1608C	p.T536T	GAAAACTGTGGAG	.	PASS	Atlas-SNP
VNN1	8876	hgsc.bcm.edu	37	6	133015257	133015257	+	Missense_Mutation	SNP	C	C	G	rs45610032	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	115	224	0	0.493562	0	C|0.992;G|0.008	0.008	strong	.	VNN1	69	.	NM_004666	exon3	c.G406C	p.V136L	TTGCCACAACATA	.	PASS	Atlas-SNP
MRPL32	64983	hgsc.bcm.edu	37	7	42971998	42971998	+	Missense_Mutation	SNP	A	A	G	rs111980169	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	51	99	0	0.53125	0	A|0.995;G|0.005	0.005	strong	.	MRPL32	25	.	NM_031903	exon1	c.A13G	p.M5V	CTGGCCATGCTGG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40360928	40360928	+	Silent	SNP	G	G	A	rs1053686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	136	55	128	0	0.404412	0	G|0.865;N|0.000	.	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon33	c.C15480T	p.R5160R	CAGGAAGCGGTCG	.	PASS	Atlas-SNP
LY6H	4062	hgsc.bcm.edu	37	8	144240257	144240257	+	Silent	SNP	C	C	G	rs9694368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	73	168	0	0.540741	0	C|0.620;G|0.380	0.380	strong	LY6H,NS,carcinoma,0,1	LY6H	12	1	NM_001135655	exon3	c.G213C	p.T71T	ACACACCGTGTCG	.	PASS	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1552107	1552107	+	Missense_Mutation	SNP	C	C	T	rs58099766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	36	63	0	0.529412	0	C|0.972;T|0.028	0.028	strong	.	TELO2	44	.	NM_016111	exon12	c.C1532T	p.A511V	GCAAGGCTCCTGC	.	PASS	Atlas-SNP
LRFN1	57622	hgsc.bcm.edu	37	19	39805188	39805188	+	Silent	SNP	C	C	T	rs115860908	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	34	44	0	0.666667	0	C|0.971;T|0.029	0.029	strong	.	LRFN1	59	.	NM_020862	exon1	c.G789A	p.L263L	CCGCCGCAGCCAG	.	PASS	Atlas-SNP
PLEKHG4	25894	hgsc.bcm.edu	37	16	67320920	67320920	+	Silent	SNP	C	C	T	rs785029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	42	66	0	0.538462	0	C|0.960;T|0.040	0.040	strong	.	PLEKHG4	94	.	NM_001129728	exon18	c.C2943T	p.L981L	TGGTCTCACTGAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511822	195511822	+	Missense_Mutation	SNP	G	G	T	rs200327729		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	308	99	424	1	0.321429	0.00235849	G|0.998;T|0.002	0.002	weak	MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,7	MUC4	1505	7	NM_018406	exon2	c.C6629A	p.P2210H	GTGACAGGAAGAG	.	PASS	Atlas-SNP
MYO1F	4542	hgsc.bcm.edu	37	19	8620636	8620636	+	Silent	SNP	C	C	T	rs73501540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	122	106	0	1	0	C|0.966;T|0.034	0.034	strong	.	MYO1F	128	.	NM_012335	exon2	c.G48A	p.Q16Q	GCCGCTCTGCTTC	.	PASS	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	37	18	59814324	59814324	+	Missense_Mutation	SNP	G	G	C	rs9320001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	132	245	0	1	0	G|0.194;C|0.806	0.806	strong	.	PIGN	62	.	NM_176787	exon9	c.C685G	p.H229D	TATTGTGCTTGTA	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79027605	79027605	+	Missense_Mutation	SNP	T	T	C	rs6893869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	172	128	0	1	0	T|0.702;C|0.298	0.298	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.T3017C	p.V1006A	CACAAGTTTCAAT	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95072907	95072907	+	Missense_Mutation	SNP	G	G	C	rs15717	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	91	161	0	0.565217	0	G|0.940;C|0.060	0.060	strong	.	NOL8	118	.	NM_017948	exon9	c.C2523G	p.D841E	AGATTCGTCATCA	.	PASS	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	37	14	68264867	68264867	+	Silent	SNP	A	A	G	rs12891164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	184	183	165	1	0.994565	0.00606061	A|0.303;G|0.697	0.697	strong	.	ZFYVE26	223	.	NM_015346	exon11	c.T2112C	p.P704P	CTCAGGAGGGCTG	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134125682	134125682	+	Missense_Mutation	SNP	G	G	A	rs1133076	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	55	53	0	1	0	G|0.442;A|0.558	0.558	strong	.	TG	416	.	NM_003235	exon44	c.G7589A	p.R2530Q	AAAGTCGAGGCCG	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19166894	19166894	+	Silent	SNP	G	G	A	rs11805253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	63	140	0	0.504	0	G|0.959;A|0.041	0.041	strong	.	TAS1R2	134	.	NM_152232	exon6	c.C1719T	p.A573A	CAGGGCGGCCAGC	.	PASS	Atlas-SNP
CARNS1	57571	hgsc.bcm.edu	37	11	67191449	67191449	+	Silent	SNP	T	T	C	rs1790747	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	88	88	0	1	0	T|0.648;C|0.352	0.352	strong	.	CARNS1	60	.	NM_001166222	exon10	c.T2230C	p.L744L	GGGCGGTTGCTGG	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58370744	58370744	+	Missense_Mutation	SNP	G	G	A	rs201869821	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	201	63	232	0	0.313433	0	G|0.999;A|0.001	0.001	weak	.	ZNF587	53	.	NM_032828	exon3	c.G964A	p.G322R	GGAGAAGGGCCTT	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730414	61730414	+	Silent	SNP	C	C	A	rs115379107	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	163	84	201	0	0.515337	0	C|0.974;A|0.026	0.026	strong	.	BEST1	85	.	NM_001139443	exon9	c.C1608A	p.T536T	CCCCACCCCAGCT	.	PASS	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	37	6	148792617	148792617	+	Silent	SNP	A	A	G	rs1883625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	101	229	0	0.476415	0	A|0.811;G|0.189	0.189	strong	.	SASH1	123	.	NM_015278	exon6	c.A492G	p.G164G	GAAAGGAATAATG	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7706989	7706989	+	Silent	SNP	C	C	T	rs75986905	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	248	123	183	0	0.495968	0	C|0.985;T|0.015	0.015	strong	.	ADCY2	337	.	NM_020546	exon8	c.C1242T	p.N414N	GGCCAACCACATG	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73711394	73711394	+	Missense_Mutation	SNP	A	A	G	rs2280792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	71	110	0	0.482993	0	A|0.795;G|0.205	0.205	strong	.	PAPLN	180	.	NM_173462	exon3	c.A97G	p.S33G	CCCTGGAGCCAGT	.	PASS	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095558	90095558	+	Missense_Mutation	SNP	C	C	T	rs76646627	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	247	13	263	1	0.0526316	0.00380228	C|0.500;T|0.500	0.500	weak	C16orf3,NS,carcinoma,0,2	C16orf3	14	2	NM_001214	exon1	c.G193A	p.G65S	GGCAGCCTACGGG	.	scavenged	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	35	55	0	0.614035	0	G|0.458;T|0.542	0.542	strong	.	ZNF493	178	.	NM_001076678	exon4	c.G968T	p.C323F	ATAAATGTGAAGA	.	PASS	Atlas-SNP
TRMT6	51605	hgsc.bcm.edu	37	20	5923203	5923203	+	Silent	SNP	T	T	C	rs394940	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	342	339	362	2	0.991228	0.00552486	T|0.772;C|0.228	0.228	strong	.	TRMT6	28	.	NM_015939	exon7	c.A897G	p.E299E	CTCTTGTTCAGAA	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642817	1642817	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	186	8	180	1	0.0430108	0.00555556	.	.	none	KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.T507C	p.G169G	CCCACAACCTGAG	.	scavenged	Atlas-SNP
TRMT11	60487	hgsc.bcm.edu	37	6	126319453	126319453	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	12	35	0	0.25	0	.	.	none	TRMT11,NS,carcinoma,-1,2	TRMT11	43	2	NM_001031712	exon5	c.C379T	p.R127X	ATCAAGCGAATAG	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7141775	7141775	+	Silent	SNP	G	G	A	rs2229431	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	260	134	274	0	0.515385	0	G|0.905;A|0.095	0.095	strong	.	INSR	265	.	NM_000208	exon13	c.C2595T	p.N865N	GACGACGTTGTTC	.	PASS	Atlas-SNP
SCP2	6342	hgsc.bcm.edu	37	1	53453714	53453714	+	Silent	SNP	G	G	T	rs7538935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	103	132	0	1	0	G|0.815;T|0.185	0.185	strong	SCP2,NS,carcinoma,0,1	SCP2	44	1	NM_002979	exon11	c.G987T	p.T329T	TGCAACGCTGGTT	.	PASS	Atlas-SNP
PCDH8	5100	hgsc.bcm.edu	37	13	53420886	53420886	+	Silent	SNP	G	G	A	rs5030684	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	15	31	0	0.428571	0	G|0.951;A|0.049	0.049	strong	.	PCDH8	95	.	NM_002590	exon1	c.C1686T	p.Y562Y	CAGCGCGTAGATG	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22156470	22156470	+	Missense_Mutation	SNP	C	C	G	rs7255075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	36	64	0	0.45	0	C|0.961;G|0.039	0.039	strong	ZNF208_ENST00000428290,NS,carcinoma,+2,3	ZNF208	817	3	NM_007153	exon4	c.G1366C	p.E456Q	ATTCTTCACATTT	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6631169	6631169	+	Silent	SNP	C	C	A	rs917634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	49	49	78	0	1	0	C|0.475;A|0.524	0.524	strong	.	NCAPD2	99	.	NM_014865	exon15	c.C1920A	p.I640I	TGGCATCATCAGC	.	PASS	Atlas-SNP
SHPK	23729	hgsc.bcm.edu	37	17	3526637	3526637	+	Missense_Mutation	SNP	C	C	T	rs150857	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	129	54	120	0	0.418605	0	C|0.763;T|0.237	0.237	strong	.	SHPK	34	.	NM_013276	exon4	c.G643A	p.E215K	ACGTCTCTACGTT	.	PASS	Atlas-SNP
LHB	3972	hgsc.bcm.edu	37	19	49519518	49519518	+	Missense_Mutation	SNP	G	G	T	rs116437960	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	48	112	0	0.403361	0	G|0.988;T|0.012	0.012	strong	.	LHB	20	.	NM_000894	exon3	c.C233A	p.T78N	CGGTAGGTGCACA	.	PASS	Atlas-SNP
TRIM39-RPP21	202658	hgsc.bcm.edu	37	6	30314567	30314567	+	Missense_Mutation	SNP	C	C	A	rs974963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	75	135	0	0.493421	0	C|0.718;A|0.282	0.282	strong	RPP21,NS,carcinoma,-1,1	.	.	1	NM_001199119	exon10	c.C1492A	p.Q498K	CAGACTCAGGGTT	.	PASS	Atlas-SNP
ALOX5	240	hgsc.bcm.edu	37	10	45878050	45878050	+	Silent	SNP	G	G	A	rs2228064	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	135	70	128	0	0.518519	0	G|0.902;A|0.098	0.098	strong	ALOX5,right_lower_lobe,carcinoma,+1,1	ALOX5	88	1	NM_000698	exon2	c.G270A	p.T90T	GAAGACGCCCCAC	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167184878	167184878	+	Missense_Mutation	SNP	T	T	C	rs9841174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	104	92	0	1	0	C|0.395;N|0.001	0.395	strong	.	SERPINI2	85	.	NM_001012303	exon4	c.A473G	p.E158G	ATCATCTCTGCAC	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5443700	5443700	+	Silent	SNP	C	C	T	rs2736588	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	198	178	1	1	0.00561798	C|0.602;T|0.398	0.398	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.C270T	p.N90N	GTTCAACGTTCGT	.	PASS	Atlas-SNP
OR10Q1	219960	hgsc.bcm.edu	37	11	57996289	57996289	+	Missense_Mutation	SNP	G	G	A	rs112800197	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	212	103	209	0	0.485849	0	G|0.991;A|0.009	0.009	strong	.	OR10Q1	79	.	NM_001004471	exon1	c.C59T	p.A20V	GTGAACGCACGGA	.	PASS	Atlas-SNP
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346197	39346197	+	Missense_Mutation	SNP	G	G	A	rs139370444	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	35	90	0	0.486111	0	G|0.992;A|0.008	0.008	strong	.	KRTAP9-1	34	.	NM_001190460	exon1	c.G59A	p.R20K	GCTGCAGGACAAC	.	PASS	Atlas-SNP
CNTD1	124817	hgsc.bcm.edu	37	17	40957849	40957849	+	Missense_Mutation	SNP	G	G	A	rs61995868	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	74	162	0	0.506849	0	G|0.891;A|0.109	0.109	strong	.	CNTD1	22	.	NM_173478	exon4	c.G527A	p.R176Q	ACTTCCGAATTAA	.	PASS	Atlas-SNP
PRKACA	5566	hgsc.bcm.edu	37	19	14204527	14204527	+	Silent	SNP	G	G	C	rs3729858	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	165	85	179	0	0.515152	0	G|0.995;C|0.005	0.005	strong	.	PRKACA	65	.	NM_002730	exon9	c.C843G	p.R281R	CCCAAAGCGCTTG	.	PASS	Atlas-SNP
IFITM3	10410	hgsc.bcm.edu	37	11	320723	320723	+	Missense_Mutation	SNP	C	C	T	rs56227617		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	4	98	0	0.0412371	0	.	.	weak	IFITM3,brain,glioma,0,1	IFITM3	132	1	NM_021034	exon1	c.G91A	p.V31M	CCAGCACAGCCAC	.	scavenged	Atlas-SNP
GBP4	115361	hgsc.bcm.edu	37	1	89655994	89655994	+	Silent	SNP	C	C	T	rs1410871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	84	130	0	0.538462	0	C|0.898;T|0.102	0.102	strong	.	GBP4	89	.	NM_052941	exon7	c.G924A	p.G308G	CAGAGTCCCCAGC	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682474	218682474	+	Silent	SNP	A	A	G	rs12694422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	70	75	0	1	0	A|0.613;G|0.387	0.387	strong	.	TNS1	251	.	NM_022648	exon24	c.T4269C	p.S1423S	GCCCCCACTGGGA	.	PASS	Atlas-SNP
CA6	765	hgsc.bcm.edu	37	1	9030964	9030964	+	Silent	SNP	C	C	T	rs3737665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	87	101	0	1	0	C|0.763;T|0.237	0.237	strong	.	CA6	47	.	NM_001270500	exon7	c.C768T	p.N256N	CCGCAACAAGACC	.	PASS	Atlas-SNP
MRPS9	64965	hgsc.bcm.edu	37	2	105705507	105705507	+	Silent	SNP	C	C	T	rs11538198	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	17	34	0	0.354167	0	C|0.797;T|0.203	0.203	strong	.	MRPS9	32	.	NM_182640	exon6	c.C555T	p.L185L	TCTGCTCCCAGAA	.	PASS	Atlas-SNP
GTDC1	79712	hgsc.bcm.edu	37	2	144966208	144966208	+	Silent	SNP	T	T	C	rs16823579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	64	41	94	0	0.640625	0	T|0.957;C|0.043	0.043	strong	.	GTDC1	61	.	NM_001006636	exon4	c.A141G	p.L47L	GAAATATAAAGCA	.	PASS	Atlas-SNP
ELK1	2002	hgsc.bcm.edu	37	X	47498400	47498400	+	Missense_Mutation	SNP	C	C	T	rs1059579	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	59	186	0	0.327778	0	C|0.847;T|0.153	0.153	strong	.	ELK1	54	.	NM_001114123	exon4	c.G548A	p.S183N	GCTGCACTGGGGA	.	PASS	Atlas-SNP
NFE2L3	9603	hgsc.bcm.edu	37	7	26224668	26224668	+	Silent	SNP	C	C	T	rs61730063	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	125	0	1	0	C|0.790;T|0.210	0.210	strong	.	NFE2L3	77	.	NM_004289	exon4	c.C1350T	p.C450C	TTATTGCACTGAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505839	195505839	+	Silent	SNP	A	A	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	6	235	0	0.0213523	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	NM_018406	exon2	c.T12612A	p.G4204G	GGCGTGACCTGTG	.	scavenged	Atlas-SNP
ARR3	407	hgsc.bcm.edu	37	X	69489530	69489530	+	Silent	SNP	C	C	T	rs3818862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	67	127	0	0.475177	0	0|0.004;T|0.119	0.119	strong	.	ARR3	41	.	NM_004312	exon3	c.C27T	p.S9S	GACCAGCTCCAAT	.	PASS	Atlas-SNP
SEMA6B	10501	hgsc.bcm.edu	37	19	4558422	4558422	+	Silent	SNP	C	C	A	rs115168835	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	31	17	17	0	0.548387	0	C|0.985;A|0.015	0.015	strong	.	SEMA6B	51	.	NM_032108	exon2	c.G48T	p.L16L	CAGCAGCAGAAGC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281136	152281136	+	Missense_Mutation	SNP	C	C	T	rs78125326	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	915	460	482	0	0.502732	0	C|0.942;T|0.058	0.058	strong	.	FLG	900	.	NM_002016	exon3	c.G6226A	p.A2076T	CACGTGCGGACTC	.	PASS	Atlas-SNP
CTNNA2	1496	hgsc.bcm.edu	37	2	80620370	80620370	+	Missense_Mutation	SNP	T	T	C	rs61754542	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	227	93	237	0	0.409692	0	T|0.992;C|0.008	0.008	strong	.	CTNNA2	462	.	NM_001164883	exon8	c.T1091C	p.I364T	TCAACATTGCGAT	.	PASS	Atlas-SNP
ANKRD45	339416	hgsc.bcm.edu	37	1	173596273	173596273	+	Silent	SNP	A	A	G	rs12059068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	58	0	1	0	A|0.781;G|0.219	0.219	strong	.	ANKRD45	36	.	NM_198493	exon4	c.T522C	p.Y174Y	TGCAATATATTTT	.	PASS	Atlas-SNP
TCF4	6925	hgsc.bcm.edu	37	18	52901894	52901894	+	Silent	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	46	70	0	0.541176	0	.	.	none	.	TCF4	178	.	NM_001243226	exon17	c.T1677C	p.D559D	CACGCCATCTTCA	.	PASS	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	37	19	50100295	50100295	+	Silent	SNP	A	A	G	rs3745475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	10	10	22	0	1	0	A|0.688;G|0.312	0.312	strong	.	PRR12	157	.	NM_020719	exon4	c.A2703G	p.P901P	AGGCCCACCAAAC	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862984	5862984	+	Missense_Mutation	SNP	G	G	C	rs10769272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	146	77	143	0	0.527397	0	G|0.607;C|0.393	0.393	strong	OR52E6,NS,carcinoma,0,1	OR52E6	70	1	NM_001005167	exon1	c.C144G	p.F48L	CACAAAGAAGATA	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43268235	43268235	+	Missense_Mutation	SNP	A	A	C	rs75257969	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	236	101	247	1	0.427966	0.00404858	A|0.835;C|0.165	0.165	strong	.	PSG8	101	.	NM_001130167	exon2	c.T263G	p.I88R	ATAATTATTTGAC	.	PASS	Atlas-SNP
CELA2B	51032	hgsc.bcm.edu	37	1	15808767	15808767	+	Missense_Mutation	SNP	G	G	A	rs3820071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	72	103	1	0.631579	0.00970874	G|0.706;A|0.294	0.294	strong	CELA2B_ENST00000422901,NS,carcinoma,-1,6	CELA2B	37	6	NM_015849	exon4	c.G235A	p.G79R	TCCTCCGGGATCT	.	scavenged	Atlas-SNP
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	142	148	0	0.986111	0	A|0.525;G|0.475	0.475	strong	.	TTBK2	82	.	NM_173500	exon2	c.T23C	p.L8P	ATATCCAGCTGCT	.	PASS	Atlas-SNP
RAD17	5884	hgsc.bcm.edu	37	5	68710032	68710032	+	Silent	SNP	G	G	A	rs145547419	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	53	113	0	0.449153	0	G|0.998;A|0.002	0.002	strong	.	RAD17	49	.	NM_133339	exon16	c.G1959A	p.L653L	TGAACTGCCTGCT	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673049	7673049	+	Missense_Mutation	SNP	C	C	G	rs77975665	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	13	53	0	0.282609	0	C|0.922;G|0.078	0.078	strong	.	PPFIBP2	87	.	NM_003621	exon23	c.C2410G	p.P804A	TACACACCACTGA	.	PASS	Atlas-SNP
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	67	75	0	0.59292	0	A|0.000;C|0.874;T|0.126	0.126	strong	PRRT4,caecum,carcinoma,0,1	PRRT4	31	1	NM_001174164	exon3	c.G401A	p.R134Q	GAGCGCCGGGATG	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73553177	73553177	+	Silent	SNP	C	C	T	rs41281332	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	120	63	105	0	0.525	0	C|0.976;T|0.024	0.024	strong	.	CDH23	365	.	NM_022124	exon46	c.C6492T	p.I2164I	TCTGATCGATGAC	.	PASS	Atlas-SNP
TRDN	10345	hgsc.bcm.edu	37	6	123759243	123759243	+	Missense_Mutation	SNP	C	C	T	rs35766971	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	58	29	64	0	0.5	0	C|0.991;T|0.009	0.009	strong	TRDN,posterior_fossa,glioma,0,1	TRDN	88	1	NM_001251987	exon12	c.G1019A	p.S340N	TTCTCACTTTTCT	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708816	168708816	+	Missense_Mutation	SNP	T	T	G	rs10945501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	28	28	43	0	1	0	T|0.545;G|0.455	0.455	strong	DACT2_ENST00000366795,rectum,carcinoma,0,2	DACT2	46	2	NM_214462	exon4	c.A1621C	p.T541P	TCCCTGTGGGCCA	.	PASS	Atlas-SNP
CPXM2	119587	hgsc.bcm.edu	37	10	125528048	125528048	+	Silent	SNP	G	G	A	rs1219725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	36	34	0	1	0	G|0.654;A|0.346	0.346	strong	.	CPXM2	120	.	NM_198148	exon9	c.C1293T	p.Y431Y	CCCTTCGTAGGCC	.	PASS	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449760	35449760	+	Silent	SNP	G	G	C	rs2651080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	115	0	0.990291	0	G|0.671;C|0.329	0.329	strong	ZNF792,NS,carcinoma,-1,2	ZNF792	46	2	NM_175872	exon4	c.C999G	p.T333T	TTCACCGGTGTGA	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134038949	134038949	+	Missense_Mutation	SNP	G	G	T	rs7927108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	16	45	0	0.4	0	G|0.966;T|0.034	0.034	strong	.	NCAPD3	141	.	NM_015261	exon25	c.C3102A	p.S1034R	CCCGAAGCTGCAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515026	195515026	+	Missense_Mutation	SNP	G	G	C	rs200763050		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	436	20	134	0	0.0458716	0	G|0.998;C|0.002	0.002	weak	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C3425G	p.T1142S	GAGGAAGTGTCGG	.	PASS	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32874919	32874919	+	Missense_Mutation	SNP	C	C	A	rs34139105	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	46	72	0	0.541176	0	C|0.927;A|0.073	0.073	strong	PRRG4,NS,carcinoma,+1,1	PRRG4	15	1	NM_024081	exon6	c.C527A	p.P176Q	TGTCTCCATTGCC	.	PASS	Atlas-SNP
CCDC153	283152	hgsc.bcm.edu	37	11	119063908	119063908	+	Missense_Mutation	SNP	C	C	T	rs2301574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	56	56	64	0	1	0	C|0.728;T|0.272	0.272	strong	CCDC153,NS,carcinoma,0,1	CCDC153	19	1	NM_001145018	exon5	c.G302A	p.R101H	TTGCTGCGGGTTT	.	PASS	Atlas-SNP
BRICD5	283870	hgsc.bcm.edu	37	16	2259673	2259673	+	Missense_Mutation	SNP	T	T	C	rs144886139	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	42	91	0	0.494118	0	T|0.993;C|0.007	0.007	strong	C16orf79,NS,carcinoma,+1,1	.	.	1	NM_182563	exon5	c.A473G	p.H158R	GTGTGGTGGGTGT	.	PASS	Atlas-SNP
GNL3L	54552	hgsc.bcm.edu	37	X	54578725	54578725	+	Silent	SNP	C	C	T	rs147602603	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	204	93	207	0	0.455882	0	C|0.998;T|0.002	0.002	strong	.	GNL3L	73	.	NM_001184819	exon13	c.C1182T	p.S394S	ATGCAGCGGGAAG	.	PASS	Atlas-SNP
FPR1	2357	hgsc.bcm.edu	37	19	52249900	52249900	+	Silent	SNP	G	G	A	rs5030879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	63	133	0	0.470149	0	G|0.895;A|0.105	0.105	strong	FPR1,colon,carcinoma,0,1	FPR1	64	1	NM_001193306	exon3	c.C348T	p.I116I	GAGGGCGATCAGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548556	32548556	+	Missense_Mutation	SNP	C	C	T	rs3830125	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	476	37	233	0	0.0777311	0	.	.	weak	.	HLA-DRB1	41	.	NM_002124	exon4	c.G730A	p.A244T	GCCCGGCCCCAAG	.	PASS	Atlas-SNP
OR5AU1	390445	hgsc.bcm.edu	37	14	21623489	21623489	+	Silent	SNP	C	C	T	rs45462402	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	57	90	0	0.483051	0	C|0.637;T|0.363	0.363	strong	.	OR5AU1	46	.	NM_001004731	exon1	c.G696A	p.G232G	GGGTGGCCCATCA	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2555008	2555008	+	Missense_Mutation	SNP	T	T	G	rs12606220	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	37	77	0	0.480519	0	T|0.885;G|0.115	0.115	strong	.	METTL4	40	.	NM_022840	exon4	c.A489C	p.L163F	CAACTGTAAAGAT	.	PASS	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	376809	376809	+	Missense_Mutation	SNP	T	T	C	rs35008248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	21	30	0	0.4375	0	T|0.914;C|0.086	0.086	strong	.	AHRR	67	.	NM_001242412	exon4	c.T341C	p.L114P	CCGTGCTGGAGGG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797211	29797211	+	Silent	SNP	C	C	T	rs41562616	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	237	123	225	1	0.518987	0.00444444	C|0.948;T|0.052	0.052	strong	.	HLA-G	90	.	NM_002127	exon5	c.C636T	p.H212H	GACACACGTGACC	.	PASS	Atlas-SNP
DNM1L	10059	hgsc.bcm.edu	37	12	32854366	32854366	+	Silent	SNP	A	A	C	rs10844308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	47	70	0	0.573171	0	A|0.858;C|0.142	0.142	strong	.	DNM1L	52	.	NM_012062	exon2	c.A120C	p.S40S	GAGCTCAGTGCTA	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17211729	17211729	+	Silent	SNP	A	A	G	rs7201590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	275	160	262	1	0.581818	0.00381679	A|0.934;G|0.066	0.066	strong	.	XYLT1	147	.	NM_022166	exon11	c.T2331C	p.N777N	GGTCACATTAGGT	.	PASS	Atlas-SNP
PLEKHG4	25894	hgsc.bcm.edu	37	16	67320223	67320223	+	Missense_Mutation	SNP	G	G	A	rs3868142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	57	115	0	0.513514	0	G|0.762;A|0.238	0.238	strong	.	PLEKHG4	94	.	NM_001129728	exon15	c.G2489A	p.R830H	AGCCTCGCTCCGA	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs45545935	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	21	98	1	0.25	0.0102041	A|0.947;G|0.053	0.053	strong	ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A481G	p.I161V	TATAAGATAAACA	.	scavenged	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5353252	5353252	+	Missense_Mutation	SNP	G	G	C	rs58819185	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	66	119	0	0.425806	0	G|0.943;C|0.057	0.057	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7270G	p.P2424A	GTGCTGGGGCCAG	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	118950208	118950208	+	Silent	SNP	G	G	T	rs80284365	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	52	77	0	0.666667	0	G|0.955;T|0.045	0.045	strong	.	PAPPA	243	.	NM_002581	exon2	c.G1191T	p.V397V	GGACGTGCTGGAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677625	100677625	+	Silent	SNP	G	G	A	rs115078078	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	257	48	140	1	0.18677	0.00714286	G|0.964;A|0.036	0.036	strong	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G2928A	p.S976S	AACCTCGACTCCT	.	scavenged	Atlas-SNP
CPNE1	8904	hgsc.bcm.edu	37	20	34214173	34214173	+	Missense_Mutation	SNP	G	G	A	rs11543239	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	77	40	66	0	0.519481	0	G|0.925;A|0.075	0.075	strong	.	CPNE1	44	.	NM_003915	exon16	c.C1619T	p.P540L	GCCTGGGGGGCCT	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13056065	13056065	+	Missense_Mutation	SNP	C	C	G	rs61739695	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	68	35	91	0	0.514706	0	C|0.986;G|0.014	0.014	strong	.	CEP192	340	.	NM_032142	exon19	c.C3476G	p.P1159R	CAAACCCTGAGGA	.	PASS	Atlas-SNP
GPD1	2819	hgsc.bcm.edu	37	12	50498475	50498475	+	Missense_Mutation	SNP	A	A	G	rs2232202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	98	41	130	0	0.418367	0	A|0.984;G|0.016	0.016	strong	.	GPD1	23	.	NM_005276	exon2	c.A160G	p.I54V	GAGATCATCAACA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134128945	134128945	+	Missense_Mutation	SNP	A	A	G	rs10091530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	34	89	0	0.453333	0	A|0.902;G|0.098;T|0.000	0.098	strong	.	TG	416	.	NM_003235	exon45	c.A7847G	p.N2616S	CTGAAAACTACGG	.	PASS	Atlas-SNP
GC	2638	hgsc.bcm.edu	37	4	72622566	72622566	+	Silent	SNP	A	A	G	rs4752	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	130	128	0	1	0	A|0.897;G|0.103	0.103	strong	.	GC	132	.	NM_001204307	exon9	c.T954C	p.C318C	TTGACAACAGTCT	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	60	103	0	0.487805	0	A|0.737;G|0.263	0.263	strong	.	ZNF543	61	.	NM_213598	exon4	c.A1717G	p.M573V	CCTTTTATGACTG	.	PASS	Atlas-SNP
C10orf118	55088	hgsc.bcm.edu	37	10	115922774	115922774	+	Missense_Mutation	SNP	G	G	A	rs1061159	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	176	87	173	0	0.494318	0	G|0.762;N|0.000	.	strong	.	C10orf118	70	.	NM_018017	exon2	c.C254T	p.T85I	GAGCCTGTGTCTG	.	PASS	Atlas-SNP
TLR7	51284	hgsc.bcm.edu	37	X	12903659	12903659	+	Missense_Mutation	SNP	A	A	T	rs179008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	81	193	0	0.468208	0	0|0.021;A|0.822;T|0.157	0.157	strong	.	TLR7	125	.	NM_016562	exon3	c.A32T	p.Q11L	AGAGACAAATTCT	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	70954682	70954682	+	Missense_Mutation	SNP	G	G	A	rs143849088	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	43	82	0	0.488636	0	G|0.996;A|0.004	0.004	strong	.	HYDIN	788	.	NM_001270974	exon46	c.C7597T	p.R2533W	GCTCCCGCTCCGC	.	PASS	Atlas-SNP
ZNF479	90827	hgsc.bcm.edu	37	7	57187997	57187997	+	Missense_Mutation	SNP	A	A	T	rs146543279	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	281	143	242	0	0.508897	0	A|0.998;T|0.002	0.002	strong	.	ZNF479	193	.	NM_033273	exon5	c.T1125A	p.H375Q	TCCAGTATGAATT	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	32014161	32014161	+	Silent	SNP	G	G	A	rs55735011	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	92	176	0	0.479167	0	G|0.959;A|0.041	0.041	strong	SFI1,NS,carcinoma,0,1	SFI1	78	1	NM_001007467	exon32	c.G3573A	p.P1191P	GGAGCCGGGGCCT	.	PASS	Atlas-SNP
NEDD4	4734	hgsc.bcm.edu	37	15	56207811	56207811	+	Missense_Mutation	SNP	T	T	G	rs62043855	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	209	94	203	0	0.449761	0	T|0.841;G|0.159	0.159	strong	.	NEDD4	167	.	NM_198400	exon1	c.A1219C	p.N407H	CAGAATTAAGCTT	.	PASS	Atlas-SNP
SLC12A4	6560	hgsc.bcm.edu	37	16	67980969	67980969	+	Silent	SNP	G	G	C	rs11860125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	30	14	22	0	0.466667	0	G|0.849;C|0.151	0.151	strong	.	SLC12A4	81	.	NM_001145962	exon16	c.C2118G	p.L706L	CACGTGGAGGTCC	.	PASS	Atlas-SNP
JMJD7-PLA2G4B	8681	hgsc.bcm.edu	37	15	42137201	42137201	+	Missense_Mutation	SNP	G	G	A	rs34807597	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	36	65	0	0.455696	0	G|0.984;A|0.016	0.016	strong	.	JMJD7-PLA2G4B	90	.	NM_005090	exon18	c.G1865A	p.R622H	GTGCCCGCTTGGG	.	PASS	Atlas-SNP
PLA1A	51365	hgsc.bcm.edu	37	3	119331892	119331892	+	Silent	SNP	C	C	G	rs2272269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	78	42	51	0	0.538462	0	C|0.730;G|0.270	0.270	strong	.	PLA1A	65	.	NM_015900	exon5	c.C591G	p.T197T	GTACACCAGGGCC	.	PASS	Atlas-SNP
SLC38A8	146167	hgsc.bcm.edu	37	16	84050218	84050218	+	Silent	SNP	G	G	A	rs13334006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	21	46	0	0.583333	0	G|0.939;A|0.061	0.061	strong	.	SLC38A8	60	.	NM_001080442	exon8	c.C1068T	p.T356T	CGTCACGGTGACC	.	PASS	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169836388	169836388	+	Silent	SNP	C	C	T	rs57509552	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	63	139	0	0.470149	0	C|0.980;T|0.020	0.020	strong	.	ABCB11	136	.	NM_003742	exon11	c.G1185A	p.E395E	TATTGTCTCAAAA	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138738204	138738204	+	Silent	SNP	G	G	A	rs11977775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	32	103	0	0.313726	0	G|0.898;A|0.102	0.102	strong	.	ZC3HAV1	75	.	NM_020119	exon12	c.C2442T	p.Y814Y	TTTTCCGTATTTG	.	PASS	Atlas-SNP
KBTBD6	89890	hgsc.bcm.edu	37	13	41706450	41706450	+	Silent	SNP	G	G	C	rs147388453	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	40	101	0	0.56338	0	G|0.988;C|0.012	0.012	strong	.	KBTBD6	83	.	NM_152903	exon1	c.C198G	p.T66T	CTCGATGGTCACA	.	PASS	Atlas-SNP
CPNE3	8895	hgsc.bcm.edu	37	8	87558846	87558846	+	Missense_Mutation	SNP	G	G	C	rs41333046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	141	265	0	0.522222	0	G|0.888;C|0.112	0.112	strong	CPNE3,NS,carcinoma,0,1	CPNE3	65	1	NM_003909	exon10	c.G756C	p.E252D	AAATGAGAAAAAA	.	PASS	Atlas-SNP
TFRC	7037	hgsc.bcm.edu	37	3	195787102	195787102	+	Silent	SNP	C	C	T	rs111276121	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	164	86	177	0	0.52439	0	C|0.997;T|0.003	0.003	strong	.	TFRC	54	.	NM_001128148	exon14	c.G1485A	p.K495K	AGAAACCTTGAAG	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25962057	25962057	+	Silent	SNP	C	C	T	rs115618637	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	47	82	0	0.415929	0	C|0.998;T|0.002	0.002	strong	.	ATP10A	270	.	NM_024490	exon9	c.G1596A	p.T532T	GTCGGGCGTGATA	.	PASS	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44189172	44189172	+	Silent	SNP	A	A	C	rs3087994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	156	156	171	0	1	0	T|0.000;G|0.000;C|0.437;A|0.562	0.437	strong	.	PDE9A	69	.	NM_002606	exon17	c.A1497C	p.A499A	TGTGGCACCGTTC	.	PASS	Atlas-SNP
KIAA0317	9870	hgsc.bcm.edu	37	14	75142606	75142606	+	Silent	SNP	G	G	A	rs35864766	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	107	62	103	0	0.579439	0	G|0.985;A|0.015	0.015	strong	.	KIAA0317	68	.	NM_001039479	exon8	c.C876T	p.G292G	GCTCACGCCTGAA	.	PASS	Atlas-SNP
USP18	11274	hgsc.bcm.edu	37	22	18644597	18644597	+	Missense_Mutation	SNP	G	G	A	rs3747038	bycluster	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	439	127	324	0	0.289294	0	.	.	weak	.	USP18	22	.	NM_017414	exon4	c.G295A	p.V99I	AGAAGCGTCCCTT	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31075439	31075439	+	Silent	SNP	G	G	A	rs34107331	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	7	7	0	0.5	0	G|0.990;A|0.010	0.010	strong	.	ZNF668	121	.	NM_001172669	exon3	c.C411T	p.C137C	CTCGGGGCACGGA	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36594404	36594404	+	Missense_Mutation	SNP	G	G	A	rs61743589	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	56	133	0	0.470588	0	G|0.981;A|0.019	0.019	strong	.	WDR62	102	.	NM_001083961	exon30	c.G3674A	p.R1225H	GCTCCCGTGCCAG	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54782393	54782393	+	Missense_Mutation	SNP	T	T	G	rs116027944	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	197	79	210	0	0.401015	0	T|0.962;G|0.038	0.038	strong	.	LILRB2	94	.	NM_005874	exon7	c.A979C	p.I327L	CTGAGATGAAGGG	.	PASS	Atlas-SNP
UGDH	7358	hgsc.bcm.edu	37	4	39515736	39515736	+	Silent	SNP	A	A	G	rs10019532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	86	187	0	0.554839	0	A|0.768;G|0.232	0.232	strong	.	UGDH	52	.	NM_003359	exon3	c.T231C	p.D77D	GATGGCATCATCA	.	PASS	Atlas-SNP
SDF2	6388	hgsc.bcm.edu	37	17	26988852	26988852	+	Missense_Mutation	SNP	C	C	T	rs35404078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	45	92	0	0.463918	0	C|0.990;T|0.010	0.010	strong	.	SDF2	17	.	NM_006923	exon1	c.G43A	p.A15T	CCACAGCGCTCCA	.	PASS	Atlas-SNP
GRID1	2894	hgsc.bcm.edu	37	10	88126072	88126072	+	Silent	SNP	G	G	A	rs61856638	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	25	16	19	0	0.64	0	G|0.654;A|0.346	0.346	strong	.	GRID1	204	.	NM_017551	exon1	c.C78T	p.I26I	CTTACCGATGTGG	.	PASS	Atlas-SNP
CA6	765	hgsc.bcm.edu	37	1	9009452	9009452	+	Silent	SNP	C	C	T	rs61746465	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	111	64	102	0	0.576577	0	C|0.988;T|0.012	0.012	strong	.	CA6	47	.	NM_001270500	exon2	c.C210T	p.G70G	GACAGGCTATGAG	.	PASS	Atlas-SNP
TMEM247	388946	hgsc.bcm.edu	37	2	46707851	46707851	+	Missense_Mutation	SNP	G	G	A	rs61995902	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	52	191	1	0.288889	0.0052356	G|0.886;A|0.114	0.114	strong	ENSG00000187600_ENST00000434431,NS,carcinoma,0,2	.	.	2	NM_001145051	exon2	c.G425A	p.R142Q	GGGAGCGGCAGCA	.	scavenged	Atlas-SNP
DENND2D	79961	hgsc.bcm.edu	37	1	111738589	111738589	+	Silent	SNP	A	A	T	rs34558744	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	33	49	0	0.471429	0	A|0.988;T|0.012	0.012	strong	.	DENND2D	50	.	NM_024901	exon6	c.T594A	p.A198A	CCCAGGAGCAGGG	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71245978	71245978	+	Silent	SNP	G	G	A	rs9446260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	39	80	0	0.47561	0	G|0.972;A|0.028	0.028	strong	.	FAM135A	181	.	NM_001162529	exon17	c.G3981A	p.S1327S	ACATTCGTTGGGC	.	PASS	Atlas-SNP
CDCA4	55038	hgsc.bcm.edu	37	14	105477613	105477613	+	Silent	SNP	T	T	C	rs7145565	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	39	84	0	0.40625	0	T|0.770;C|0.230	0.230	strong	.	CDCA4	18	.	NM_017955	exon2	c.A654G	p.P218P	AGGGCCTGGGGTG	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45759045	45759045	+	Silent	SNP	C	C	T	rs11870	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	72	32	26	0	0.444444	0	C|0.721;T|0.279	0.279	strong	.	C21orf2	10	.	NM_004928	exon1	c.G33A	p.R11R	CTTGGCCCGGGTC	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9321501	9321501	+	Missense_Mutation	SNP	C	C	T	rs3213832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	75	44	68	0	0.586667	0	C|0.907;T|0.093	0.093	strong	.	PZP	422	.	NM_002864	exon17	c.G2071A	p.V691M	CAGACACGGAAGG	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20652291	20652291	+	Silent	SNP	C	C	T	rs143680068	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	298	138	316	1	0.463087	0.00316456	C|1.000;T|0.000	0.000	strong	.	SLC6A5	151	.	NM_004211	exon10	c.C1554T	p.F518F	CGGCTTCGTCATC	.	PASS	Atlas-SNP
KIAA1279	26128	hgsc.bcm.edu	37	10	70775329	70775329	+	Silent	SNP	G	G	A	rs16926021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	24	53	0	0.461538	0	G|0.946;A|0.054	0.054	strong	.	KIAA1279	35	.	NM_015634	exon7	c.G1023A	p.Q341Q	TAAACAGTCTGAA	.	PASS	Atlas-SNP
DNM1L	10059	hgsc.bcm.edu	37	12	32875406	32875406	+	Silent	SNP	A	A	G	rs10844318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	56	104	0	0.444444	0	A|0.859;G|0.141	0.141	strong	.	DNM1L	52	.	NM_012062	exon9	c.A918G	p.T306T	GAAAACAAGAATA	.	PASS	Atlas-SNP
JMJD7-PLA2G4B	8681	hgsc.bcm.edu	37	15	42139875	42139875	+	Missense_Mutation	SNP	A	A	G	rs34424865	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	49	92	0	0.538462	0	A|0.984;G|0.016	0.016	strong	.	JMJD7-PLA2G4B	90	.	NM_001198588	exon24	c.A2669G	p.Q890R	GGCGGCAGCTGGG	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47398549	47398549	+	Silent	SNP	G	G	A	rs3826579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	210	94	185	0	0.447619	0	G|0.718;A|0.282	0.282	strong	.	MYO5B	178	.	NM_001080467	exon27	c.C3591T	p.Y1197Y	ACTATTGTAGGCC	.	PASS	Atlas-SNP
SLC24A1	9187	hgsc.bcm.edu	37	15	65917355	65917355	+	Missense_Mutation	SNP	T	T	G	rs35571449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	36	18	38	0	0.5	0	T|0.948;G|0.052	0.052	strong	.	SLC24A1	58	.	NM_004727	exon2	c.T937G	p.L313V	GTCCTGTTGCATA	.	PASS	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	28	47	0	0.509091	0	G|0.763;A|0.237	0.237	strong	.	MRGPRF	22	.	NM_001098515	exon3	c.C375T	p.C125C	GAACATGCAGAGC	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136590746	136590746	+	Missense_Mutation	SNP	C	C	T	rs3754689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	67	79	0	1	0	C|0.681;T|0.319	0.319	strong	LCT,colon,carcinoma,+1,2	LCT	309	2	NM_002299	exon2	c.G655A	p.V219I	GGACAACAGAGAG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187542356	187542356	+	Missense_Mutation	SNP	C	C	T	rs56790426	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	71	139	0	0.473333	0	C|0.993;T|0.007	0.007	strong	.	FAT1	500	.	NM_005245	exon10	c.G5384A	p.R1795Q	GCTGCTCGAATCA	.	PASS	Atlas-SNP
OR14I1	401994	hgsc.bcm.edu	37	1	248844695	248844695	+	Missense_Mutation	SNP	A	A	T	rs114135727	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	24	43	0	0.470588	0	A|0.982;T|0.018	0.018	strong	.	OR14I1	64	.	NM_001004734	exon1	c.T911A	p.V304E	ATCTTCACAAAGA	.	PASS	Atlas-SNP
EVC2	132884	hgsc.bcm.edu	37	4	5570221	5570221	+	Silent	SNP	G	G	A	rs12511039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	49	98	0	0.49	0	G|0.656;A|0.344	0.344	strong	EVC2,NS,lymphoid_neoplasm,0,1	EVC2	202	1	NM_147127	exon20	c.C3507T	p.H1169H	AGCTGCGTGGTCC	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113352397	113352397	+	Missense_Mutation	SNP	G	G	A	rs2074388	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	123	123	132	0	1	0	G|0.353;A|0.647	0.647	strong	.	ALPK1	125	.	NM_001102406	exon11	c.G1694A	p.G565D	GCAATGGTGAGGG	.	PASS	Atlas-SNP
BLOC1S2	282991	hgsc.bcm.edu	37	10	102046402	102046402	+	Silent	SNP	G	G	C	rs12250221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	53	22	75	0	0.415094	0	G|0.949;C|0.051	0.051	strong	.	BLOC1S2	10	.	NM_173809	exon1	c.C15G	p.A5A	GCCCTCGGCTGCC	.	PASS	Atlas-SNP
ADCK2	90956	hgsc.bcm.edu	37	7	140373326	140373326	+	Missense_Mutation	SNP	A	A	G	rs2968558	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	14	14	13	0	1	0	A|0.744;G|0.256	0.256	strong	.	ADCK2	37	.	NM_052853	exon1	c.A196G	p.S66G	GTTCTGAGTCGGC	.	PASS	Atlas-SNP
HSD17B4	3295	hgsc.bcm.edu	37	5	118877677	118877677	+	Silent	SNP	C	C	T	rs12714	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	79	193	0	0.512987	0	C|0.960;T|0.040	0.040	strong	.	HSD17B4	63	.	NM_001199291	exon25	c.C2274T	p.Y758Y	AGACTACGCCAAG	.	PASS	Atlas-SNP
VAV2	7410	hgsc.bcm.edu	37	9	136662928	136662928	+	Silent	SNP	A	A	G	rs7865299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	91	113	1	1	0.00884956	A|0.741;G|0.259	0.259	strong	.	VAV2	165	.	NM_001134398	exon10	c.T840C	p.L280L	GATCAGAAGCCTG	.	PASS	Atlas-SNP
C4orf40	401137	hgsc.bcm.edu	37	4	71024268	71024268	+	Missense_Mutation	SNP	A	A	G	rs116632053	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	100	209	0	0.469484	0	A|0.986;G|0.014	0.014	strong	.	C4orf40	19	.	NM_214711	exon3	c.A299G	p.N100S	AGTTGAATGTTCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6530138	6530138	+	Missense_Mutation	SNP	G	G	A	rs2555152	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	175	83	142	0	0.474286	0	G|0.962;A|0.038	0.038	strong	.	DNHD1	198	.	NM_173589	exon4	c.G949A	p.D317N	CCACCCGACAAGG	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	37	20	18445963	18445963	+	Silent	SNP	A	A	G	rs6035051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	84	54	0	1	0	A|0.419;G|0.581	0.581	strong	DZANK1,caecum,carcinoma,+1,1	DZANK1	65	1	NM_001099407	exon2	c.T40C	p.L14L	CTCGTAATGGTAT	.	PASS	Atlas-SNP
PNPLA3	80339	hgsc.bcm.edu	37	22	44324730	44324730	+	Silent	SNP	C	C	T	rs738408	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	77	179	0	0.450292	0	C|0.802;T|0.198	0.198	strong	PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	NM_025225	exon3	c.C447T	p.P149P	CATCCCCTTCTAC	.	PASS	Atlas-SNP
RBM33	155435	hgsc.bcm.edu	37	7	155531080	155531080	+	Missense_Mutation	SNP	A	A	G	rs3735576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	102	76	0	0.990291	0	A|0.633;G|0.367	0.367	strong	.	RBM33	157	.	NM_053043	exon11	c.A1720G	p.T574A	ACACACACACAGC	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97058567	97058567	+	Silent	SNP	A	A	G	rs2273622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	211	107	180	1	0.507109	0.00555556	A|0.841;G|0.159	0.159	strong	FHL5,NS,malignant_melanoma,+2,1	FHL5	73	1	NM_020482	exon6	c.A624G	p.P208P	CTATCCATTCTGC	.	scavenged	Atlas-SNP
SLC8A3	6547	hgsc.bcm.edu	37	14	70512964	70512964	+	Silent	SNP	G	G	A	rs144234198	byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	71	94	0	0.47973	0	G|1.000;A|0.000	0.000	strong	SLC8A3_ENST00000357887,colon,carcinoma,0,2	SLC8A3	234	2	NM_183002	exon8	c.C2484T	p.N828N	GACGGCGTTGCTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179552895	179552895	+	Missense_Mutation	SNP	C	C	T	rs72650028	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	147	78	157	0	0.530612	0	C|0.991;T|0.009	0.009	strong	.	TTN	18412	.	NM_001267550	exon127	c.G32254A	p.V10752I	TATAAACTGAAAT	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51912760	51912760	+	Silent	SNP	T	T	G	rs34704431	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	31	42	0	0.563636	0	T|0.955;G|0.045	0.045	strong	EPS15,NS,carcinoma,-2,1	EPS15	72	1	NM_001981	exon10	c.A669C	p.A223A	TTTTTCTGCAGGG	.	PASS	Atlas-SNP
SHCBP1L	81626	hgsc.bcm.edu	37	1	182922003	182922003	+	Missense_Mutation	SNP	G	G	T	rs13373887	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	28	33	0	0.756757	0	G|0.965;T|0.035	0.035	strong	.	SHCBP1L	64	.	NM_030933	exon1	c.C266A	p.A89E	TCCTCCGCCGCCG	.	PASS	Atlas-SNP
FAM21A	387680	hgsc.bcm.edu	37	10	51827934	51827934	+	Missense_Mutation	SNP	G	G	A	rs55875820	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	30	0	1	0	G|0.689;A|0.311	0.311	strong	FAM21A,NS,carcinoma,0,1	FAM21A	32	1	NM_001005751	exon2	c.G73A	p.V25M	TGGTCGGTGGAGG	.	PASS	Atlas-SNP
GMFG	9535	hgsc.bcm.edu	37	19	39826131	39826131	+	Missense_Mutation	SNP	G	G	T	rs1801733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	179	74	165	0	0.413408	0	G|0.980;T|0.020	0.020	strong	.	GMFG	16	.	NM_004877	exon2	c.C44A	p.T15K	TTTTCTGTTAGCT	.	PASS	Atlas-SNP
KDM1A	23028	hgsc.bcm.edu	37	1	23409803	23409803	+	Silent	SNP	G	G	A	rs150794224	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	69	43	89	0	0.623188	0	G|0.997;A|0.003	0.003	strong	.	KDM1A	49	.	NM_001009999	exon21	c.G2577A	p.T859T	GTATACGCTGCCT	.	PASS	Atlas-SNP
FAM129C	199786	hgsc.bcm.edu	37	19	17643125	17643125	+	Silent	SNP	C	C	T	rs73504248	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	219	219	168	0	1	0	C|0.976;T|0.024	0.024	strong	.	FAM129C	110	.	NM_001098524	exon4	c.C333T	p.H111H	GGGCCACCCACCC	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49308261	49308261	+	Silent	SNP	C	C	T	rs143088014	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	25	62	0	0.373134	0	C|0.999;T|0.001	0.001	strong	.	CCDC65	41	.	NM_033124	exon3	c.C375T	p.D125D	TGTTGACCAGCTC	.	PASS	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149547273	149547273	+	Silent	SNP	G	G	A	rs112719493	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	228	227	238	0	0.995614	0	G|0.960;A|0.040	0.040	strong	.	ZNF862	97	.	NM_001099220	exon5	c.G963A	p.S321S	GCTGTCGGAGGAG	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108754214	108754214	+	Missense_Mutation	SNP	T	T	C	rs3762697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	37	122	0	0.4625	0	T|0.839;C|0.161	0.161	strong	.	MORC1	211	.	NM_014429	exon15	c.A1432G	p.M478V	TACCCATGGCTTG	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17930772	17930772	+	Missense_Mutation	SNP	C	C	T	rs3753115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	107	463	0	0.327217	0	C|0.584;T|0.416	0.416	strong	.	ASAH1	71	.	NM_001127505	exon3	c.G187A	p.V63I	TTATAACAGCAGG	.	PASS	Atlas-SNP
NTRK3	4916	hgsc.bcm.edu	37	15	88680684	88680684	+	Silent	SNP	G	G	A	rs1128994	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	83	83	92	0	1	0	G|0.705;A|0.295	0.295	strong	.	NTRK3	587	.	NM_001243101	exon7	c.C573T	p.N191N	ATCAGCGTTGATG	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154282235	154282235	+	Silent	SNP	T	T	C	rs1421813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	110	60	110	0	0.545455	0	T|0.893;C|0.107	0.107	strong	.	GEMIN5	120	.	NM_015465	exon20	c.A2730G	p.G910G	ACCTTTTCCTGTT	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32754386	32754386	+	Missense_Mutation	SNP	C	C	A	rs9621427	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	249	117	259	1	0.46988	0.003861	C|0.903;A|0.097	0.097	strong	.	RFPL3	91	.	NM_001098535	exon1	c.C328A	p.L110M	CCCAAGCTGAAGA	.	PASS	Atlas-SNP
FBXL5	26234	hgsc.bcm.edu	37	4	15627092	15627092	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	6	131	0	0.0447761	0	.	.	none	.	FBXL5	52	.	NM_012161	exon9	c.T1633C	p.Y545H	CACAATACGCAAA	.	PASS	Atlas-SNP
FBXO22	26263	hgsc.bcm.edu	37	15	76205550	76205550	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	20	11	16	0	0.55	0	.	.	none	FBXO22_ENST00000453211,NS,carcinoma,0,3	FBXO22	60	3	NM_012170	exon3	c.C286T	p.R96C	AATGTTCGCATCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512734	195512734	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	327	27	399	2	0.0825688	0.00501253	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A5717C	p.H1906P	GTGACATGAAGAG	.	scavenged	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100510903	100510903	+	Missense_Mutation	SNP	A	A	G	rs3792683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	17	51	0	0.333333	0	A|0.901;G|0.099	0.099	strong	MTTP,NS,carcinoma,-1,1	MTTP	127	1	NM_000253	exon5	c.A497G	p.N166S	CCACCAATGAGGT	.	PASS	Atlas-SNP
PAPSS1	9061	hgsc.bcm.edu	37	4	108552787	108552787	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	45	100	0	0.401786	0	.	.	none	.	PAPSS1	57	.	NM_005443	exon11	c.A1736G	p.H579R	ACTTACTGTTCAG	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464046	39464046	+	Missense_Mutation	SNP	G	G	C	rs2074286	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	152	127	0	1	0	G|0.675;C|0.325	0.325	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C1460G	p.A487G	CAGGGAGCCTCTT	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20846950	20846950	+	Missense_Mutation	SNP	C	C	T	rs8022805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	142	73	117	0	0.514085	0	C|0.963;T|0.037	0.037	strong	.	TEP1	224	.	NM_007110	exon37	c.G5315A	p.R1772Q	AGCAGCCGGCAGT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416775	105416775	+	Silent	SNP	C	C	A	rs60880494	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	82	316	0	0.384977	0	A|0.015;C|0.985	0.015	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G5013T	p.S1671S	TGGGGCCGACACC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103398453	103398453	+	Missense_Mutation	SNP	C	C	A	rs141118373	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	108	199	0	0.524272	0	C|0.991;A|0.009	0.009	strong	.	.	.	.	NM_001146197	exon4	c.G4594T	p.G1532C	AAGGACCCATTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509122	195509122	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	307	59	185	0	0.192182	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9329T	p.P3110L	GAGGAAGGGCTAG	.	PASS	Atlas-SNP
PEX19	5824	hgsc.bcm.edu	37	1	160253413	160253413	+	Silent	SNP	G	G	A	rs141911166	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	103	53	81	0	0.514563	0	G|1.000;A|0.000	0.000	strong	PEX19,NS,carcinoma,0,3	PEX19	34	3	NM_002857	exon2	c.C87T	p.F29F	TTTATCGAAATCA	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117303858	117303858	+	Silent	SNP	T	T	C	rs11216382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	41	134	0	0.460674	0	T|0.826;C|0.174	0.174	strong	DSCAML1,NS,carcinoma,-2,1	DSCAML1	286	1	NM_020693	exon29	c.A5202G	p.Q1734Q	ACCCAGTTGCTTG	.	PASS	Atlas-SNP
HPS5	11234	hgsc.bcm.edu	37	11	18327684	18327684	+	Silent	SNP	G	G	T	rs1140047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	169	71	137	0	0.420118	0	G|0.215;T|0.590	0.590	strong	.	HPS5	70	.	NM_181507	exon7	c.C822A	p.L274L	TTACCTGAGAGTA	.	PASS	Atlas-SNP
KRT16	3868	hgsc.bcm.edu	37	17	39767947	39767947	+	Silent	SNP	C	C	T	rs144914208	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	379	169	390	0	0.44591	0	C|0.978;T|0.022	0.022	strong	KRT16,colon,carcinoma,-1,1	KRT16	45	1	NM_005557	exon2	c.G558A	p.A186A	GGGCTGCGCATTC	.	PASS	Atlas-SNP
PUS7L	83448	hgsc.bcm.edu	37	12	44130205	44130205	+	Silent	SNP	G	G	A	rs12309260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	52	72	0	0.541667	0	G|0.988;A|0.012	0.012	strong	.	PUS7L	73	.	NM_001098614	exon7	c.C1704T	p.D568D	ATTCTCGTCATCA	.	PASS	Atlas-SNP
PTK6	5753	hgsc.bcm.edu	37	20	62166313	62166313	+	Silent	SNP	C	C	T	rs310640	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	46	46	38	0	1	0	C|0.869;T|0.131	0.131	strong	.	PTK6	33	.	NM_005975	exon2	c.G330A	p.P110P	GGCACTCGGCTTC	.	PASS	Atlas-SNP
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278075	126278075	+	Silent	SNP	C	C	T	rs2230279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	100	186	0	0.469484	0	C|0.657;T|0.343	0.343	strong	.	ST3GAL4	25	.	NM_001254757	exon7	c.C423T	p.Y141Y	CAAGTACGATGTG	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1403894	1403894	+	Missense_Mutation	SNP	A	A	G	rs145079480	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	276	108	290	0	0.391304	0	A|0.972;G|0.028	0.028	strong	.	ATAD3C	23	.	NM_001039211	exon12	c.A1220G	p.E407G	AGGACGAGCAACC	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20698270	20698270	+	Missense_Mutation	SNP	A	A	G	rs2301641	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	84	57	86	0	0.678571	0	A|0.625;G|0.375	0.375	strong	.	ABCB5	357	.	NM_001163941	exon14	c.A1678G	p.K560E	GAAAGCAAGTCAG	.	PASS	Atlas-SNP
ITGB3	3690	hgsc.bcm.edu	37	17	45369777	45369777	+	Silent	SNP	A	A	G	rs4642	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	46	89	0	0.528736	0	A|0.710;G|0.290	0.290	strong	ITGB3_ENST00000435993,colon,carcinoma,0,2	ITGB3	157	2	NM_000212	exon10	c.A1533G	p.E511E	GGACGAATGCAGC	.	PASS	Atlas-SNP
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606150	1606150	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	42	266	1	0.411765	0.0037594	.	.	none	.	KRTAP5-1	74	.	NM_001005922	exon1	c.C330T	p.G110G	ACAAGAGCCACAG	.	PASS	Atlas-SNP
RGPD8	727851	hgsc.bcm.edu	37	2	113147751	113147751	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	720	230	627	0	0.319444	0	.	.	none	.	RGPD8	81	.	NM_001164463	exon20	c.T2771G	p.F924C	ATGCCAAATTTAA	.	PASS	Atlas-SNP
LRRN4	164312	hgsc.bcm.edu	37	20	6021703	6021703	+	Missense_Mutation	SNP	C	C	T	rs116777692	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	198	78	177	0	0.393939	0	C|0.990;T|0.010	0.010	strong	.	LRRN4	54	.	NM_152611	exon5	c.G2188A	p.D730N	AATCATCAAAGGC	.	PASS	Atlas-SNP
MYO19	80179	hgsc.bcm.edu	37	17	34859831	34859831	+	Silent	SNP	G	G	A	rs73276768	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	45	19	37	0	0.422222	0	G|0.996;A|0.004	0.004	strong	.	MYO19	130	.	NM_001163735	exon21	c.C1935T	p.L645L	CTCCACGAGGCCA	.	PASS	Atlas-SNP
TMEM140	55281	hgsc.bcm.edu	37	7	134849690	134849690	+	Missense_Mutation	SNP	T	T	C	rs76023601	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	214	98	146	0	0.457944	0	T|0.998;C|0.002	0.002	strong	.	TMEM140	18	.	NM_018295	exon2	c.T497C	p.I166T	TGCTTATAGCCAT	.	PASS	Atlas-SNP
FAM196A	642938	hgsc.bcm.edu	37	10	128974220	128974220	+	Missense_Mutation	SNP	G	G	A	rs11594560	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	83	138	0	0.525316	0	G|0.829;A|0.171	0.171	strong	.	FAM196A	55	.	NM_001039762	exon4	c.C440T	p.A147V	TCTTTCGCATCTG	.	PASS	Atlas-SNP
OVCH2	341277	hgsc.bcm.edu	37	11	7727886	7727886	+	Missense_Mutation	SNP	C	C	T	rs7927138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	82	37	70	0	0.451219	0	C|0.636;T|0.364	0.364	strong	OVCH2,NS,carcinoma,0,2	OVCH2	47	2	NM_198185	exon1	c.G56A	p.R19Q	TTACCTCGTTCAA	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112899702	112899702	+	Silent	SNP	A	A	G	rs6886628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	255	132	241	0	0.517647	0	A|0.681;G|0.319	0.319	strong	.	YTHDC2	118	.	NM_022828	exon20	c.A2589G	p.T863T	TTGCACACTAGCT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92623877	92623877	+	Silent	SNP	G	G	A	rs12277422	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	93	49	100	0	0.526882	0	A|0.259;G|0.741	0.259	strong	.	FAT3	1822	.	NM_001008781	exon25	c.G13272A	p.P4424P	TCTCCCGGAGGAC	.	PASS	Atlas-SNP
C16orf71	146562	hgsc.bcm.edu	37	16	4790304	4790304	+	Missense_Mutation	SNP	C	C	T	rs17137230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	103	156	0	0.536458	0	C|0.980;T|0.020	0.020	strong	.	C16orf71	46	.	NM_139170	exon4	c.C427T	p.P143S	GAGGAGCCCCCCA	.	PASS	Atlas-SNP
PELP1	27043	hgsc.bcm.edu	37	17	4576623	4576623	+	Silent	SNP	G	G	A	rs191748391	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	194	97	161	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	PELP1	102	.	NM_014389	exon15	c.C1767T	p.A589A	AGACGGGGCCAGC	.	PASS	Atlas-SNP
PAQR8	85315	hgsc.bcm.edu	37	6	52269046	52269046	+	Silent	SNP	C	C	G	rs3799274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	92	45	84	0	0.48913	0	T|0.000;G|0.131;C|0.869	0.131	strong	PAQR8,NS,carcinoma,0,1	PAQR8	31	1	NM_133367	exon2	c.C1035G	p.V345V	CAAAGTCAAGGCC	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116340269	116340269	+	Silent	SNP	C	C	T	rs28444388	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	17	36	0	0.404762	0	C|0.967;T|0.033	0.033	strong	.	MET	412	.	NM_000245	exon2	c.C1131T	p.I377I	CAAGATCGTCAAC	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100731748	100731748	+	Silent	SNP	T	T	G	rs61730718	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	34	18	36	0	0.529412	0	T|0.931;G|0.069	0.069	strong	.	TRIM56	123	.	NM_030961	exon3	c.T1155G	p.G385G	AGCTGGTACCCAG	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595017	55595017	+	Missense_Mutation	SNP	G	G	T	rs117277709		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	134	49	181	0	0.365672	0	.	.	weak	OR5L2,NS,carcinoma,-1,2	OR5L2	135	2	NM_001004739	exon1	c.G323T	p.G108V	CATGTGGAGTCAC	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19467322	19467322	+	Silent	SNP	G	G	A	rs139618268	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	67	34	57	0	0.507463	0	G|0.999;A|0.001	0.001	strong	.	UBR4	415	.	NM_020765	exon58	c.C8553T	p.S2851S	CAGAGAGGAAGAG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242039198	242039198	+	Missense_Mutation	SNP	T	T	C	rs3796093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	130	51	101	0	0.392308	0	T|0.899;C|0.101	0.101	strong	.	MTERFD2	33	.	NM_182501	exon2	c.A133G	p.T45A	AGGCTGTAGTCAG	.	PASS	Atlas-SNP
IRAK1	3654	hgsc.bcm.edu	37	X	153284746	153284746	+	Missense_Mutation	SNP	G	G	A	rs11465829	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	113	47	86	0	0.415929	0	G|0.984;0|0.014	.	strong	.	IRAK1	107	.	NM_001569	exon3	c.C338T	p.T113I	GCAGTGGTGCCTG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037579	33037579	+	Missense_Mutation	SNP	A	A	T	rs36013091	alternate_allele	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	138	137	166	0	0.992754	0	.	.	alt	.	HLA-DPA1	20	.	NM_033554	exon2	c.T185A	p.M62K	TAGAACATCTCAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	568	91	479	0	0.160211	0	.	.	weak	FLG,NS,malignant_melanoma,+1,1	FLG	900	1	NM_002016	exon3	c.T6671A	p.L2224Q	CCCACCAGTGAGT	.	scavenged	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27436247	27436247	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	85	47	80	0	0.552941	0	.	.	none	.	SLC4A7	119	.	NM_003615	exon20	c.A2852G	p.Y951C	AGGTGATAGCCAG	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104638926	104638926	+	Silent	SNP	G	G	A	rs2275595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	102	52	90	0	0.509804	0	G|0.932;A|0.068	0.068	strong	.	KIF26A	84	.	NM_015656	exon7	c.G1341A	p.S447S	CTGCTCGGGGACC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46760102	46760102	+	Silent	SNP	C	C	T	rs6008778	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	65	34	41	0	0.523077	0	C|0.948;T|0.052	0.052	strong	.	CELSR1	242	.	NM_014246	exon34	c.G8826A	p.T2942T	CTGCTCCGTCAGC	.	PASS	Atlas-SNP
CARKD	55739	hgsc.bcm.edu	37	13	111279817	111279817	+	Missense_Mutation	SNP	A	A	G	rs3742191	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	160	82	157	0	0.5125	0	A|0.955;G|0.045	0.045	strong	.	CARKD	36	.	NM_018210	exon5	c.A418G	p.K140E	GTGGAGAAGTGGC	.	PASS	Atlas-SNP
PELP1	27043	hgsc.bcm.edu	37	17	4574751	4574751	+	Missense_Mutation	SNP	T	T	A	rs9436	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	41	80	0	0.394231	0	T|0.893;A|0.107	0.107	strong	.	PELP1	102	.	NM_014389	exon17	c.A3376T	p.T1126S	GCTCTGTGGGAGG	.	PASS	Atlas-SNP
APC	324	hgsc.bcm.edu	37	5	112176556	112176556	+	Silent	SNP	G	G	A	rs34506289	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	41	114	0	0.376147	0	G|0.992;A|0.008	0.008	strong	.	APC	4158	.	NM_001127510	exon17	c.G5265A	p.A1755A	ATCTGCGTCTTCT	.	PASS	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	47	131	0	0.431193	0	C|0.618;A|0.382	0.382	strong	.	CRISP3	67	.	NM_001190986	exon5	c.G469T	p.A157S	CCACTGCGTTGGG	.	PASS	Atlas-SNP
WDR25	79446	hgsc.bcm.edu	37	14	100996312	100996312	+	Silent	SNP	T	T	C	rs13065	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	148	148	129	0	1	0	T|0.409;C|0.591	0.591	strong	WDR25,NS,carcinoma,0,1	WDR25	37	1	NM_001161476	exon7	c.T1569C	p.Y523Y	CACCTATCACCCC	.	PASS	Atlas-SNP
RNFT2	84900	hgsc.bcm.edu	37	12	117187907	117187907	+	Silent	SNP	T	T	C	rs111256849	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	6	6	4	0	1	0	T|0.767;C|0.233	0.233	strong	RNFT2,NS,carcinoma,0,4	RNFT2	28	4	NM_001109903	exon4	c.T345C	p.H115H	CCACCATTTCCAC	.	PASS	Atlas-SNP
RAB40AL	282808	hgsc.bcm.edu	37	X	102192315	102192315	+	Missense_Mutation	SNP	G	G	C	rs61745030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	256	254	305	0	0.992188	0	G|0.821;C|0.179	0.179	strong	.	RAB40AL	33	.	NM_001031834	exon1	c.G69C	p.R23S	CGACAGGGACGTA	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117244374	117244374	+	Silent	SNP	T	T	C	rs7770158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	154	82	147	0	0.532468	0	T|0.747;C|0.253	0.253	strong	.	RFX6	141	.	NM_173560	exon14	c.T1542C	p.N514N	GAACAATGCATCC	.	PASS	Atlas-SNP
ACTRT2	140625	hgsc.bcm.edu	37	1	2938697	2938697	+	Silent	SNP	T	T	G	rs3795262	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	161	83	118	0	0.515528	0	T|0.796;G|0.204	0.204	strong	.	ACTRT2	69	.	NM_080431	exon1	c.T447G	p.S149S	CGCCTCTGCCTGT	.	PASS	Atlas-SNP
TTC31	64427	hgsc.bcm.edu	37	2	74710491	74710491	+	Missense_Mutation	SNP	C	C	T	rs6707475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	71	75	0	1	0	C|0.514;T|0.486	0.486	strong	.	TTC31	23	.	NM_022492	exon2	c.C83T	p.A28V	CTGCTGCACCCAA	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376172	52376172	+	Missense_Mutation	SNP	T	T	A	rs9807853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	50	103	0	0.47619	0	T|0.898;A|0.102	0.102	strong	ZNF577,bladder,carcinoma,-1,1	ZNF577	63	1	NM_032679	exon7	c.A1071T	p.R357S	ACATTCTCTGCAT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382402	43382402	+	Silent	SNP	G	G	A	rs17423717	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	333	27	323	0	0.0810811	0	G|0.996;A|0.004	0.004	strong	PSG1_ENST00000312439,NS,carcinoma,-1,4	PSG1	196	4	NM_001184826	exon2	c.C93T	p.P31P	AGTGGTGGGCAGG	.	scavenged	Atlas-SNP
CREB3L3	84699	hgsc.bcm.edu	37	19	4171825	4171825	+	Silent	SNP	G	G	A	rs115268777	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	125	68	123	0	0.544	0	G|0.988;A|0.012	0.012	strong	.	CREB3L3	53	.	NM_032607	exon10	c.G1245A	p.T415T	TTCGACGGAGGAG	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17472785	17472785	+	Silent	SNP	G	G	A	rs116325774	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	284	136	272	2	0.478873	0.00735294	G|0.994;A|0.006	0.006	strong	GAB4,NS,carcinoma,-1,1	GAB4	95	1	NM_001037814	exon2	c.C456T	p.G152G	CCTGAAGCCACAG	.	scavenged	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	37	12	7015075	7015075	+	Missense_Mutation	SNP	A	A	C	rs2071072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	51	99	0	0.485714	0	A|0.951;C|0.049	0.049	strong	.	LRRC23	46	.	NM_001135217	exon3	c.A193C	p.N65H	ACAGGCAATGGGC	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	37	11	82880341	82880341	+	Silent	SNP	G	G	A	rs12284052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	206	206	264	0	1	0	G|0.783;A|0.217	0.217	strong	.	PCF11	220	.	NM_015885	exon8	c.G2964A	p.Q988Q	TGGTCAGCCAGGG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882811	152882811	+	Missense_Mutation	SNP	G	G	A	rs75111974	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	205	112	126	0	0.546341	0	G|0.980;A|0.020	0.020	strong	.	IVL	100	.	NM_005547	exon2	c.G538A	p.E180K	CAGCAGGAGGGGC	.	PASS	Atlas-SNP
RDH8	50700	hgsc.bcm.edu	37	19	10131401	10131401	+	Silent	SNP	T	T	C	rs2233796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	60	113	0	0.454545	0	T|0.974;C|0.026	0.026	strong	.	RDH8	51	.	NM_015725	exon4	c.T519C	p.D173D	CAACGATGTCTAT	.	PASS	Atlas-SNP
TRIM49	57093	hgsc.bcm.edu	37	11	89531619	89531619	+	Silent	SNP	A	A	G	rs77416436		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	84	336	0	0.466667	0	.	.	weak	.	TRIM49	45	.	NM_020358	exon8	c.T1038C	p.H346H	CCCTACATGGACC	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117685255	117685255	+	Silent	SNP	G	G	A	rs41410247	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	157	72	159	0	0.458599	0	G|0.995;A|0.005	0.005	strong	.	NOS1	240	.	NM_001204218	exon19	c.C2823T	p.L941L	TTCCAGGAGGGTG	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257835	110257835	+	Silent	SNP	C	C	T	rs78183574	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	578	286	537	2	0.49481	0.00372439	C|0.907;T|0.093	0.093	strong	GSTM5,brain,glioma,0,2	GSTM5	89	2	NM_000851	exon7	c.C540T	p.N180N	CCTAAACTTGAAG	.	PASS	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	37	3	171395468	171395468	+	Silent	SNP	A	A	G	rs2124147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	152	151	134	0	0.993421	0	A|0.510;G|0.490	0.490	strong	.	PLD1	134	.	NM_002662	exon17	c.T1884C	p.R628R	TAAACTACGGATG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	36	71	0	0.486486	0	G|0.878;C|0.122	0.122	strong	.	UTP20	222	.	NM_014503	exon59	c.G7834C	p.E2612Q	AAGGAAGAGCTCG	.	PASS	Atlas-SNP
DBX1	120237	hgsc.bcm.edu	37	11	20178717	20178717	+	Silent	SNP	G	G	T	rs831464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	52	26	42	0	0.5	0	G|0.881;T|0.119	0.119	strong	DBX1,NS,carcinoma,0,1	DBX1	39	1	NM_001029865	exon3	c.C538A	p.R180R	TGCCCCGCCGAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511608	195511608	+	Silent	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	18	505	1	0.107784	0.0019802	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.A6843G	p.V2281V	TGTGGATACTGAG	.	scavenged	Atlas-SNP
ZDHHC7	55625	hgsc.bcm.edu	37	16	85011548	85011548	+	Missense_Mutation	SNP	C	C	T	rs13334011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	187	91	181	0	0.486631	0	C|0.962;T|0.038	0.038	strong	.	ZDHHC7	55	.	NM_001145548	exon7	c.G712A	p.V238I	CTCGGACACAGGA	.	PASS	Atlas-SNP
PCBP3	54039	hgsc.bcm.edu	37	21	47329352	47329352	+	Silent	SNP	T	T	C	rs2277812	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	74	74	56	0	1	0	T|0.204;C|0.796	0.796	strong	.	PCBP3	82	.	NM_001130141	exon6	c.T423C	p.C141C	CCAGTGTGGGTCC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15791081	15791081	+	Missense_Mutation	SNP	T	T	C	rs146740964	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	374	93	264	0	0.248663	0	T|0.989;C|0.011	0.011	strong	.	CYP4F12	89	.	NM_023944	exon4	c.T371C	p.F124S	ATCTCTTCATCAG	.	PASS	Atlas-SNP
EHHADH	1962	hgsc.bcm.edu	37	3	184910042	184910042	+	Missense_Mutation	SNP	A	A	G	rs11927618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	67	126	0	0.523438	0	A|0.975;G|0.025	0.025	strong	.	EHHADH	73	.	NM_001966	exon7	c.T2144C	p.L715S	CCTGCCAAGCTTT	.	PASS	Atlas-SNP
FAM13A	10144	hgsc.bcm.edu	37	4	89653257	89653257	+	Silent	SNP	G	G	A	rs1801915	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	254	116	272	0	0.456693	0	G|0.831;A|0.169	0.169	strong	.	FAM13A	181	.	NM_014883	exon22	c.C2739T	p.D913D	GAATTGGTCCAGA	.	PASS	Atlas-SNP
PTPN12	5782	hgsc.bcm.edu	37	7	77247821	77247821	+	Missense_Mutation	SNP	G	G	A	rs9640663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	35	35	41	0	1	0	G|0.277;A|0.722	0.722	strong	PTPN12,rectum,carcinoma,0,1	PTPN12	83	1	NM_002835	exon12	c.G964A	p.V322I	AACATGGTCAGCT	.	PASS	Atlas-SNP
PCSK9	255738	hgsc.bcm.edu	37	1	55523855	55523855	+	Missense_Mutation	SNP	G	G	A	rs28362263	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	168	91	154	0	0.541667	0	G|0.975;A|0.025	0.025	strong	.	PCSK9	76	.	NM_174936	exon8	c.G1327A	p.A443T	GTGGCCGCCCTGC	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12848822	12848822	+	Missense_Mutation	SNP	T	T	C	rs11718898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	193	193	190	0	1	0	C|0.622;N|0.000	0.622	strong	.	CAND2	138	.	NM_001162499	exon3	c.T230C	p.V77A	TGGTGGTCAAAGT	.	PASS	Atlas-SNP
PRSS38	339501	hgsc.bcm.edu	37	1	228003843	228003843	+	Silent	SNP	C	C	T	rs113353225	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	246	139	195	1	0.565041	0.00512821	C|0.982;T|0.018	0.018	strong	.	PRSS38	55	.	NM_183062	exon2	c.C201T	p.P67P	TGCGCCCGAGAGG	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247013203	247013203	+	Silent	SNP	G	G	A	rs74976688		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	231	101	201	0	0.437229	0	.	.	weak	.	AHCTF1	187	.	NM_015446	exon33	c.C6132T	p.N2044N	TTCCTCGTTTGGC	.	PASS	Atlas-SNP
ECT2L	345930	hgsc.bcm.edu	37	6	139170412	139170412	+	Missense_Mutation	SNP	A	A	G	rs75962473	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	132	69	120	0	0.522727	0	A|0.992;G|0.008	0.008	strong	.	ECT2L	75	.	NM_001195037	exon8	c.A910G	p.M304V	ATGGTGATGGAGA	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882610	152882610	+	Missense_Mutation	SNP	A	A	G	rs2229496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	131	130	109	0	0.992366	0	A|0.668;G|0.332	0.332	strong	.	IVL	100	.	NM_005547	exon2	c.A337G	p.T113A	GAGAAAACACAAA	.	PASS	Atlas-SNP
KRTAP24-1	643803	hgsc.bcm.edu	37	21	31654809	31654809	+	Missense_Mutation	SNP	C	C	T	rs77638540	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	172	86	168	0	0.5	0	C|0.951;T|0.049	0.049	strong	.	KRTAP24-1	44	.	NM_001085455	exon1	c.G442A	p.G148S	TGGAACCGTTGCG	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95081569	95081569	+	Silent	SNP	T	T	C	rs16908298	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	241	156	284	0	0.647303	0	T|0.969;C|0.031	0.031	strong	.	NOL8	118	.	NM_017948	exon5	c.A351G	p.L117L	CTTTTCTAACAAG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	51	204	0	0.22973	0	.	.	none	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	NM_014644	exon40	c.G6633A	p.A2211A	GCTGCACGCTGAT	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12401021	12401021	+	Missense_Mutation	SNP	C	C	T	rs80272295	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	55	144	0	0.429688	0	C|0.885;T|0.115	0.115	strong	.	VWDE	123	.	NM_001135924	exon14	c.G3025A	p.G1009R	GTTTCCCACCCAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105414316	105414316	+	Missense_Mutation	SNP	G	G	A	rs145541349	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	259	128	303	2	0.494208	0.00660066	G|0.988;A|0.012	0.012	strong	AHNAK2_ENST00000333244,colon,carcinoma,+1,2	AHNAK2	719	2	NM_138420	exon7	c.C7472T	p.P2491L	AATGACGGCATCT	.	scavenged	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56388033	56388033	+	Silent	SNP	T	T	C	rs12439907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	11	31	0	0.37931	0	T|0.747;C|0.253	0.253	strong	.	RFX7	170	.	NM_022841	exon9	c.A1893G	p.L631L	GAAAGTTAAGTTC	.	PASS	Atlas-SNP
NEURL4	84461	hgsc.bcm.edu	37	17	7221454	7221454	+	Silent	SNP	G	G	A	rs73239601	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	43	97	0	0.494253	0	G|0.999;A|0.001	0.001	strong	.	NEURL4	192	.	NM_032442	exon25	c.C3990T	p.A1330A	ACTAGCGGCAGGT	.	PASS	Atlas-SNP
FSTL4	23105	hgsc.bcm.edu	37	5	132535225	132535225	+	Silent	SNP	G	G	A	rs61740558	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	118	68	113	0	0.576271	0	G|0.980;A|0.020	0.020	strong	FSTL4,colon,carcinoma,0,2	FSTL4	74	2	NM_015082	exon16	c.C2091T	p.D697D	GCGCCCGTCGGGG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280907	152280907	+	Missense_Mutation	SNP	G	G	T	rs77249082	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	820	371	462	2	0.452439	0.004329	G|0.500;T|0.500	0.500	strong	.	FLG	900	.	NM_002016	exon3	c.C6455A	p.S2152Y	TGGTGGGACCCCT	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62018239	62018239	+	Silent	SNP	G	G	A	rs2227907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	110	125	0	0.982143	0	G|0.844;A|0.156	0.156	strong	.	SCN4A	205	.	NM_000334	exon24	c.C5403T	p.A1801A	GGGTCCGGCGTCC	.	PASS	Atlas-SNP
RAB17	64284	hgsc.bcm.edu	37	2	238494681	238494681	+	Silent	SNP	G	G	A	rs34052613	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	222	122	209	0	0.54955	0	G|0.890;A|0.110	0.110	strong	.	RAB17	17	.	NM_022449	exon2	c.C117T	p.Y39Y	CTTCACGTACCGA	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	716287	716287	+	Silent	SNP	C	C	A	rs9934288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	51	81	0	0.481132	0	C|0.854;A|0.146	0.146	strong	.	WDR90	107	.	NM_145294	exon37	c.C4677A	p.T1559T	GACAACCTTCCGT	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263406	80263406	+	Missense_Mutation	SNP	C	C	T	rs1138357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	75	167	0	0.438596	0	C|0.708;T|0.292	0.292	strong	.	BCL2A1	28	.	NM_001114735	exon1	c.G56A	p.C19Y	AGGACGCACTGCA	.	PASS	Atlas-SNP
CHST5	23563	hgsc.bcm.edu	37	16	75564172	75564172	+	Silent	SNP	C	C	G	rs74355367	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	114	52	95	0	0.45614	0	C|0.955;G|0.045	0.045	strong	.	CHST5	47	.	NM_024533	exon3	c.G111C	p.L37L	CTGTGCCAGGAGG	.	PASS	Atlas-SNP
ZNF554	115196	hgsc.bcm.edu	37	19	2823100	2823100	+	Missense_Mutation	SNP	G	G	A	rs181024964	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	71	34	60	0	0.478873	0	G|0.998;A|0.002	0.002	strong	.	ZNF554	47	.	NM_001102651	exon2	c.G116A	p.R39H	TGCCCCGCTGGTC	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169611765	169611765	+	Silent	SNP	C	C	T	rs17054482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	62	156	0	0.484375	0	C|0.962;T|0.038	0.038	strong	.	PALLD	179	.	NM_001166108	exon7	c.C1347T	p.N449N	GCAAAACACAGCC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1058635	1058635	+	Missense_Mutation	SNP	C	C	T	rs73505232	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	49	92	0	0.510417	0	C|0.952;T|0.048	0.048	strong	.	ABCA7	174	.	NM_019112	exon38	c.C5168T	p.S1723L	TCCAGTCACCCCT	.	PASS	Atlas-SNP
ARPC1B	10095	hgsc.bcm.edu	37	7	98984354	98984354	+	Missense_Mutation	SNP	G	G	C	rs1045012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	89	46	71	0	0.516854	0	G|0.926;C|0.074	0.074	strong	.	ARPC1B	41	.	NM_005720	exon3	c.G111C	p.K37N	TGAAAAGAGCGGT	.	PASS	Atlas-SNP
MMP25	64386	hgsc.bcm.edu	37	16	3109032	3109032	+	Missense_Mutation	SNP	G	G	A	rs7188234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	52	98	0	0.525253	0	G|0.889;A|0.111	0.111	strong	.	MMP25	35	.	NM_022468	exon10	c.G1622A	p.G541E	CCGCAGGACGTTG	.	PASS	Atlas-SNP
GPAM	57678	hgsc.bcm.edu	37	10	113920465	113920465	+	Silent	SNP	G	G	A	rs2277207	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	229	237	0	1	0	G|0.445;A|0.555	0.555	strong	.	GPAM	68	.	NM_001244949	exon16	c.C1656T	p.N552N	CTCATCGTTCCTG	.	PASS	Atlas-SNP
ANKFN1	162282	hgsc.bcm.edu	37	17	54450073	54450073	+	Missense_Mutation	SNP	G	G	A	rs115263675	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	35	63	0	0.460526	0	G|0.982;A|0.018	0.018	strong	.	ANKFN1	115	.	NM_153228	exon6	c.G677A	p.S226N	GGGTGAGTGAACT	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141719078	141719078	+	Missense_Mutation	SNP	A	A	G	rs114936410	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	38	15	46	0	0.394737	0	A|0.990;G|0.010	0.010	strong	.	MGAM	767	.	NM_004668	exon4	c.A407G	p.H136R	AGAATCATAGCTA	.	PASS	Atlas-SNP
LGSN	51557	hgsc.bcm.edu	37	6	64004905	64004905	+	Missense_Mutation	SNP	T	T	A	rs2459568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	362	163	302	0	0.450276	0	T|0.988;A|0.012	0.012	strong	.	LGSN	82	.	NM_016571	exon2	c.A76T	p.N26Y	ATGTGTTCATGCT	.	PASS	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	37	14	94756750	94756750	+	Missense_Mutation	SNP	T	T	C	rs941591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	91	45	80	0	0.494505	0	T|0.700;C|0.300	0.300	strong	SERPINA10,NS,carcinoma,0,1	SERPINA10	83	1	NM_001100607	exon2	c.A181G	p.S61G	CCTCACTGGCCTT	.	PASS	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	37	18	59814268	59814268	+	Silent	SNP	G	G	A	rs9320000	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	167	166	260	0	0.994012	0	G|0.397;A|0.603	0.603	strong	.	PIGN	62	.	NM_176787	exon9	c.C741T	p.H247H	ATAGAAGTGGTTA	.	PASS	Atlas-SNP
CCDC28A	25901	hgsc.bcm.edu	37	6	139094936	139094936	+	Missense_Mutation	SNP	C	C	A	rs34538642	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	270	126	203	0	0.466667	0	C|0.946;A|0.054	0.054	strong	.	CCDC28A	34	.	NM_015439	exon1	c.C125A	p.S42Y	GCGGGTCCCGGGA	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21258523	21258523	+	Missense_Mutation	SNP	C	C	T	rs61741625	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	106	58	120	0	0.54717	0	C|0.997;T|0.003	0.003	strong	.	APOB	761	.	NM_000384	exon7	c.G751A	p.A251T	TCTTAGCGTCCAG	.	PASS	Atlas-SNP
SLC27A5	10998	hgsc.bcm.edu	37	19	59023174	59023174	+	Missense_Mutation	SNP	A	A	G	rs35350976	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	47	66	0	0.489583	0	A|0.840;G|0.160	0.160	strong	.	SLC27A5	58	.	NM_012254	exon1	c.T149C	p.M50T	GCTAACATGGCCA	.	PASS	Atlas-SNP
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	22	43	0	0.407407	0	G|0.714;A|0.286	0.286	strong	OXTR,NS,carcinoma,0,1	OXTR	31	1	NM_000916	exon3	c.C690T	p.N230N	CCGCAAGTTCTGC	.	PASS	Atlas-SNP
NUP155	9631	hgsc.bcm.edu	37	5	37294473	37294473	+	Silent	SNP	T	T	C	rs1045908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	158	78	146	0	0.493671	0	T|0.750;C|0.250	0.250	strong	NUP155,NS,carcinoma,0,1	NUP155	116	1	NM_153485	exon33	c.A3888G	p.L1296L	TCTAGGTAATGGT	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220417266	220417266	+	Missense_Mutation	SNP	C	C	T	rs59332477	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	42	42	48	0	1	0	C|0.582;T|0.418	0.418	strong	.	OBSL1	120	.	NM_015311	exon18	c.G5300A	p.R1767Q	TCCTGTCGGATGC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17084269	17084269	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	799	59	693	0	0.0738423	0	.	.	none	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon13	c.C1748T	p.A583V	CAGCCTGCAATCT	.	PASS	Atlas-SNP
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524957	10524957	+	Silent	SNP	G	G	T	rs34430103	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	213	210	199	0	0.985915	0	G|0.848;T|0.152	0.152	strong	.	ATF7IP2	40	.	NM_024997	exon3	c.G480T	p.G160G	TGAGGGGGCTTGT	.	PASS	Atlas-SNP
MATK	4145	hgsc.bcm.edu	37	19	3789321	3789321	+	Nonsense_Mutation	SNP	G	G	A	rs74830030	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	122	68	113	0	0.557377	0	G|0.980;A|0.020	0.020	strong	.	MATK	108	.	NM_002378	exon2	c.C25T	p.R9X	CTCTTCGTTCAGC	.	PASS	Atlas-SNP
PKN3	29941	hgsc.bcm.edu	37	9	131467782	131467782	+	Silent	SNP	C	C	T	rs55665019	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	15	11	10	0	0.733333	0	C|0.909;T|0.091	0.091	strong	.	PKN3	62	.	NM_013355	exon2	c.C225T	p.H75H	GCTGCACGCCCGA	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13913885	13913885	+	Silent	SNP	A	A	G	rs3213936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	99	99	106	0	1	0	A|0.439;G|0.561	0.561	strong	.	DNAH5	868	.	NM_001369	exon11	c.T1503C	p.I501I	CCCTTCAATTGTG	.	PASS	Atlas-SNP
PCDHGC5	56097	hgsc.bcm.edu	37	5	140890573	140890573	+	Missense_Mutation	SNP	C	C	T	rs148119281		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	233	3	219	0	0.0128755	0	C|1.000;T|0.000	0.000	weak	PCDHG_cluster,NS,carcinoma,-1,24	PCDHGC5	199	24	NM_018929	exon4	c.C2668T	p.R890C	AGCGCCCGCTACG	.	scavenged	Atlas-SNP
CDYL	9425	hgsc.bcm.edu	37	6	4943846	4943846	+	Silent	SNP	T	T	C	rs11963443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	97	46	81	0	0.474227	0	T|0.895;C|0.105	0.105	strong	.	CDYL	74	.	NM_004824	exon5	c.T1188C	p.I396I	AGCCATTGGTCTA	.	PASS	Atlas-SNP
CPA1	1357	hgsc.bcm.edu	37	7	130021488	130021488	+	Silent	SNP	G	G	C	rs1126899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	117	115	71	0	0.982906	0	C|0.552;G|0.448	0.552	strong	.	CPA1	73	.	NM_001868	exon3	c.G165C	p.G55G	GCGGGGGCCTGCC	.	PASS	Atlas-SNP
CIRH1A	84916	hgsc.bcm.edu	37	16	69191012	69191012	+	Missense_Mutation	SNP	G	G	A	rs8056684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	155	69	111	0	0.445161	0	G|0.990;A|0.010	0.010	strong	.	CIRH1A	48	.	NM_032830	exon12	c.G1313A	p.R438H	TCCTTCGCTCTGC	.	PASS	Atlas-SNP
S100A3	6274	hgsc.bcm.edu	37	1	153520898	153520898	+	Missense_Mutation	SNP	G	G	A	rs61731550	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	28	58	0	0.54902	0	G|0.991;A|0.009	0.009	strong	.	S100A3	7	.	NM_002960	exon2	c.C64T	p.R22C	CACAGCGCCCTGC	.	PASS	Atlas-SNP
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	242	89	239	0	0.367769	0	C|0.378;0|0.003	.	strong	.	H2BFWT	33	.	NM_001002916	exon1	c.G368A	p.R123H	GCCAGGCGACCAG	.	PASS	Atlas-SNP
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	173	73	167	0	0.421965	0	G|0.710;A|0.290	0.290	strong	.	AKR1C3	21	.	NM_001253908	exon2	c.G90A	p.P30P	GGTTCCGAGAAGT	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33568455	33568455	+	Silent	SNP	T	T	C	rs61746163	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	171	89	201	0	0.520468	0	T|0.994;C|0.006	0.006	strong	.	MYH7B	145	.	NM_020884	exon8	c.T543C	p.A181A	AGTGGCTGCTTAC	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894961	1894961	+	Missense_Mutation	SNP	A	A	G	rs9806945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	60	147	0	0.431655	0	A|0.839;G|0.161	0.161	strong	.	.	.	.	NM_001163560	exon10	c.T782C	p.I261T	TCTGGTATATCTT	.	PASS	Atlas-SNP
C9orf78	51759	hgsc.bcm.edu	37	9	132597021	132597021	+	Silent	SNP	C	C	T	rs3814547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	51	108	0	0.34	0	C|0.765;T|0.235	0.235	strong	C9orf78,NS,carcinoma,0,1	C9orf78	26	1	NM_016520	exon2	c.G108A	p.E36E	CTGTACCTCTCTG	.	PASS	Atlas-SNP
SLC7A14	57709	hgsc.bcm.edu	37	3	170184949	170184949	+	Missense_Mutation	SNP	G	G	A	rs73040363	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	183	91	183	0	0.497268	0	G|0.942;A|0.058	0.058	strong	.	SLC7A14	110	.	NM_020949	exon8	c.C2210T	p.A737V	GCCTTCGCATCTG	.	PASS	Atlas-SNP
TAF1A	9015	hgsc.bcm.edu	37	1	222734803	222734803	+	Silent	SNP	G	G	C	rs1134898	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	200	94	211	0	0.47	0	G|0.637;C|0.363	0.363	strong	.	TAF1A	35	.	NM_001201536	exon10	c.C1143G	p.G381G	ATGAAAGCCTGGC	.	PASS	Atlas-SNP
PTP4A1	7803	hgsc.bcm.edu	37	6	64289968	64289968	+	Silent	SNP	G	G	T	rs1618240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	29	16	32	0	0.551724	0	G|0.980;T|0.020	0.020	strong	.	PTP4A1	13	.	NM_003463	exon6	c.G411T	p.R137R	AAAGCGGCGTGGA	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19651307	19651307	+	Missense_Mutation	SNP	G	G	A	rs73320125	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	39	123	0	0.357798	0	G|0.953;A|0.047	0.047	strong	.	TMPRSS15	189	.	NM_002772	exon23	c.C2738T	p.A913V	CAACCAGCAATAG	.	PASS	Atlas-SNP
GOLM1	51280	hgsc.bcm.edu	37	9	88651370	88651370	+	Missense_Mutation	SNP	T	T	C	rs2297002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	73	136	0	0.651786	0	T|0.830;C|0.170	0.170	strong	GOLM1,NS,carcinoma,0,1	GOLM1	36	1	NM_016548	exon7	c.A650G	p.H217R	TCTGTGTGTGGCA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124417889	124417889	+	Silent	SNP	C	C	T	rs4930721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	73	36	78	0	0.493151	0	C|0.719;T|0.281	0.281	strong	.	DNAH10	888	.	NM_207437	exon76	c.C12954T	p.S4318S	CGAGAGCGAGCCC	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13409390	13409390	+	Silent	SNP	C	C	T	rs16025	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	150	148	168	2	0.986667	0.0119048	C|0.871;T|0.129	0.129	strong	CACNA1A_ENST00000360228,NS,carcinoma,0,4	CACNA1A	715	4	NM_001127221	exon19	c.G3060A	p.R1020R	GTCCTCCCTCCGC	.	scavenged	Atlas-SNP
GYPC	2995	hgsc.bcm.edu	37	2	127453664	127453664	+	Silent	SNP	A	A	C	rs1050967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	124	123	153	0	0.991935	0	A|0.405;C|0.595	0.595	strong	.	GYPC	27	.	NM_002101	exon4	c.A333C	p.G111G	GCAGGGAGACCCT	.	PASS	Atlas-SNP
GARS	2617	hgsc.bcm.edu	37	7	30673401	30673401	+	Silent	SNP	A	A	G	rs4593	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	48	28	37	0	0.583333	0	A|0.940;G|0.060	0.060	strong	.	GARS	52	.	NM_002047	exon17	c.A2145G	p.T715T	CATCACATGGGCT	.	PASS	Atlas-SNP
CTTN	2017	hgsc.bcm.edu	37	11	70279766	70279766	+	Silent	SNP	C	C	T	rs643301	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	140	71	123	0	0.507143	0	C|0.811;T|0.189	0.189	strong	.	CTTN	162	.	NM_005231	exon17	c.C1458T	p.Y486Y	CACCTACGATGAG	.	PASS	Atlas-SNP
ZNF135	7694	hgsc.bcm.edu	37	19	58572959	58572959	+	Silent	SNP	G	G	A	rs2288274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	102	211	1	0.445415	0.00473934	G|0.716;A|0.284	0.284	strong	ZNF135_ENST00000401053,colon,carcinoma,+1,3	ZNF135	159	3	NM_007134	exon2	c.G81A	p.T27T	AGTGACGTTTGAG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Silent	SNP	G	G	A	rs1771484	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	68	156	0	0.53125	0	G|0.718;A|0.282	0.282	strong	.	OBSCN	2142	.	NM_001271223	exon9	c.G2889A	p.E963E	CTGTGAGGCCAGG	.	PASS	Atlas-SNP
MLL	4297	hgsc.bcm.edu	37	11	118373861	118373861	+	Silent	SNP	C	C	T	rs2071702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	40	22	45	0	0.55	0	C|0.930;T|0.070	0.070	strong	.	MLL	548	.	NM_001197104	exon27	c.C7254T	p.N2418N	TATCAACGAACAT	.	PASS	Atlas-SNP
CLDN23	137075	hgsc.bcm.edu	37	8	8560151	8560151	+	Silent	SNP	G	G	A	rs61754959	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	22	18	12	0	0.818182	0	G|0.968;A|0.032	0.032	strong	.	CLDN23	5	.	NM_194284	exon1	c.G243A	p.R81R	GGCGCGGGCACTC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149493519	149493519	+	Nonsense_Mutation	SNP	C	C	T	rs57595625	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	139	73	135	0	0.52518	0	C|0.972;T|0.028	0.028	strong	.	.	.	.	NM_198455	exon44	c.C6595T	p.Q2199X	ATGGTGCAGGCGA	.	PASS	Atlas-SNP
SMIM5	643008	hgsc.bcm.edu	37	17	73636368	73636368	+	Silent	SNP	C	C	T	rs117954398	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	62	125	0	0.439716	0	C|0.994;T|0.006	0.006	strong	.	.	.	.	NM_001162995	exon2	c.C87T	p.P29P	TGAGCCCGTGGAG	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952560	14952560	+	Missense_Mutation	SNP	G	G	T	rs12985894	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	109	61	105	0	0.559633	0	G|0.856;T|0.144	0.144	strong	.	OR7A10	33	.	NM_001005190	exon1	c.C130A	p.L44I	TGATGAGCAGGTT	.	PASS	Atlas-SNP
C9orf3	84909	hgsc.bcm.edu	37	9	97563076	97563076	+	Missense_Mutation	SNP	C	C	T	rs34557833	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	141	88	130	0	0.624114	0	C|0.995;T|0.005	0.005	strong	.	C9orf3	100	.	NM_001193331	exon5	c.C1156T	p.R386C	CCCTGCCGCTTCC	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36767024	36767024	+	Missense_Mutation	SNP	T	T	C	rs28608091	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	108	57	135	0	0.527778	0	T|0.627;C|0.373	0.373	strong	.	KCNU1	359	.	NM_001031836	exon21	c.T2302C	p.W768R	TTTCTCTGGAATT	.	PASS	Atlas-SNP
LHFPL1	340596	hgsc.bcm.edu	37	X	111914244	111914244	+	Silent	SNP	A	A	G	rs7064462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	62	83	0	0.62	0	A|0.714;0|0.003	.	strong	.	LHFPL1	28	.	NM_178175	exon2	c.T375C	p.F125F	TCCAACAAACTGC	.	PASS	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80373453	80373453	+	Missense_Mutation	SNP	G	G	A	rs61742456	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	54	32	35	0	0.592593	0	G|0.997;A|0.003	0.003	strong	.	.	.	.	NM_175902	exon2	c.C125T	p.P42L	AGCCACGGCCTCT	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	37	11	48149352	48149352	+	Missense_Mutation	SNP	G	G	A	rs2229703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	38	73	0	0.395833	0	G|0.964;A|0.036	0.036	strong	PTPRJ_ENST00000418331,rectum,carcinoma,-1,5	PTPRJ	225	5	NM_001098503	exon7	c.G1114A	p.V372I	TTTGACGTCACCG	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104070041	104070041	+	Missense_Mutation	SNP	G	G	A	rs79431579	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	185	92	203	0	0.497297	0	G|0.985;A|0.015	0.015	strong	.	CENPE	253	.	NM_001813	exon28	c.C3803T	p.T1268I	TCCTGAGTATTTA	.	PASS	Atlas-SNP
FPR1	2357	hgsc.bcm.edu	37	19	52249672	52249672	+	Missense_Mutation	SNP	A	A	C	rs1042229	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	44	18	47	0	0.409091	0	G|0.018;C|0.428;A|0.554	0.428	strong	FPR1,NS,carcinoma,0,1	FPR1	64	1	NM_001193306	exon3	c.T576G	p.N192K	GGCCACATTTATC	.	PASS	Atlas-SNP
ACCSL	390110	hgsc.bcm.edu	37	11	44069589	44069589	+	Missense_Mutation	SNP	G	G	A	rs3094398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	70	30	51	0	0.428571	0	G|0.977;A|0.023	0.023	strong	.	ACCSL	57	.	NM_001031854	exon1	c.G3A	p.M1I	GAGTATGAGTCAT	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	37	2	224862842	224862842	+	Silent	SNP	A	A	G	rs12457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	105	45	103	0	0.428571	0	A|0.718;G|0.282	0.282	strong	.	SERPINE2	103	.	NM_001136530	exon3	c.T513C	p.N171N	GGTTTCATTTTTA	.	PASS	Atlas-SNP
CCDC116	164592	hgsc.bcm.edu	37	22	21989230	21989230	+	Missense_Mutation	SNP	C	C	T	rs41279987	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	62	27	56	0	0.435484	0	C|0.974;T|0.026	0.026	strong	CCDC116,NS,carcinoma,-1,1	CCDC116	56	1	NM_152612	exon4	c.C878T	p.P293L	ACTGTCCGCTCCG	.	PASS	Atlas-SNP
CALCRL	10203	hgsc.bcm.edu	37	2	188250275	188250275	+	Missense_Mutation	SNP	A	A	T	rs13391909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	104	53	112	0	0.509615	0	A|0.954;T|0.046	0.046	strong	.	CALCRL	73	.	NM_001271751	exon3	c.T48A	p.F16L	TACCATAAAAAAA	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19482788	19482788	+	Missense_Mutation	SNP	T	T	C	rs145733997	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	192	95	204	0	0.494792	0	T|0.999;C|0.001	0.001	strong	.	UBR4	415	.	NM_020765	exon42	c.A6049G	p.I2017V	TGACAATTGCTAA	.	PASS	Atlas-SNP
RAD51D	5892	hgsc.bcm.edu	37	17	33445549	33445549	+	Silent	SNP	G	G	A	rs9901455	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	57	57	64	0	1	0	G|0.828;A|0.172	0.172	strong	.	RAD51D	53	.	NM_002878	exon3	c.C234T	p.S78S	GGCAGTGGAGGTC	.	PASS	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2398017	2398017	+	Silent	SNP	G	G	A	rs2295077	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	37	37	49	0	1	0	G|0.719;A|0.281	0.281	strong	.	TGM6	126	.	NM_198994	exon10	c.G1476A	p.K492K	CACCAAGCCCAGC	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48250031	48250031	+	Silent	SNP	T	T	C	rs11860868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	55	27	31	0	0.490909	0	T|0.927;C|0.073	0.073	strong	.	ABCC11	177	.	NM_033151	exon6	c.A945G	p.P315P	CGCCAGTGGGAAA	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11719	11719	+	Silent	SNP	G	G	A	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	12	12	10	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.G960A	p.G320G	CCACGGGCTTACA	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16899865	16899865	+	Missense_Mutation	SNP	A	A	G	rs2608738	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	112	49	105	0	0.4375	0	A|0.798;G|0.202	0.202	strong	NWD1_ENST00000524140,colon,carcinoma,0,2	NWD1	303	2	NM_001007525	exon13	c.A2804G	p.H935R	CGCTGCACTTGTG	.	PASS	Atlas-SNP
RNF157	114804	hgsc.bcm.edu	37	17	74163821	74163821	+	Silent	SNP	G	G	A	rs2289603	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	229	229	230	0	1	0	G|0.818;A|0.182	0.182	strong	.	RNF157	66	.	NM_052916	exon4	c.C354T	p.Y118Y	AACATTGTAGTGG	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6554126	6554126	+	Missense_Mutation	SNP	C	C	A	rs115745154	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	51	27	31	0	0.529412	0	C|0.986;A|0.014	0.014	strong	.	GRID2IP	82	.	NM_001145118	exon8	c.G1303T	p.V435L	CCAGCACAGGGTA	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90046508	90046508	+	Silent	SNP	A	A	T	rs138029547	bycluster;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	80	45	66	0	0.5625	0	A|0.999;G|0.001	.	strong	.	GPR98	605	.	NM_032119	exon53	c.A11115T	p.S3705S	TACCTCAGGAGTG	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80935345	80935345	+	Missense_Mutation	SNP	T	T	C	rs6539524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	76	76	61	0	1	0	T|0.587;C|0.413	0.413	strong	.	PTPRQ	119	.	NM_001145026	exon18	c.T2650C	p.F884L	GAAGGGTTTGTTG	.	PASS	Atlas-SNP
WWP1	11059	hgsc.bcm.edu	37	8	87439926	87439926	+	Silent	SNP	C	C	T	rs60177164	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	96	50	106	0	0.520833	0	C|0.862;T|0.138	0.138	strong	.	WWP1	97	.	NM_007013	exon11	c.C1212T	p.T404T	TAACACCAGAACA	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7951819	7951819	+	Missense_Mutation	SNP	A	A	G	rs4792147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	79	79	65	0	1	0	A|0.391;C|0.000;G|0.609	0.609	strong	.	ALOX15B	66	.	NM_001141	exon14	c.A1967G	p.Q656R	GGAACCAGGGCCT	.	PASS	Atlas-SNP
CDT1	81620	hgsc.bcm.edu	37	16	88874632	88874632	+	Silent	SNP	C	C	G	rs572275	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	126	126	117	0	1	0	C|0.482;G|0.518	0.518	strong	.	CDT1	30	.	NM_030928	exon10	c.C1587G	p.L529L	GGACCTCGCCCAC	.	PASS	Atlas-SNP
ZAR1L	646799	hgsc.bcm.edu	37	13	32885658	32885658	+	Silent	SNP	G	G	A	rs371193	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	11	11	8	0	1	0	A|0.173;C|0.006	0.173	strong	.	ZAR1L	17	.	NM_001136571	exon1	c.C405T	p.P135P	GGTGGCGGGCGAA	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163137983	163137983	+	Missense_Mutation	SNP	T	T	C	rs10930046	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	119	72	166	0	0.605042	0	T|0.838;C|0.162	0.162	strong	.	IFIH1	102	.	NM_022168	exon7	c.A1379G	p.H460R	AAATAATGCCTCA	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56459342	56459342	+	Missense_Mutation	SNP	C	C	T	rs306507	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	127	154	0	0.992188	0	C|0.326;T|0.674	0.674	strong	.	NLRP8	225	.	NM_176811	exon1	c.C74T	p.P25L	ATATTCCGCCCTG	.	PASS	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110539	33110539	+	Missense_Mutation	SNP	C	C	A	rs144941975	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	100	40	121	0	0.4	0	C|0.998;A|0.002	0.002	strong	.	N4BP2L2	90	.	NM_014887	exon2	c.G626T	p.G209V	TTATGACCCTCAT	.	PASS	Atlas-SNP
ICA1	3382	hgsc.bcm.edu	37	7	8198226	8198226	+	Missense_Mutation	SNP	A	A	C	rs7798010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	128	66	108	0	0.515625	0	A|0.880;C|0.120	0.120	strong	.	ICA1	65	.	NM_001136020	exon7	c.T636G	p.F212L	TTGACAAACATCC	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36657940	36657940	+	Silent	SNP	T	T	A	rs3735385	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	88	33	119	0	0.375	0	T|0.975;A|0.025	0.025	strong	.	AOAH	79	.	NM_001637	exon10	c.A714T	p.P238P	ATCTTTTGGATCG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	430	402	383	0	0.934884	0	G|0.640;C|0.360	0.360	strong	FLG,brain,glioma,0,1	FLG	900	1	NM_002016	exon3	c.C3500G	p.A1167G	GGGTGTGCACGAA	.	PASS	Atlas-SNP
LRRC14	9684	hgsc.bcm.edu	37	8	145745268	145745268	+	Silent	SNP	G	G	A	rs116791876	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	144	85	147	0	0.590278	0	G|0.994;A|0.006	0.006	strong	.	LRRC14	25	.	NM_001272036	exon3	c.G159A	p.T53T	ACACACGTGGCCC	.	PASS	Atlas-SNP
ACBD5	91452	hgsc.bcm.edu	37	10	27508758	27508758	+	Silent	SNP	T	T	C	rs10764690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	199	98	174	0	0.492462	0	T|0.634;C|0.366	0.366	strong	ACBD5_ENST00000396271,NS,adenoma,0,2	ACBD5	75	2	NM_145698	exon6	c.A519G	p.P173P	GGCGTTTGGAGTA	.	PASS	Atlas-SNP
KIF23	9493	hgsc.bcm.edu	37	15	69714347	69714347	+	Silent	SNP	T	T	C	rs34969957	bycluster;byfrequency;by1000genomes	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	180	90	175	0	0.5	0	T|0.985;C|0.015	0.015	strong	.	KIF23	57	.	NM_138555	exon5	c.T333C	p.Y111Y	TACATATGGTGTG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	bycluster;byfrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	41	18	40	6	0.439024	0.15	T|0.870;A|0.130	0.130	strong	UBXN11,NS,carcinoma,0,1	UBXN11	54	1	NM_183008	exon16	c.A1480T	p.S494C	CGGGACTGGGGCC	.	scavenged	Atlas-SNP
BACE1	23621	hgsc.bcm.edu	37	11	117186285	117186285	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	87	4	151	0	0.045977	0	.	.	none	.	BACE1	33	.	NM_138972	exon1	c.A227G	p.Y76C	TCCACGTAGTAGC	.	PASS	Atlas-SNP
